https://launchpad.net/ubuntu/+source/apbs/3.4.1-5build5/+build/27660350 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-058 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 19 Jan 18:59:30 ntpdate[1842]: adjust time server 10.131.248.1 offset -0.007461 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27660350 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27660350 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27660350 Starting target for build PACKAGEBUILD-27660350 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27660350 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27660350 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27660350 Updating target for build PACKAGEBUILD-27660350 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1408 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [14.9 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6019 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [187 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [68.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [829 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [338 kB] Fetched 24.8 MB in 3s (9217 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring usrmerge util-linux uuid-runtime xz-utils zlib1g 150 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After this operation, 54.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.38-3ubuntu1 [2114 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.38-3ubuntu1 [20.3 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-5build1 [142 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-5build1 [346 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-5build1 [81.3 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-5build1 [33.2 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu3 [1910 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3 amd64 1.3.4+ds-1build1 [95.7 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3 [41.3 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.6.0-14.14 [1580 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcc1-0 amd64 13.2.0-10ubuntu1 [48.0 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgprofng0 amd64 2.41.90.20240115-1ubuntu1 [851 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libctf0 amd64 2.41.90.20240115-1ubuntu1 [94.6 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libctf-nobfd0 amd64 2.41.90.20240115-1ubuntu1 [96.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.41.90.20240115-1ubuntu1 [2474 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbinutils amd64 2.41.90.20240115-1ubuntu1 [576 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 binutils-common amd64 2.41.90.20240115-1ubuntu1 [238 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 binutils amd64 2.41.90.20240115-1ubuntu1 [17.9 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-base amd64 13.2.0-10ubuntu1 [46.1 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-s1 amd64 13.2.0-10ubuntu1 [62.5 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgomp1 amd64 13.2.0-10ubuntu1 [142 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libitm1 amd64 13.2.0-10ubuntu1 [29.5 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libatomic1 amd64 13.2.0-10ubuntu1 [10.5 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libasan8 amd64 13.2.0-10ubuntu1 [2835 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblsan0 amd64 13.2.0-10ubuntu1 [1203 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtsan2 amd64 13.2.0-10ubuntu1 [2607 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libubsan1 amd64 13.2.0-10ubuntu1 [1105 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhwasan0 amd64 13.2.0-10ubuntu1 [1262 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libquadmath0 amd64 13.2.0-10ubuntu1 [153 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13 amd64 13.2.0-10ubuntu1 [12.2 MB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-10ubuntu1 [2337 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-13-dev amd64 13.2.0-10ubuntu1 [2687 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13 amd64 13.2.0-10ubuntu1 [21.5 MB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13 amd64 13.2.0-10ubuntu1 [10.7 MB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++6 amd64 13.2.0-10ubuntu1 [772 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g amd64 1:1.3.dfsg-3ubuntu1 [63.3 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsframe1 amd64 2.41.90.20240115-1ubuntu1 [14.6 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.38-3ubuntu1 [3248 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu6 [84.5 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.16 [93.9 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu1 [795 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.2-6ubuntu1 [93.9 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 coreutils amd64 9.4-2ubuntu2 [1693 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma5 amd64 5.4.5-0.3 [141 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.1-4ubuntu1 [18.6 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha2-0ubuntu7 [48.2 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit-common all 1:3.1.2-1 [5512 B] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.4-1 [16.8 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit1 amd64 1:3.1.2-1 [46.7 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.2-6ubuntu1 [122 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libkmod2 amd64 30+20230601-2ubuntu1 [51.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libselinux1 amd64 3.5-1build2 [78.5 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.2-6ubuntu1 [132 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-iconv-perl amd64 1.7-8build1 [13.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-charwidth-perl amd64 0.04-11build1 [9266 B] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libperl5.38 amd64 5.38.2-3 [4871 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl amd64 5.38.2-3 [231 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-base amd64 5.38.2-3 [1823 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblocale-gettext-perl amd64 1.07-6build1 [15.5 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.36 amd64 5.36.0-10ubuntu1 [4782 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [736 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debconf-i18n all 1.5.83 [238 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debconf all 1.5.83 [147 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam0g amd64 1.5.2-9.1ubuntu2 [65.7 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.4-2ubuntu1 [49.3 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255.2-3ubuntu1 [12.5 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255.2-3ubuntu1 [107 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255.2-3ubuntu1 [4022 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255.2-3ubuntu1 [2506 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.2-6ubuntu1 [34.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libcryptsetup12 amd64 2:2.6.1-6ubuntu1 [242 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.2-6ubuntu1 [145 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.2-6ubuntu1 [118 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255.2-3ubuntu1 [495 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255.2-3ubuntu1 [190 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0 amd64 2.7.10 [980 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg amd64 1.22.2ubuntu2 [1309 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-3ubuntu1 [201 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ncurses-bin amd64 6.4+20240113-1 [188 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.2-6ubuntu1 [1120 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu1 [11.3 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.38-3ubuntu1 [680 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ncurses-base all 6.4+20240113-1 [25.4 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-3ubuntu1 [33.7 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt amd64 2.7.10 [1371 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt-utils amd64 2.7.10 [217 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.4-2 [24.4 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-2ubuntu2 [298 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.4-1build1 [64.3 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgnutls30 amd64 3.8.1-4ubuntu7 [991 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu2 [48.3 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu2 [285 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.2-6ubuntu1 [63.3 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.2-6ubuntu1 [32.9 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.1-5 [12.9 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage-common all 3.5-1build1 [9982 B] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage2 amd64 3.5-1build1 [92.9 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libncursesw6 amd64 6.4+20240113-1 [148 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtinfo6 amd64 6.4+20240113-1 [108 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-3ubuntu1 [844 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-2ubuntu1 [59.0 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20231126-1 [126 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-2ubuntu1 [708 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 usrmerge all 38ubuntu1 [58.8 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 readline-common all 8.2-3 [56.2 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline8 amd64 8.2-3 [152 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.44.2-1 [685 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu3 [1188 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2023d-1ubuntu2 [321 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.2-6ubuntu1 [73.5 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.40-3 [204 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 psmisc amd64 23.6-2 [178 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 xz-utils amd64 5.4.5-0.3 [276 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-2ubuntu1 [1122 B] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-2ubuntu1 [5166 B] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-2ubuntu1 [29.0 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg-dev all 1.22.2ubuntu2 [1168 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 libdpkg-perl all 1.22.2ubuntu2 [321 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 45 [12.4 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.32.2-1 [32.1 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.32.2-1 [67.1 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main amd64 optipng amd64 0.7.7-3 [83.3 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu1 [34.9 kB] Preconfiguring packages ... Fetched 123 MB in 1s (123 MB/s) (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../00-libnsl-dev_1.3.0-3_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-3) over (1.3.0-2build2) ... Preparing to unpack .../01-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.36-4) over (1:4.4.36-2) ... Preparing to unpack .../02-libc6-dev_2.38-3ubuntu1_amd64.deb ... Unpacking libc6-dev:amd64 (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../03-libc-dev-bin_2.38-3ubuntu1_amd64.deb ... Unpacking libc-dev-bin (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../04-libtirpc-common_1.3.4+ds-1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1build1) over (1.3.3+ds-1) ... Preparing to unpack .../05-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) over (1.3.3+ds-1) ... Preparing to unpack .../06-libgssapi-krb5-2_1.20.1-5build1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../07-libkrb5-3_1.20.1-5build1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../08-libk5crypto3_1.20.1-5build1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../09-libkrb5support0_1.20.1-5build1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../10-libssl3_3.0.10-1ubuntu3_amd64.deb ... Unpacking libssl3:amd64 (3.0.10-1ubuntu3) over (3.0.10-1ubuntu2) ... Setting up libssl3:amd64 (3.0.10-1ubuntu3) ... (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.4+ds-1build1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.4+ds-1build1) over (1.3.3+ds-1) ... Preparing to unpack .../libnsl2_1.3.0-3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3) over (1.3.0-2build2) ... Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.36-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../0-linux-libc-dev_6.6.0-14.14_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.6.0-14.14) over (6.5.0-9.9) ... Preparing to unpack .../1-libcc1-0_13.2.0-10ubuntu1_amd64.deb ... Unpacking libcc1-0:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../2-libgprofng0_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking libgprofng0:amd64 (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../3-libctf0_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking libctf0:amd64 (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../4-libctf-nobfd0_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../5-binutils-x86-64-linux-gnu_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../6-libbinutils_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking libbinutils:amd64 (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../7-binutils-common_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking binutils-common:amd64 (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../8-binutils_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking binutils (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../9-gcc-13-base_13.2.0-10ubuntu1_amd64.deb ... Unpacking gcc-13-base:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Setting up gcc-13-base:amd64 (13.2.0-10ubuntu1) ... (Reading database ... 13649 files and directories currently installed.) Preparing to unpack .../libgcc-s1_13.2.0-10ubuntu1_amd64.deb ... Unpacking libgcc-s1:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:amd64 (13.2.0-10ubuntu1) ... (Reading database ... 13649 files and directories currently installed.) Preparing to unpack .../00-libgomp1_13.2.0-10ubuntu1_amd64.deb ... Unpacking libgomp1:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../01-libitm1_13.2.0-10ubuntu1_amd64.deb ... Unpacking libitm1:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../02-libatomic1_13.2.0-10ubuntu1_amd64.deb ... Unpacking libatomic1:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../03-libasan8_13.2.0-10ubuntu1_amd64.deb ... Unpacking libasan8:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../04-liblsan0_13.2.0-10ubuntu1_amd64.deb ... Unpacking liblsan0:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../05-libtsan2_13.2.0-10ubuntu1_amd64.deb ... Unpacking libtsan2:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../06-libubsan1_13.2.0-10ubuntu1_amd64.deb ... Unpacking libubsan1:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../07-libhwasan0_13.2.0-10ubuntu1_amd64.deb ... Unpacking libhwasan0:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../08-libquadmath0_13.2.0-10ubuntu1_amd64.deb ... Unpacking libquadmath0:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../09-g++-13_13.2.0-10ubuntu1_amd64.deb ... Unpacking g++-13 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../10-libstdc++-13-dev_13.2.0-10ubuntu1_amd64.deb ... Unpacking libstdc++-13-dev:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../11-libgcc-13-dev_13.2.0-10ubuntu1_amd64.deb ... Unpacking libgcc-13-dev:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../12-gcc-13_13.2.0-10ubuntu1_amd64.deb ... Unpacking gcc-13 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../13-cpp-13_13.2.0-10ubuntu1_amd64.deb ... Unpacking cpp-13 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../14-libstdc++6_13.2.0-10ubuntu1_amd64.deb ... Unpacking libstdc++6:amd64 (13.2.0-10ubuntu1) over (13.2.0-4ubuntu3) ... Setting up libstdc++6:amd64 (13.2.0-10ubuntu1) ... (Reading database ... 13647 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3ubuntu1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.3.dfsg-3ubuntu1) over (1:1.2.13.dfsg-1ubuntu5) ... Setting up zlib1g:amd64 (1:1.3.dfsg-3ubuntu1) ... (Reading database ... 13647 files and directories currently installed.) Preparing to unpack .../libsframe1_2.41.90.20240115-1ubuntu1_amd64.deb ... Unpacking libsframe1:amd64 (2.41.90.20240115-1ubuntu1) over (2.41-5ubuntu1) ... Preparing to unpack .../libzstd1_1.5.5+dfsg2-2_amd64.deb ... Unpacking libzstd1:amd64 (1.5.5+dfsg2-2) over (1.5.5+dfsg2-1ubuntu2) ... Setting up libzstd1:amd64 (1.5.5+dfsg2-2) ... (Reading database ... 13647 files and directories currently installed.) Preparing to unpack .../libc6_2.38-3ubuntu1_amd64.deb ... Unpacking libc6:amd64 (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Setting up libc6:amd64 (2.38-3ubuntu1) ... (Reading database ... 13647 files and directories currently installed.) Preparing to unpack .../base-files_13ubuntu6_amd64.deb ... Unpacking base-files (13ubuntu6) over (13ubuntu3) ... Setting up base-files (13ubuntu6) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/10-help-text ... (Reading database ... 13647 files and directories currently installed.) Preparing to unpack .../debianutils_5.16_amd64.deb ... Unpacking debianutils (5.16) over (5.8-1) ... Setting up debianutils (5.16) ... (Reading database ... 13646 files and directories currently installed.) Preparing to unpack .../bash_5.2.21-2ubuntu1_amd64.deb ... Unpacking bash (5.2.21-2ubuntu1) over (5.2.15-2ubuntu1) ... Setting up bash (5.2.21-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 13646 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.2-6ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.39.2-6ubuntu1) over (1:2.39.1-4ubuntu2) ... Setting up bsdutils (1:2.39.2-6ubuntu1) ... (Reading database ... 13646 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-2ubuntu2_amd64.deb ... Unpacking coreutils (9.4-2ubuntu2) over (9.1-1ubuntu2) ... Setting up coreutils (9.4-2ubuntu2) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_amd64.deb ... Unpacking diffutils (1:3.10-1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libgpg-error-l10n_1.47-3build1_all.deb ... Unpacking libgpg-error-l10n (1.47-3build1) over (1.47-2) ... Preparing to unpack .../libgpg-error0_1.47-3build1_amd64.deb ... Unpacking libgpg-error0:amd64 (1.47-3build1) over (1.47-2) ... Setting up libgpg-error0:amd64 (1.47-3build1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.10.2-3ubuntu1) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.5-0.3_amd64.deb ... Unpacking liblzma5:amd64 (5.4.5-0.3) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.4.5-0.3) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-4ubuntu1_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-4ubuntu1) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.1-4ubuntu1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libapparmor1_4.0.0~alpha2-0ubuntu7_amd64.deb ... Unpacking libapparmor1:amd64 (4.0.0~alpha2-0ubuntu7) over (4.0.0~alpha2-0ubuntu5) ... Preparing to unpack .../libaudit-common_1%3a3.1.2-1_all.deb ... Unpacking libaudit-common (1:3.1.2-1) over (1:3.1.1-1) ... Setting up libaudit-common (1:3.1.2-1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-1) over (0.8.3-1build2) ... Setting up libcap-ng0:amd64 (0.8.4-1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-1) over (1:3.1.1-1) ... Setting up libaudit1:amd64 (1:3.1.2-1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.2-6ubuntu1_amd64.deb ... Unpacking libblkid1:amd64 (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Setting up libblkid1:amd64 (2.39.2-6ubuntu1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libkmod2_30+20230601-2ubuntu1_amd64.deb ... Unpacking libkmod2:amd64 (30+20230601-2ubuntu1) over (30+20230519-1ubuntu3) ... Preparing to unpack .../libpcre2-8-0_10.42-4ubuntu1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4ubuntu1) over (10.42-4) ... Setting up libpcre2-8-0:amd64 (10.42-4ubuntu1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-1build2_amd64.deb ... Unpacking libselinux1:amd64 (3.5-1build2) over (3.5-1) ... Setting up libselinux1:amd64 (3.5-1build2) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.2-6ubuntu1_amd64.deb ... Unpacking libmount1:amd64 (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Setting up libmount1:amd64 (2.39.2-6ubuntu1) ... (Reading database ... 13651 files and directories currently installed.) Preparing to unpack .../0-libtext-iconv-perl_1.7-8build1_amd64.deb ... Unpacking libtext-iconv-perl:amd64 (1.7-8build1) over (1.7-8) ... Preparing to unpack .../1-libtext-charwidth-perl_0.04-11build1_amd64.deb ... Unpacking libtext-charwidth-perl:amd64 (0.04-11build1) over (0.04-11) ... Preparing to unpack .../2-perl_5.38.2-3_amd64.deb ... Unpacking perl (5.38.2-3) over (5.36.0-9ubuntu1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../3-perl-modules-5.38_5.38.2-3_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3) ... Selecting previously unselected package libperl5.38:amd64. Preparing to unpack .../4-libperl5.38_5.38.2-3_amd64.deb ... Unpacking libperl5.38:amd64 (5.38.2-3) ... Preparing to unpack .../5-perl-base_5.38.2-3_amd64.deb ... Unpacking perl-base (5.38.2-3) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-3) ... (Reading database ... 15590 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6build1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6build1) over (1.07-6) ... Preparing to unpack .../perl-modules-5.36_5.36.0-10ubuntu1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-10ubuntu1) over (5.36.0-9ubuntu1) ... Preparing to unpack .../libperl5.36_5.36.0-10ubuntu1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-10ubuntu1) over (5.36.0-9ubuntu1) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4) over (5.3.28+dfsg2-2) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4) ... (Reading database ... 15588 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.23-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../libgdbm-compat4_1.23-5_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../debconf-i18n_1.5.83_all.deb ... Unpacking debconf-i18n (1.5.83) over (1.5.82) ... Preparing to unpack .../debconf_1.5.83_all.deb ... Unpacking debconf (1.5.83) over (1.5.82) ... Setting up debconf (1.5.83) ... (Reading database ... 15587 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.2-9.1ubuntu2_amd64.deb ... Unpacking libpam0g:amd64 (1.5.2-9.1ubuntu2) over (1.5.2-6ubuntu1) ... Setting up libpam0g:amd64 (1.5.2-9.1ubuntu2) ... (Reading database ... 15586 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-2ubuntu1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.4-2ubuntu1) over (2.5.4-1ubuntu3) ... Setting up libseccomp2:amd64 (2.5.4-2ubuntu1) ... (Reading database ... 15586 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_255.2-3ubuntu1_amd64.deb ... Unpacking systemd-sysv (255.2-3ubuntu1) over (253.5-1ubuntu6) ... Preparing to unpack .../1-systemd-dev_255.2-3ubuntu1_all.deb ... Unpacking systemd-dev (255.2-3ubuntu1) over (253.5-1ubuntu6) ... Preparing to unpack .../2-systemd_255.2-3ubuntu1_amd64.deb ... Unpacking systemd (255.2-3ubuntu1) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../3-libsystemd-shared_255.2-3ubuntu1_amd64.deb ... Unpacking libsystemd-shared:amd64 (255.2-3ubuntu1) over (253.5-1ubuntu6) ... Preparing to unpack .../4-libargon2-1_0~20190702+dfsg-4_amd64.deb ... Unpacking libargon2-1:amd64 (0~20190702+dfsg-4) over (0~20190702+dfsg-3) ... Preparing to unpack .../5-libuuid1_2.39.2-6ubuntu1_amd64.deb ... Unpacking libuuid1:amd64 (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Setting up libuuid1:amd64 (2.39.2-6ubuntu1) ... (Reading database ... 15748 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.6.1-6ubuntu1_amd64.deb ... Unpacking libcryptsetup12:amd64 (2:2.6.1-6ubuntu1) over (2:2.6.1-4ubuntu3) ... Preparing to unpack .../libfdisk1_2.39.2-6ubuntu1_amd64.deb ... Unpacking libfdisk1:amd64 (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Preparing to unpack .../mount_2.39.2-6ubuntu1_amd64.deb ... Unpacking mount (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Preparing to unpack .../libsystemd0_255.2-3ubuntu1_amd64.deb ... Unpacking libsystemd0:amd64 (255.2-3ubuntu1) over (253.5-1ubuntu6) ... Setting up libsystemd0:amd64 (255.2-3ubuntu1) ... (Reading database ... 15748 files and directories currently installed.) Preparing to unpack .../libudev1_255.2-3ubuntu1_amd64.deb ... Unpacking libudev1:amd64 (255.2-3ubuntu1) over (253.5-1ubuntu6) ... Setting up libudev1:amd64 (255.2-3ubuntu1) ... (Reading database ... 15748 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.2-2) over (0.8.1-1) ... Setting up libxxhash0:amd64 (0.8.2-2) ... (Reading database ... 15748 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.10_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.7.10) over (2.7.3) ... Setting up libapt-pkg6.0:amd64 (2.7.10) ... (Reading database ... 15748 files and directories currently installed.) Preparing to unpack .../tar_1.35+dfsg-3_amd64.deb ... Unpacking tar (1.35+dfsg-3) over (1.34+dfsg-1.2ubuntu1) ... Setting up tar (1.35+dfsg-3) ... (Reading database ... 15748 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.2ubuntu2_amd64.deb ... Unpacking dpkg (1.22.2ubuntu2) over (1.22.0ubuntu1) ... Setting up dpkg (1.22.2ubuntu2) ... (Reading database ... 15746 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-4_amd64.deb ... Unpacking grep (3.11-4) over (3.11-2) ... Setting up grep (3.11-4) ... (Reading database ... 15746 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-3ubuntu1_amd64.deb ... Unpacking login (1:4.13+dfsg1-3ubuntu1) over (1:4.13+dfsg1-1ubuntu1) ... Setting up login (1:4.13+dfsg1-3ubuntu1) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (Reading database ... 15746 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.4+20230625-2) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... 15746 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-2_amd64.deb ... Unpacking sed (4.9-2) over (4.9-1) ... Setting up sed (4.9-2) ... (Reading database ... 15746 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.2-6ubuntu1_amd64.deb ... Unpacking util-linux (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Setting up util-linux (2.39.2-6ubuntu1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271ubuntu1_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271ubuntu1) over (0.270ubuntu1) ... Setting up libdebconfclient0:amd64 (0.271ubuntu1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.6.1) ... Setting up base-passwd (3.6.3) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66ubuntu1_all.deb ... Unpacking init-system-helpers (1.66ubuntu1) over (1.65.2ubuntu1) ... Setting up init-system-helpers (1.66ubuntu1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../libc-bin_2.38-3ubuntu1_amd64.deb ... Unpacking libc-bin (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Setting up libc-bin (2.38-3ubuntu1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.4+20230625-2) ... Setting up ncurses-base (6.4+20240113-1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-3ubuntu1_amd64.deb ... Unpacking sysvinit-utils (3.08-3ubuntu1) over (3.07-1ubuntu1) ... Setting up sysvinit-utils (3.08-3ubuntu1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../archives/apt_2.7.10_amd64.deb ... Unpacking apt (2.7.10) over (2.7.3) ... Setting up apt (2.7.10) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../apt-utils_2.7.10_amd64.deb ... Unpacking apt-utils (2.7.10) over (2.7.3) ... Preparing to unpack .../ubuntu-keyring_2023.11.28.1_all.deb ... Unpacking ubuntu-keyring (2023.11.28.1) over (2021.03.26) ... Setting up ubuntu-keyring (2023.11.28.1) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-2) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-2) ... (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-2ubuntu2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-2ubuntu2) over (0.25.0-4ubuntu1) ... Setting up libp11-kit0:amd64 (0.25.3-2ubuntu2) ... Selecting previously unselected package libunistring5:amd64. (Reading database ... 15747 files and directories currently installed.) Preparing to unpack .../libunistring5_1.1-2_amd64.deb ... Unpacking libunistring5:amd64 (1.1-2) ... Setting up libunistring5:amd64 (1.1-2) ... (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.4-1build1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.4-1build1) over (2.3.4-1) ... Setting up libidn2-0:amd64 (2.3.4-1build1) ... (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.8.1-4ubuntu7_amd64.deb ... Unpacking libgnutls30:amd64 (3.8.1-4ubuntu7) over (3.8.1-4ubuntu1) ... Setting up libgnutls30:amd64 (3.8.1-4ubuntu7) ... (Reading database ... 15753 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-9.1ubuntu2_amd64.deb ... Unpacking libpam-modules-bin (1.5.2-9.1ubuntu2) over (1.5.2-6ubuntu1) ... Setting up libpam-modules-bin (1.5.2-9.1ubuntu2) ... (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.2-9.1ubuntu2_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.2-9.1ubuntu2) over (1.5.2-6ubuntu1) ... Setting up libpam-modules:amd64 (1.5.2-9.1ubuntu2) ... Setting up libapparmor1:amd64 (4.0.0~alpha2-0ubuntu7) ... Setting up libargon2-1:amd64 (0~20190702+dfsg-4) ... Setting up libcryptsetup12:amd64 (2:2.6.1-6ubuntu1) ... Setting up libfdisk1:amd64 (2.39.2-6ubuntu1) ... Setting up libkmod2:amd64 (30+20230601-2ubuntu1) ... Setting up libsystemd-shared:amd64 (255.2-3ubuntu1) ... Setting up systemd-dev (255.2-3ubuntu1) ... Setting up mount (2.39.2-6ubuntu1) ... Setting up systemd (255.2-3ubuntu1) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (255.2-3ubuntu1) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../init_1.66ubuntu1_amd64.deb ... Unpacking init (1.66ubuntu1) over (1.65.2ubuntu1) ... Preparing to unpack .../libsmartcols1_2.39.2-6ubuntu1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Setting up libsmartcols1:amd64 (2.39.2-6ubuntu1) ... (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../uuid-runtime_2.39.2-6ubuntu1_amd64.deb ... Unpacking uuid-runtime (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Preparing to unpack .../libattr1_1%3a2.5.1-5_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-5) over (1:2.5.1-4) ... Setting up libattr1:amd64 (1:2.5.1-5) ... (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2) over (1.1.0-1) ... Setting up libmd0:amd64 (1.1.0-2) ... (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.2-9.1ubuntu2_all.deb ... Unpacking libpam-runtime (1.5.2-9.1ubuntu2) over (1.5.2-6ubuntu1) ... Setting up libpam-runtime (1.5.2-9.1ubuntu2) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1build1_all.deb ... Unpacking libsemanage-common (3.5-1build1) over (3.5-1) ... Setting up libsemanage-common (3.5-1build1) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) over (3.5-1) ... Setting up libsepol2:amd64 (3.5-2) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1build1_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1build1) over (3.5-1) ... Setting up libsemanage2:amd64 (3.5-1build1) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.4+20230625-2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4+20230625-2) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-3ubuntu1_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-3ubuntu1) over (1:4.13+dfsg1-1ubuntu1) ... Setting up passwd (1:4.13+dfsg1-3ubuntu1) ... (Reading database ... 15751 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-2ubuntu1_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-2ubuntu1) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../01-mawk_1.3.4.20231126-1_amd64.deb ... Unpacking mawk (1.3.4.20231126-1) over (1.3.4.20230730-1) ... Preparing to unpack .../02-procps_2%3a4.0.4-2ubuntu1_amd64.deb ... Unpacking procps (2:4.0.4-2ubuntu1) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../03-usrmerge_38ubuntu1_all.deb ... Unpacking usrmerge (38ubuntu1) over (35ubuntu1) ... Preparing to unpack .../04-krb5-locales_1.20.1-5build1_all.deb ... Unpacking krb5-locales (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../05-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) over (8.2-1.3) ... Preparing to unpack .../06-libreadline8_8.2-3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-3) over (8.2-1.3) ... Preparing to unpack .../07-libsqlite3-0_3.44.2-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.44.2-1) over (3.42.0-1) ... Preparing to unpack .../08-openssl_3.0.10-1ubuntu3_amd64.deb ... Unpacking openssl (3.0.10-1ubuntu3) over (3.0.10-1ubuntu2) ... Preparing to unpack .../09-tzdata_2023d-1ubuntu2_all.deb ... Unpacking tzdata (2023d-1ubuntu2) over (2023c-9ubuntu1) ... Preparing to unpack .../10-bash-completion_1%3a2.11-8_all.deb ... Unpacking bash-completion (1:2.11-8) over (1:2.11-7) ... Preparing to unpack .../11-bsdextrautils_2.39.2-6ubuntu1_amd64.deb ... Unpacking bsdextrautils (2.39.2-6ubuntu1) over (2.39.1-4ubuntu2) ... Preparing to unpack .../12-libpng16-16_1.6.40-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.40-3) over (1.6.40-1) ... Preparing to unpack .../13-psmisc_23.6-2_amd64.deb ... Unpacking psmisc (23.6-2) over (23.6-1) ... Preparing to unpack .../14-xz-utils_5.4.5-0.3_amd64.deb ... Unpacking xz-utils (5.4.5-0.3) over (5.4.1-0.2) ... Preparing to unpack .../15-g++_4%3a13.2.0-2ubuntu1_amd64.deb ... Unpacking g++ (4:13.2.0-2ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../16-gcc_4%3a13.2.0-2ubuntu1_amd64.deb ... Unpacking gcc (4:13.2.0-2ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../17-cpp_4%3a13.2.0-2ubuntu1_amd64.deb ... Unpacking cpp (4:13.2.0-2ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../18-dpkg-dev_1.22.2ubuntu2_all.deb ... Unpacking dpkg-dev (1.22.2ubuntu2) over (1.22.0ubuntu1) ... Preparing to unpack .../19-libdpkg-perl_1.22.2ubuntu2_all.deb ... Unpacking libdpkg-perl (1.22.2ubuntu2) over (1.22.0ubuntu1) ... Preparing to unpack .../20-lto-disabled-list_45_all.deb ... Unpacking lto-disabled-list (45) over (43) ... Preparing to unpack .../21-libfakeroot_1.32.2-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.32.2-1) over (1.32.1-1) ... Preparing to unpack .../22-fakeroot_1.32.2-1_amd64.deb ... Unpacking fakeroot (1.32.2-1) over (1.32.1-1) ... Preparing to unpack .../23-optipng_0.7.7-3_amd64.deb ... Unpacking optipng (0.7.7-3) over (0.7.7-2build1) ... Preparing to unpack .../24-pinentry-curses_1.2.1-3ubuntu1_amd64.deb ... Unpacking pinentry-curses (1.2.1-3ubuntu1) over (1.2.1-1ubuntu1) ... Setting up libtext-iconv-perl:amd64 (1.7-8build1) ... Setting up libtext-charwidth-perl:amd64 (0.04-11build1) ... Setting up lto-disabled-list (45) ... Setting up apt-utils (2.7.10) ... Setting up bsdextrautils (2.39.2-6ubuntu1) ... Setting up cpp-13 (13.2.0-10ubuntu1) ... Setting up init (1.66ubuntu1) ... Setting up psmisc (23.6-2) ... Setting up libtirpc-common (1.3.4+ds-1build1) ... Setting up libsqlite3-0:amd64 (3.44.2-1) ... Setting up binutils-common:amd64 (2.41.90.20240115-1ubuntu1) ... Installing new version of config file /etc/gprofng.rc ... Setting up linux-libc-dev:amd64 (6.6.0-14.14) ... Setting up libctf-nobfd0:amd64 (2.41.90.20240115-1ubuntu1) ... Setting up krb5-locales (1.20.1-5build1) ... Setting up libgomp1:amd64 (13.2.0-10ubuntu1) ... Setting up libsframe1:amd64 (2.41.90.20240115-1ubuntu1) ... Setting up libfakeroot:amd64 (1.32.2-1) ... Setting up libkrb5support0:amd64 (1.20.1-5build1) ... Setting up tzdata (2023d-1ubuntu2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 19 18:59:56 UTC 2024. Universal Time is now: Fri Jan 19 18:59:56 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.32.2-1) ... Setting up perl-modules-5.36 (5.36.0-10ubuntu1) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.4.5-0.3) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libquadmath0:amd64 (13.2.0-10ubuntu1) ... Setting up libproc2-0:amd64 (2:4.0.4-2ubuntu1) ... Setting up libpng16-16:amd64 (1.6.40-3) ... Setting up libatomic1:amd64 (13.2.0-10ubuntu1) ... Setting up usrmerge (38ubuntu1) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5build1) ... Setting up libubsan1:amd64 (13.2.0-10ubuntu1) ... Setting up uuid-runtime (2.39.2-6ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libhwasan0:amd64 (13.2.0-10ubuntu1) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... Setting up cpp (4:13.2.0-2ubuntu1) ... Setting up libasan8:amd64 (13.2.0-10ubuntu1) ... Setting up procps (2:4.0.4-2ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20231126-1) ... Setting up libkrb5-3:amd64 (1.20.1-5build1) ... Setting up libtsan2:amd64 (13.2.0-10ubuntu1) ... Setting up libbinutils:amd64 (2.41.90.20240115-1ubuntu1) ... Setting up libc-dev-bin (2.38-3ubuntu1) ... Setting up openssl (3.0.10-1ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3) ... Setting up libcc1-0:amd64 (13.2.0-10ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6build1) ... Setting up liblsan0:amd64 (13.2.0-10ubuntu1) ... Setting up libitm1:amd64 (13.2.0-10ubuntu1) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libctf0:amd64 (2.41.90.20240115-1ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu1) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up debconf-i18n (1.5.83) ... Setting up libgprofng0:amd64 (2.41.90.20240115-1ubuntu1) ... Setting up optipng (0.7.7-3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5build1) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libgcc-13-dev:amd64 (13.2.0-10ubuntu1) ... Setting up libperl5.36:amd64 (5.36.0-10ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.41.90.20240115-1ubuntu1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1build1) ... Setting up libperl5.38:amd64 (5.38.2-3) ... Setting up binutils (2.41.90.20240115-1ubuntu1) ... Setting up perl (5.38.2-3) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ... Setting up gcc-13 (13.2.0-10ubuntu1) ... Setting up libdpkg-perl (1.22.2ubuntu2) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up gcc (4:13.2.0-2ubuntu1) ... Setting up dpkg-dev (1.22.2ubuntu2) ... Setting up libnsl-dev:amd64 (1.3.0-3) ... Setting up libc6-dev:amd64 (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:amd64 (13.2.0-10ubuntu1) ... Setting up g++-13 (13.2.0-10ubuntu1) ... Setting up g++ (4:13.2.0-2ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.16) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27660350 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27660350 --arch=amd64 --dist=noble-proposed --nolog -A apbs_3.4.1-5build5.dsc Initiating build PACKAGEBUILD-27660350 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-058.buildd +==============================================================================+ | apbs 3.4.1-5build5 (amd64) Fri, 19 Jan 2024 18:59:57 +0000 | +==============================================================================+ Package: apbs Version: 3.4.1-5build5 Source Version: 3.4.1-5build5 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27660350/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-BfNPLZ/resolver-YzaSk2' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- apbs_3.4.1-5build5.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/apbs-BfNPLZ/apbs-3.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-BfNPLZ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, build-essential, fakeroot, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, build-essential, fakeroot, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [524 B] Get:5 copy:/<>/apt_archive ./ Packages [597 B] Fetched 2078 B in 0s (200 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file fonts-font-awesome fonts-lato fonts-mathjax gettext gettext-base gfortran-13 groff-base ibverbs-providers intltool-debian libamd3 libarchive-zip-perl libarchive13 libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libbsd0 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcurl4 libcxsparse4 libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 libklu2 liblapack-dev liblapack3 libldap2 libldl3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libparu0 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib librbio4 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libspex2 libspqr4 libssh-4 libsub-override-perl libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7 libsuperlu-dev libsuperlu6 libtool libuchardet0 libucx0 libumfpack6 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libyaml-0-2 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config pkgconf pkgconf-bin po-debconf pybind11-dev pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster python3-babel python3-build python3-certifi python3-chardet python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-installer python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-toml python3-tz python3-urllib3 python3-wheel python3-yaml python3.12 python3.12-dev python3.12-minimal sgml-base sphinx-common sphinx-rtd-theme-common swig swig4.0 xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit gettext-doc libasprintf-dev libgettextpo-dev gfortran-13-multilib gfortran-13-doc libcoarrays-dev groff lrzip liblapack-doc libhwloc-contrib-plugins libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc libtool-doc openmpi-doc pciutils libsuperlu-doc gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv python3-pip docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-installer-doc python-jinja2-doc python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-stemmer dvipng fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.12-venv python3.12-doc binfmt-support sgml-base-doc swig-doc swig-examples swig4.0-examples swig4.0-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules libgraphblas-dev xauth libmail-sendmail-perl libeigen3-dev libpaper-utils python3-pil python3-numpy The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file fonts-font-awesome fonts-lato fonts-mathjax gettext gettext-base gfortran-13 groff-base ibverbs-providers intltool-debian libamd3 libarchive-zip-perl libarchive13 libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libbsd0 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcurl4 libcxsparse4 libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 libklu2 liblapack-dev liblapack3 libldap2 libldl3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libparu0 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib librbio4 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libspex2 libspqr4 libssh-4 libsub-override-perl libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7 libsuperlu-dev libsuperlu6 libtool libuchardet0 libucx0 libumfpack6 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libyaml-0-2 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config pkgconf pkgconf-bin po-debconf pybind11-dev pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster python3-babel python3-build python3-certifi python3-chardet python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-installer python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-toml python3-tz python3-urllib3 python3-wheel python3-yaml python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common sphinx-rtd-theme-common swig swig4.0 xml-core zlib1g-dev 0 upgraded, 195 newly installed, 0 to remove and 0 not upgraded. Need to get 122 MB of archives. After this operation, 468 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [820 B] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.12-minimal amd64 3.12.1-2 [830 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libexpat1 amd64 2.5.0-2 [85.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 python3.12-minimal amd64 3.12.1-2 [2381 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-minimal amd64 3.12.1-0ubuntu1 [26.9 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 netbase all 6.4 [13.1 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [2034 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 python3.12 amd64 3.12.1-2 [638 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpython3-stdlib amd64 3.12.1-0ubuntu1 [9654 B] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3 amd64 3.12.1-0ubuntu1 [22.9 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-lato all 2.015-1 [2781 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 sgml-base all 1.31 [11.4 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libbsd0 amd64 0.11.8-1 [41.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libelf1 amd64 0.190-1 [57.0 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libicu74 amd64 74.2-1ubuntu1 [10.9 MB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libxml2 amd64 2.9.14+dfsg-1.3build3 [762 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libyaml-0-2 amd64 0.2.5-1 [52.8 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 python3-pkg-resources all 68.1.2-2 [167 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 python3-pygments all 2.15.1+dfsg-1 [820 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-yaml amd64 6.0.1-2 [184 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic-mgc amd64 1:5.45-2 [307 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic1 amd64 1:5.45-2 [86.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 file amd64 1:5.45-2 [21.9 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-14 [38.3 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.8-1 [75.3 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 groff-base amd64 1.23.0-3 [1023 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libcbor0.10 amd64 0.10.2-1.1ubuntu1 [25.7 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libedit2 amd64 3.1-20230828-1 [95.8 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libfido2-1 amd64 1.14.0-1 [84.9 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libnghttp2-14 amd64 1.58.0-1 [73.2 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libnuma1 amd64 2.0.16-1 [22.6 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libpsl5 amd64 0.21.2-1build1 [56.8 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libuv1 amd64 1.46.0-3 [114 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-data all 2:1.8.7-1 [115 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-6 amd64 2:1.8.7-1 [642 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 man-db amd64 2.12.0-3 [1230 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 openssh-client amd64 1:9.4p1-1ubuntu2 [888 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14 [422 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive13 amd64 3.7.2-1ubuntu2 [378 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libbrotli1 amd64 1.1.0-2 [332 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4 [20.1 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4 [53.3 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libldap2 amd64 2.6.6+dfsg-1~exp1ubuntu2 [194 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libssh-4 amd64 0.10.6-2 [220 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libcurl4 amd64 8.5.0-2ubuntu1 [397 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libjsoncpp25 amd64 1.9.5-6 [82.3 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 librhash0 amd64 1.4.3-3 [128 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 cmake-data all 3.28.1-1 [2621 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 cmake amd64 3.28.1-1 [14.5 MB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libdebhelper-perl all 13.11.9ubuntu1 [97.7 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1 amd64 0.190-1 [260 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 dwz amd64 0.15-1 [112 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14 [865 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 debhelper all 13.11.9ubuntu1 [968 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 python3-lib2to3 all 3.11.5-1 [79.0 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 python3-distutils all 3.11.5-1 [131 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 python3-setuptools all 68.1.2-2 [396 kB] Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 dh-python all 6.20231223 [128 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 xml-core all 0.19 [20.3 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 docutils-common all 0.20.1+dfsg-3 [132 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgfortran5 amd64 13.2.0-10ubuntu1 [890 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgfortran-13-dev amd64 13.2.0-10ubuntu1 [941 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gfortran-13 amd64 13.2.0-10ubuntu1 [11.4 MB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libnl-3-200 amd64 3.7.0-0.3 [55.5 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [189 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libibverbs1 amd64 48.0-1 [67.8 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 ibverbs-providers amd64 48.0-1 [369 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsuitesparseconfig7 amd64 1:7.5.1+dfsg-1 [12.7 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libamd3 amd64 1:7.5.1+dfsg-1 [27.1 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.11.0-2build1 [237 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.11.0-2build1 [2623 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe amd64 libarpack2 amd64 3.9.1-1 [105 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.11.0-2build1 [170 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.11.0-2build1 [5104 kB] Get:97 http://ftpmaster.internal/ubuntu noble/universe amd64 libarpack2-dev amd64 3.9.1-1 [122 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libbtf2 amd64 1:7.5.1+dfsg-1 [13.4 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libcamd3 amd64 1:7.5.1+dfsg-1 [23.8 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libccolamd3 amd64 1:7.5.1+dfsg-1 [25.9 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcolamd3 amd64 1:7.5.1+dfsg-1 [19.4 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libcholmod5 amd64 1:7.5.1+dfsg-1 [667 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libcxsparse4 amd64 1:7.5.1+dfsg-1 [74.9 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-2.1-7 amd64 2.1.12-stable-9 [144 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-9 [91.2 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-9 [64.0 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-9 [7802 B] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-9 [15.8 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-dev amd64 2.1.12-stable-9 [273 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libexpat1-dev amd64 2.5.0-2 [137 kB] Get:111 http://ftpmaster.internal/ubuntu noble/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [178 kB] Get:112 http://ftpmaster.internal/ubuntu noble/universe amd64 libpsm2-2 amd64 11.2.185-2 [196 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 librdmacm1 amd64 48.0-1 [70.7 kB] Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 libfabric1 amd64 1.17.0-3 [665 kB] Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc15 amd64 2.10.0-1 [171 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-sphinxdoc all 7.2.6-3 [149 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libjson-perl all 4.10000-1 [81.9 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libklu2 amd64 1:7.5.1+dfsg-1 [79.0 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libldl3 amd64 1:7.5.1+dfsg-1 [13.1 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 libltdl7 amd64 2.4.7-7 [40.5 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 libltdl-dev amd64 2.4.7-7 [169 kB] Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 libmaloc1 amd64 1.5-1 [81.4 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 libmaloc-dev amd64 1.5-1 [104 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.5 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [216 kB] Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 libmunge2 amd64 0.5.15-3ubuntu1 [14.6 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 libpciaccess0 amd64 0.17-3 [18.9 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu1 [11.5 kB] Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1 [38.3 kB] Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc-plugins amd64 2.10.0-1 [15.8 kB] Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 libpmix2 amd64 5.0.1-4 [695 kB] Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 libucx0 amd64 1.15.0-1 [989 kB] Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 libopenmpi3 amd64 4.1.6-5ubuntu1 [3177 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libumfpack6 amd64 1:7.5.1+dfsg-1 [268 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libparu0 amd64 1:7.5.1+dfsg-1 [50.0 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 libnuma-dev amd64 2.0.16-1 [36.3 kB] Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 libhwloc-dev amd64 2.10.0-1 [267 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 libpmix-dev amd64 5.0.1-4 [4013 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.12 amd64 3.12.1-2 [2355 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.12-dev amd64 3.12.1-2 [5528 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpython3-dev amd64 3.12.1-0ubuntu1 [9920 B] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 librbio4 amd64 1:7.5.1+dfsg-1 [26.5 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libspex2 amd64 1:7.5.1+dfsg-1 [35.0 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libspqr4 amd64 1:7.5.1+dfsg-1 [135 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libsuitesparse-mongoose3 amd64 1:7.5.1+dfsg-1 [33.5 kB] Get:151 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libsuitesparse-dev amd64 1:7.5.1+dfsg-1 [1535 kB] Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 libsuperlu6 amd64 6.0.1+dfsg1-1 [184 kB] Get:153 http://ftpmaster.internal/ubuntu noble/universe amd64 libsuperlu-dev amd64 6.0.1+dfsg1-1 [20.7 kB] Get:154 http://ftpmaster.internal/ubuntu noble/universe amd64 openmpi-common all 4.1.6-5ubuntu1 [178 kB] Get:155 http://ftpmaster.internal/ubuntu noble/universe amd64 openmpi-bin amd64 4.1.6-5ubuntu1 [124 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B] Get:159 http://ftpmaster.internal/ubuntu noble/universe amd64 pybind11-dev all 2.11.1-2 [159 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 python3-packaging all 23.2-1 [40.6 kB] Get:161 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pyproject-hooks all 1.0.0-2 [9434 B] Get:162 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] Get:163 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-wheel all 0.42.0-1 [53.1 kB] Get:164 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-build all 0.10.0-1 [17.6 kB] Get:165 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-installer all 0.7.0+dfsg1-2 [18.1 kB] Get:166 http://ftpmaster.internal/ubuntu noble/universe amd64 pybuild-plugin-pyproject all 6.20231223 [1762 B] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 python-babel-localedata all 2.10.3-3build1 [6357 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 python3-tz all 2023.3.post1-2 [31.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main amd64 python3-babel all 2.10.3-3build1 [87.5 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 python3-certifi all 2023.11.17-1 [165 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 python3.12-dev amd64 3.12.1-2 [505 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-dev amd64 3.12.1-0ubuntu1 [26.7 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main amd64 python3-roman all 3.3-3 [9632 B] Get:175 http://ftpmaster.internal/ubuntu noble/main amd64 python3-docutils all 0.20.1+dfsg-3 [393 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main amd64 python3-idna all 3.3-2 [45.4 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main amd64 python3-imagesize all 1.4.1-1 [6844 B] Get:178 http://ftpmaster.internal/ubuntu noble/main amd64 python3-markupsafe amd64 2.1.3-1build1 [13.6 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main amd64 python3-jinja2 all 3.1.2-1 [107 kB] Get:180 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pybind11 all 2.11.1-2 [167 kB] Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-urllib3 all 2.0.7-1 [113 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main amd64 python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:183 http://ftpmaster.internal/ubuntu noble/main amd64 python3-snowballstemmer all 2.2.0-4 [59.7 kB] Get:184 http://ftpmaster.internal/ubuntu noble/main amd64 sphinx-common all 7.2.6-3 [741 kB] Get:185 http://ftpmaster.internal/ubuntu noble/main amd64 python3-alabaster all 0.7.12-1 [17.8 kB] Get:186 http://ftpmaster.internal/ubuntu noble/main amd64 python3-sphinx all 7.2.6-3 [557 kB] Get:187 http://ftpmaster.internal/ubuntu noble/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] Get:188 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] Get:189 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [23.1 kB] Get:190 http://ftpmaster.internal/ubuntu noble/universe amd64 swig4.0 amd64 4.1.0-0.3 [1171 kB] Get:191 http://ftpmaster.internal/ubuntu noble/universe amd64 swig all 4.1.0-0.3 [5990 B] Get:192 http://ftpmaster.internal/ubuntu noble/main amd64 libibverbs-dev amd64 48.0-1 [676 kB] Get:193 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] Get:194 http://ftpmaster.internal/ubuntu noble/universe amd64 libopenmpi-dev amd64 4.1.6-5ubuntu1 [1713 kB] Get:195 http://ftpmaster.internal/ubuntu noble/universe amd64 mpi-default-dev amd64 1.15 [3118 B] Preconfiguring packages ... Fetched 122 MB in 2s (78.7 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 15778 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.1-2_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.1-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.1-2_amd64.deb ... Unpacking python3.12-minimal (3.12.1-2) ... Setting up libpython3.12-minimal:amd64 (3.12.1-2) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.12-minimal (3.12.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 16096 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_amd64.deb ... Unpacking python3-minimal (3.12.1-0ubuntu1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../3-libpython3.12-stdlib_3.12.1-2_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.1-2) ... Selecting previously unselected package python3.12. Preparing to unpack .../4-python3.12_3.12.1-2_amd64.deb ... Unpacking python3.12 (3.12.1-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../5-libpython3-stdlib_3.12.1-0ubuntu1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.1-0ubuntu1) ... Setting up python3-minimal (3.12.1-0ubuntu1) ... Selecting previously unselected package python3. (Reading database ... 16537 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.1-0ubuntu1_amd64.deb ... Unpacking python3 (3.12.1-0ubuntu1) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../001-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../002-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../003-libbsd0_0.11.8-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.8-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../004-libelf1_0.190-1_amd64.deb ... Unpacking libelf1:amd64 (0.190-1) ... Selecting previously unselected package libicu74:amd64. Preparing to unpack .../005-libicu74_74.2-1ubuntu1_amd64.deb ... Unpacking libicu74:amd64 (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../006-libxml2_2.9.14+dfsg-1.3build3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3build3) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../007-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../008-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../009-python3-pygments_2.15.1+dfsg-1_all.deb ... Unpacking python3-pygments (2.15.1+dfsg-1) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../010-python3-yaml_6.0.1-2_amd64.deb ... Unpacking python3-yaml (6.0.1-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../011-libmagic-mgc_1%3a5.45-2_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../012-libmagic1_1%3a5.45-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2) ... Selecting previously unselected package file. Preparing to unpack .../013-file_1%3a5.45-2_amd64.deb ... Unpacking file (1:5.45-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../014-gettext-base_0.21-14_amd64.deb ... Unpacking gettext-base (0.21-14) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../015-libuchardet0_0.0.8-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../016-groff-base_1.23.0-3_amd64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../017-libcbor0.10_0.10.2-1.1ubuntu1_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-1.1ubuntu1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../018-libedit2_3.1-20230828-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20230828-1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../019-libfido2-1_1.14.0-1_amd64.deb ... Unpacking libfido2-1:amd64 (1.14.0-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../020-libnghttp2-14_1.58.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.58.0-1) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../021-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../022-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../023-libpsl5_0.21.2-1build1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1build1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../024-libuv1_1.46.0-3_amd64.deb ... Unpacking libuv1:amd64 (1.46.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../025-libxau6_1%3a1.0.9-1build5_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1build5) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../026-libxdmcp6_1%3a1.1.3-0ubuntu5_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../027-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../028-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../029-libx11-6_2%3a1.8.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../030-libxext6_2%3a1.3.4-1build1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../031-man-db_2.12.0-3_amd64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../032-openssh-client_1%3a9.4p1-1ubuntu2_amd64.deb ... Unpacking openssh-client (1:9.4p1-1ubuntu2) ... Selecting previously unselected package m4. Preparing to unpack .../033-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../034-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../035-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../036-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../037-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../038-libarchive13_3.7.2-1ubuntu2_amd64.deb ... Unpacking libarchive13:amd64 (3.7.2-1ubuntu2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../039-libbrotli1_1.1.0-2_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../040-libsasl2-modules-db_2.1.28+dfsg1-4_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-4) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../041-libsasl2-2_2.1.28+dfsg1-4_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../042-libldap2_2.6.6+dfsg-1~exp1ubuntu2_amd64.deb ... Unpacking libldap2:amd64 (2.6.6+dfsg-1~exp1ubuntu2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../043-librtmp1_2.4+20151223.gitfa8646d.1-2build4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Selecting previously unselected package libssh-4:amd64. Preparing to unpack .../044-libssh-4_0.10.6-2_amd64.deb ... Unpacking libssh-4:amd64 (0.10.6-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../045-libcurl4_8.5.0-2ubuntu1_amd64.deb ... Unpacking libcurl4:amd64 (8.5.0-2ubuntu1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../046-libjsoncpp25_1.9.5-6_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../047-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package cmake-data. Preparing to unpack .../048-cmake-data_3.28.1-1_all.deb ... Unpacking cmake-data (3.28.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../049-cmake_3.28.1-1_amd64.deb ... Unpacking cmake (3.28.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../050-libdebhelper-perl_13.11.9ubuntu1_all.deb ... Unpacking libdebhelper-perl (13.11.9ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../051-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../052-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../053-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../054-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../055-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../056-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libdw1:amd64. Preparing to unpack .../057-libdw1_0.190-1_amd64.deb ... Unpacking libdw1:amd64 (0.190-1) ... Selecting previously unselected package debugedit. Preparing to unpack .../058-debugedit_1%3a5.0-5_amd64.deb ... Unpacking debugedit (1:5.0-5) ... Selecting previously unselected package dwz. Preparing to unpack .../059-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../060-gettext_0.21-14_amd64.deb ... Unpacking gettext (0.21-14) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../061-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../062-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../063-debhelper_13.11.9ubuntu1_all.deb ... Unpacking debhelper (13.11.9ubuntu1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../064-python3-lib2to3_3.11.5-1_all.deb ... Unpacking python3-lib2to3 (3.11.5-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../065-python3-distutils_3.11.5-1_all.deb ... Unpacking python3-distutils (3.11.5-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../066-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../067-dh-python_6.20231223_all.deb ... Unpacking dh-python (6.20231223) ... Selecting previously unselected package xml-core. Preparing to unpack .../068-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package docutils-common. Preparing to unpack .../069-docutils-common_0.20.1+dfsg-3_all.deb ... Unpacking docutils-common (0.20.1+dfsg-3) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../070-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../071-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../072-libgfortran5_13.2.0-10ubuntu1_amd64.deb ... Unpacking libgfortran5:amd64 (13.2.0-10ubuntu1) ... Selecting previously unselected package libgfortran-13-dev:amd64. Preparing to unpack .../073-libgfortran-13-dev_13.2.0-10ubuntu1_amd64.deb ... Unpacking libgfortran-13-dev:amd64 (13.2.0-10ubuntu1) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../074-gfortran-13_13.2.0-10ubuntu1_amd64.deb ... Unpacking gfortran-13 (13.2.0-10ubuntu1) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../075-libnl-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../076-libnl-route-3-200_3.7.0-0.3_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../077-libibverbs1_48.0-1_amd64.deb ... Unpacking libibverbs1:amd64 (48.0-1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../078-ibverbs-providers_48.0-1_amd64.deb ... Unpacking ibverbs-providers:amd64 (48.0-1) ... Selecting previously unselected package libsuitesparseconfig7:amd64. Preparing to unpack .../079-libsuitesparseconfig7_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libsuitesparseconfig7:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libamd3:amd64. Preparing to unpack .../080-libamd3_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libamd3:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../081-libblas3_3.11.0-2build1_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2build1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../082-liblapack3_3.11.0-2build1_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2build1) ... Selecting previously unselected package libarpack2:amd64. Preparing to unpack .../083-libarpack2_3.9.1-1_amd64.deb ... Unpacking libarpack2:amd64 (3.9.1-1) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../084-libblas-dev_3.11.0-2build1_amd64.deb ... Unpacking libblas-dev:amd64 (3.11.0-2build1) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../085-liblapack-dev_3.11.0-2build1_amd64.deb ... Unpacking liblapack-dev:amd64 (3.11.0-2build1) ... Selecting previously unselected package libarpack2-dev:amd64. Preparing to unpack .../086-libarpack2-dev_3.9.1-1_amd64.deb ... Unpacking libarpack2-dev:amd64 (3.9.1-1) ... Selecting previously unselected package libbtf2:amd64. Preparing to unpack .../087-libbtf2_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libbtf2:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libcamd3:amd64. Preparing to unpack .../088-libcamd3_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libcamd3:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libccolamd3:amd64. Preparing to unpack .../089-libccolamd3_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libccolamd3:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libcolamd3:amd64. Preparing to unpack .../090-libcolamd3_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libcolamd3:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libcholmod5:amd64. Preparing to unpack .../091-libcholmod5_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libcholmod5:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libcxsparse4:amd64. Preparing to unpack .../092-libcxsparse4_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libcxsparse4:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../093-libevent-2.1-7_2.1.12-stable-9_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.12-stable-9) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../094-libevent-core-2.1-7_2.1.12-stable-9_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-9) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../095-libevent-extra-2.1-7_2.1.12-stable-9_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.12-stable-9) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../096-libevent-pthreads-2.1-7_2.1.12-stable-9_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-9) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../097-libevent-openssl-2.1-7_2.1.12-stable-9_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.12-stable-9) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../098-libevent-dev_2.1.12-stable-9_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-9) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../099-libexpat1-dev_2.5.0-2_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.5.0-2) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../100-libpsm-infinipath1_3.3+20.604758e7-6.3_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../101-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../102-librdmacm1_48.0-1_amd64.deb ... Unpacking librdmacm1:amd64 (48.0-1) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../103-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../104-libhwloc15_2.10.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.10.0-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../105-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../106-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../107-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../108-libjs-sphinxdoc_7.2.6-3_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-3) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../109-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package libklu2:amd64. Preparing to unpack .../110-libklu2_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libklu2:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libldl3:amd64. Preparing to unpack .../111-libldl3_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libldl3:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../112-libltdl7_2.4.7-7_amd64.deb ... Unpacking libltdl7:amd64 (2.4.7-7) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../113-libltdl-dev_2.4.7-7_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.7-7) ... Selecting previously unselected package libmaloc1. Preparing to unpack .../114-libmaloc1_1.5-1_amd64.deb ... Unpacking libmaloc1 (1.5-1) ... Selecting previously unselected package libmaloc-dev. Preparing to unpack .../115-libmaloc-dev_1.5-1_amd64.deb ... Unpacking libmaloc-dev (1.5-1) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../116-libnl-3-dev_3.7.0-0.3_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../117-libnl-route-3-dev_3.7.0-0.3_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.7.0-0.3) ... Selecting previously unselected package libmunge2:amd64. Preparing to unpack .../118-libmunge2_0.5.15-3ubuntu1_amd64.deb ... Unpacking libmunge2:amd64 (0.5.15-3ubuntu1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../119-libpciaccess0_0.17-3_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-3) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../120-libxnvctrl0_510.47.03-0ubuntu1_amd64.deb ... Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../121-ocl-icd-libopencl1_2.3.2-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../122-libhwloc-plugins_2.10.0-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.10.0-1) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../123-libpmix2_5.0.1-4_amd64.deb ... Unpacking libpmix2:amd64 (5.0.1-4) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../124-libucx0_1.15.0-1_amd64.deb ... Unpacking libucx0:amd64 (1.15.0-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../125-libopenmpi3_4.1.6-5ubuntu1_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.6-5ubuntu1) ... Selecting previously unselected package libumfpack6:amd64. Preparing to unpack .../126-libumfpack6_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libumfpack6:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libparu0:amd64. Preparing to unpack .../127-libparu0_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libparu0:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../128-libpkgconf3_1.8.1-2_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-2) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../129-libnuma-dev_2.0.16-1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.16-1) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../130-libhwloc-dev_2.10.0-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.10.0-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../131-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... Selecting previously unselected package libpmix-dev:amd64. Preparing to unpack .../132-libpmix-dev_5.0.1-4_amd64.deb ... Unpacking libpmix-dev:amd64 (5.0.1-4) ... Selecting previously unselected package libpython3.12:amd64. Preparing to unpack .../133-libpython3.12_3.12.1-2_amd64.deb ... Unpacking libpython3.12:amd64 (3.12.1-2) ... Selecting previously unselected package libpython3.12-dev:amd64. Preparing to unpack .../134-libpython3.12-dev_3.12.1-2_amd64.deb ... Unpacking libpython3.12-dev:amd64 (3.12.1-2) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../135-libpython3-dev_3.12.1-0ubuntu1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.12.1-0ubuntu1) ... Selecting previously unselected package librbio4:amd64. Preparing to unpack .../136-librbio4_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking librbio4:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libspex2:amd64. Preparing to unpack .../137-libspex2_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libspex2:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libspqr4:amd64. Preparing to unpack .../138-libspqr4_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libspqr4:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libsuitesparse-mongoose3:amd64. Preparing to unpack .../139-libsuitesparse-mongoose3_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libsuitesparse-mongoose3:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libsuitesparse-dev:amd64. Preparing to unpack .../140-libsuitesparse-dev_1%3a7.5.1+dfsg-1_amd64.deb ... Unpacking libsuitesparse-dev:amd64 (1:7.5.1+dfsg-1) ... Selecting previously unselected package libsuperlu6:amd64. Preparing to unpack .../141-libsuperlu6_6.0.1+dfsg1-1_amd64.deb ... Unpacking libsuperlu6:amd64 (6.0.1+dfsg1-1) ... Selecting previously unselected package libsuperlu-dev:amd64. Preparing to unpack .../142-libsuperlu-dev_6.0.1+dfsg1-1_amd64.deb ... Unpacking libsuperlu-dev:amd64 (6.0.1+dfsg1-1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../143-openmpi-common_4.1.6-5ubuntu1_all.deb ... Unpacking openmpi-common (4.1.6-5ubuntu1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../144-openmpi-bin_4.1.6-5ubuntu1_amd64.deb ... Unpacking openmpi-bin (4.1.6-5ubuntu1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../145-pkgconf-bin_1.8.1-2_amd64.deb ... Unpacking pkgconf-bin (1.8.1-2) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../146-pkgconf_1.8.1-2_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-2) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../147-pkg-config_1.8.1-2_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-2) ... Selecting previously unselected package pybind11-dev. Preparing to unpack .../148-pybind11-dev_2.11.1-2_all.deb ... Unpacking pybind11-dev (2.11.1-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../149-python3-packaging_23.2-1_all.deb ... Unpacking python3-packaging (23.2-1) ... Selecting previously unselected package python3-pyproject-hooks. Preparing to unpack .../150-python3-pyproject-hooks_1.0.0-2_all.deb ... Unpacking python3-pyproject-hooks (1.0.0-2) ... Selecting previously unselected package python3-toml. Preparing to unpack .../151-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../152-python3-wheel_0.42.0-1_all.deb ... Unpacking python3-wheel (0.42.0-1) ... Selecting previously unselected package python3-build. Preparing to unpack .../153-python3-build_0.10.0-1_all.deb ... Unpacking python3-build (0.10.0-1) ... Selecting previously unselected package python3-installer. Preparing to unpack .../154-python3-installer_0.7.0+dfsg1-2_all.deb ... Unpacking python3-installer (0.7.0+dfsg1-2) ... Selecting previously unselected package pybuild-plugin-pyproject. Preparing to unpack .../155-pybuild-plugin-pyproject_6.20231223_all.deb ... Unpacking pybuild-plugin-pyproject (6.20231223) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../156-python-babel-localedata_2.10.3-3build1_all.deb ... Unpacking python-babel-localedata (2.10.3-3build1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../157-python3-tz_2023.3.post1-2_all.deb ... Unpacking python3-tz (2023.3.post1-2) ... Selecting previously unselected package python3-babel. Preparing to unpack .../158-python3-babel_2.10.3-3build1_all.deb ... Unpacking python3-babel (2.10.3-3build1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../159-python3-certifi_2023.11.17-1_all.deb ... Unpacking python3-certifi (2023.11.17-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../160-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../161-python3.12-dev_3.12.1-2_amd64.deb ... Unpacking python3.12-dev (3.12.1-2) ... Selecting previously unselected package python3-dev. Preparing to unpack .../162-python3-dev_3.12.1-0ubuntu1_amd64.deb ... Unpacking python3-dev (3.12.1-0ubuntu1) ... Selecting previously unselected package python3-roman. Preparing to unpack .../163-python3-roman_3.3-3_all.deb ... Unpacking python3-roman (3.3-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../164-python3-docutils_0.20.1+dfsg-3_all.deb ... Unpacking python3-docutils (0.20.1+dfsg-3) ... Selecting previously unselected package python3-idna. Preparing to unpack .../165-python3-idna_3.3-2_all.deb ... Unpacking python3-idna (3.3-2) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../166-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../167-python3-markupsafe_2.1.3-1build1_amd64.deb ... Unpacking python3-markupsafe (2.1.3-1build1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../168-python3-jinja2_3.1.2-1_all.deb ... Unpacking python3-jinja2 (3.1.2-1) ... Selecting previously unselected package python3-pybind11. Preparing to unpack .../169-python3-pybind11_2.11.1-2_all.deb ... Unpacking python3-pybind11 (2.11.1-2) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../170-python3-urllib3_2.0.7-1_all.deb ... Unpacking python3-urllib3 (2.0.7-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../171-python3-requests_2.31.0+dfsg-1ubuntu1_all.deb ... Unpacking python3-requests (2.31.0+dfsg-1ubuntu1) ... Selecting previously unselected package python3-snowballstemmer. Preparing to unpack .../172-python3-snowballstemmer_2.2.0-4_all.deb ... Unpacking python3-snowballstemmer (2.2.0-4) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../173-sphinx-common_7.2.6-3_all.deb ... Unpacking sphinx-common (7.2.6-3) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../174-python3-alabaster_0.7.12-1_all.deb ... Unpacking python3-alabaster (0.7.12-1) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../175-python3-sphinx_7.2.6-3_all.deb ... Unpacking python3-sphinx (7.2.6-3) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../176-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Selecting previously unselected package python3-sphinxcontrib.jquery. Preparing to unpack .../177-python3-sphinxcontrib.jquery_4.1-5_all.deb ... Unpacking python3-sphinxcontrib.jquery (4.1-5) ... Selecting previously unselected package python3-sphinx-rtd-theme. Preparing to unpack .../178-python3-sphinx-rtd-theme_2.0.0+dfsg-1_all.deb ... Unpacking python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Selecting previously unselected package swig4.0. Preparing to unpack .../179-swig4.0_4.1.0-0.3_amd64.deb ... Unpacking swig4.0 (4.1.0-0.3) ... Selecting previously unselected package swig. Preparing to unpack .../180-swig_4.1.0-0.3_all.deb ... Unpacking swig (4.1.0-0.3) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../181-libibverbs-dev_48.0-1_amd64.deb ... Unpacking libibverbs-dev:amd64 (48.0-1) ... Selecting previously unselected package libjs-mathjax. Preparing to unpack .../182-libjs-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking libjs-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package libopenmpi-dev:amd64. Preparing to unpack .../183-libopenmpi-dev_4.1.6-5ubuntu1_amd64.deb ... Unpacking libopenmpi-dev:amd64 (4.1.6-5ubuntu1) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../184-mpi-default-dev_1.15_amd64.deb ... Unpacking mpi-default-dev (1.15) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../185-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libmaloc1 (1.5-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpciaccess0:amd64 (0.17-3) ... Setting up libxau6:amd64 (1:1.0.9-1build5) ... Setting up libpsl5:amd64 (0.21.2-1build1) ... Setting up fonts-lato (2.015-1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up libcbor0.10:amd64 (0.10.2-1.1ubuntu1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libdebhelper-perl (13.11.9ubuntu1) ... Setting up libbrotli1:amd64 (1.1.0-2) ... Setting up libcxsparse4:amd64 (1:7.5.1+dfsg-1) ... Setting up libnghttp2-14:amd64 (1.58.0-1) ... Setting up libmagic1:amd64 (1:5.45-2) ... Setting up gettext-base (0.21-14) ... Setting up m4 (1.4.19-4) ... Setting up libldl3:amd64 (1:7.5.1+dfsg-1) ... Setting up file (1:5.45-2) ... Setting up python-babel-localedata (2.10.3-3build1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4) ... Setting up libbtf2:amd64 (1:7.5.1+dfsg-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-2) ... Setting up libuv1:amd64 (1.46.0-3) ... Setting up libmunge2:amd64 (0.5.15-3ubuntu1) ... Setting up libexpat1-dev:amd64 (2.5.0-2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libhwloc15:amd64 (2.10.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-9) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-9) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libltdl7:amd64 (2.4.7-7) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4) ... Setting up libssh-4:amd64 (0.10.6-2) ... Setting up libgfortran5:amd64 (13.2.0-10ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libicu74:amd64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.6-5ubuntu1) ... Setting up libsuitesparseconfig7:amd64 (1:7.5.1+dfsg-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.28.1-1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.3) ... Setting up libfido2-1:amd64 (1.14.0-1) ... Setting up libgfortran-13-dev:amd64 (13.2.0-10ubuntu1) ... Setting up libbsd0:amd64 (0.11.8-1) ... Setting up libelf1:amd64 (0.190-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3build3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libmaloc-dev (1.5-1) ... Setting up libldap2:amd64 (2.6.6+dfsg-1~exp1ubuntu2) ... Setting up libblas-dev:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-9) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:amd64 (0.190-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-9) ... Setting up liblapack3:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14) ... Setting up swig (4.1.0-0.3) ... Setting up libamd3:amd64 (1:7.5.1+dfsg-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.1-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:amd64 (1:7.5.1+dfsg-1) ... Setting up libarchive13:amd64 (3.7.2-1ubuntu2) ... Setting up libsuitesparse-mongoose3:amd64 (1:7.5.1+dfsg-1) ... Setting up python3.12 (3.12.1-2) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libarpack2:amd64 (3.9.1-1) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-9) ... Setting up libsuperlu6:amd64 (6.0.1+dfsg1-1) ... Setting up libcamd3:amd64 (1:7.5.1+dfsg-1) ... Setting up pkgconf:amd64 (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.16-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-7) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up gfortran-13 (13.2.0-10ubuntu1) ... Setting up librbio4:amd64 (1:7.5.1+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-9) ... Setting up liblapack-dev:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up pkg-config:amd64 (1.8.1-2) ... Setting up libjs-sphinxdoc (7.2.6-3) ... Setting up libccolamd3:amd64 (1:7.5.1+dfsg-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-3) ... Setting up xml-core (0.19) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:amd64 (8.5.0-2ubuntu1) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libhwloc-dev:amd64 (2.10.0-1) ... Setting up libsuperlu-dev:amd64 (6.0.1+dfsg1-1) ... Setting up libpython3.12:amd64 (3.12.1-2) ... Setting up libpython3-stdlib:amd64 (3.12.1-0ubuntu1) ... Setting up libibverbs1:amd64 (48.0-1) ... Setting up libcholmod5:amd64 (1:7.5.1+dfsg-1) ... Setting up libarpack2-dev:amd64 (3.9.1-1) ... Setting up libspex2:amd64 (1:7.5.1+dfsg-1) ... Setting up ibverbs-providers:amd64 (48.0-1) ... Setting up libspqr4:amd64 (1:7.5.1+dfsg-1) ... Setting up openssh-client (1:9.4p1-1ubuntu2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up python3 (3.12.1-0ubuntu1) ... Setting up libpython3.12-dev:amd64 (3.12.1-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.1.3-1build1) ... Setting up python3-tz (2023.3.post1-2) ... Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libklu2:amd64 (1:7.5.1+dfsg-1) ... Setting up sphinx-common (7.2.6-3) ... Setting up python3-idna (3.3-2) ... Setting up python3.12-dev (3.12.1-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-2) ... Setting up python3-urllib3 (2.0.7-1) ... Setting up libumfpack6:amd64 (1:7.5.1+dfsg-1) ... Setting up cmake (3.28.1-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up librdmacm1:amd64 (48.0-1) ... Setting up libucx0:amd64 (1.15.0-1) ... Setting up libpython3-dev:amd64 (3.12.1-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.10.3-3build1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.12-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up debhelper (13.11.9ubuntu1) ... Setting up libparu0:amd64 (1:7.5.1+dfsg-1) ... Setting up libibverbs-dev:amd64 (48.0-1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1) ... Setting up python3-wheel (0.42.0-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-pygments (2.15.1+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.12.1-0ubuntu1) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up python3-build (0.10.0-1) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20231223) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libsuitesparse-dev:amd64 (1:7.5.1+dfsg-1) ... Setting up libpmix2:amd64 (5.0.1-4) ... Setting up pybuild-plugin-pyproject (6.20231223) ... Setting up libopenmpi3:amd64 (4.1.6-5ubuntu1) ... Setting up libpmix-dev:amd64 (5.0.1-4) ... Setting up openmpi-bin (4.1.6-5ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.6-5ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for systemd (255.2-3ubuntu1) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-3) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.41.90.20240115-1ubuntu1 dpkg-dev_1.22.2ubuntu2 g++-13_13.2.0-10ubuntu1 gcc-13_13.2.0-10ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-10ubuntu1 libstdc++6_13.2.0-10ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.10 apt-utils_2.7.10 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41.90.20240115-1ubuntu1 binutils-common_2.41.90.20240115-1ubuntu1 binutils-x86-64-linux-gnu_2.41.90.20240115-1ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 cmake_3.28.1-1 cmake-data_3.28.1-1 coreutils_9.4-2ubuntu2 cpp_4:13.2.0-2ubuntu1 cpp-13_13.2.0-10ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.83 debconf-i18n_1.5.83 debhelper_13.11.9ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.2ubuntu2 dpkg-dev_1.22.2ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1 fonts-lato_2.015-1 fonts-mathjax_2.7.9+dfsg-1 g++_4:13.2.0-2ubuntu1 g++-13_13.2.0-10ubuntu1 gcc_4:13.2.0-2ubuntu1 gcc-13_13.2.0-10ubuntu1 gcc-13-base_13.2.0-10ubuntu1 gettext_0.21-14 gettext-base_0.21-14 gfortran-13_13.2.0-10ubuntu1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 ibverbs-providers_48.0-1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libamd3_1:7.5.1+dfsg-1 libapparmor1_4.0.0~alpha2-0ubuntu7 libapt-pkg6.0_2.7.10 libarchive-zip-perl_1.68-1 libarchive13_3.7.2-1ubuntu2 libargon2-1_0~20190702+dfsg-4 libarpack2_3.9.1-1 libarpack2-dev_3.9.1-1 libasan8_13.2.0-10ubuntu1 libassuan0_2.5.6-1 libatomic1_13.2.0-10ubuntu1 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41.90.20240115-1ubuntu1 libblas-dev_3.11.0-2build1 libblas3_3.11.0-2build1 libblkid1_2.39.2-6ubuntu1 libbrotli1_1.1.0-2 libbsd0_0.11.8-1 libbtf2_1:7.5.1+dfsg-1 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-3ubuntu1 libc-dev-bin_2.38-3ubuntu1 libc6_2.38-3ubuntu1 libc6-dev_2.38-3ubuntu1 libcamd3_1:7.5.1+dfsg-1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4ubuntu1 libcbor0.10_0.10.2-1.1ubuntu1 libcc1-0_13.2.0-10ubuntu1 libccolamd3_1:7.5.1+dfsg-1 libcholmod5_1:7.5.1+dfsg-1 libcolamd3_1:7.5.1+dfsg-1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.41.90.20240115-1ubuntu1 libctf0_2.41.90.20240115-1ubuntu1 libcurl4_8.5.0-2ubuntu1 libcxsparse4_1:7.5.1+dfsg-1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.11.9ubuntu1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.2ubuntu2 libdw1_0.190-1 libedit2_3.1-20230828-1 libelf1_0.190-1 libevent-2.1-7_2.1.12-stable-9 libevent-core-2.1-7_2.1.12-stable-9 libevent-dev_2.1.12-stable-9 libevent-extra-2.1-7_2.1.12-stable-9 libevent-openssl-2.1-7_2.1.12-stable-9 libevent-pthreads-2.1-7_2.1.12-stable-9 libexpat1_2.5.0-2 libexpat1-dev_2.5.0-2 libext2fs2_1.47.0-2ubuntu1 libfabric1_1.17.0-3 libfakeroot_1.32.2-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfido2-1_1.14.0-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-10ubuntu1 libgcc-s1_13.2.0-10ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran-13-dev_13.2.0-10ubuntu1 libgfortran5_13.2.0-10ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.1-4ubuntu7 libgomp1_13.2.0-10ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgprofng0_2.41.90.20240115-1ubuntu1 libgssapi-krb5-2_1.20.1-5build1 libhogweed6_3.9.1-2 libhwasan0_13.2.0-10ubuntu1 libhwloc-dev_2.10.0-1 libhwloc-plugins_2.10.0-1 libhwloc15_2.10.0-1 libibverbs-dev_48.0-1 libibverbs1_48.0-1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.4-1build1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libitm1_13.2.0-10ubuntu1 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-mathjax_2.7.9+dfsg-1 libjs-sphinxdoc_7.2.6-3 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-c5_0.17-1 libjson-perl_4.10000-1 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-2 libklu2_1:7.5.1+dfsg-1 libkmod2_30+20230601-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 liblapack-dev_3.11.0-2build1 liblapack3_3.11.0-2build1 libldap2_2.6.6+dfsg-1~exp1ubuntu2 libldl3_1:7.5.1+dfsg-1 liblocale-gettext-perl_1.07-6build1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13.2.0-10ubuntu1 libltdl-dev_2.4.7-7 libltdl7_2.4.7-7 liblz4-1_1.9.4-1 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmaloc-dev_1.5-1 libmaloc1_1.5-1 libmd0_1.1.0-2 libmount1_2.39.2-6ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libmunge2_0.5.15-3ubuntu1 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnl-3-200_3.7.0-0.3 libnl-3-dev_3.7.0-0.3 libnl-route-3-200_3.7.0-0.3 libnl-route-3-dev_3.7.0-0.3 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libnuma-dev_2.0.16-1 libnuma1_2.0.16-1 libopenmpi-dev_4.1.6-5ubuntu1 libopenmpi3_4.1.6-5ubuntu1 libp11-kit0_0.25.3-2ubuntu2 libpam-modules_1.5.2-9.1ubuntu2 libpam-modules-bin_1.5.2-9.1ubuntu2 libpam-runtime_1.5.2-9.1ubuntu2 libpam0g_1.5.2-9.1ubuntu2 libparu0_1:7.5.1+dfsg-1 libpciaccess0_0.17-3 libpcre2-8-0_10.42-4ubuntu1 libperl5.36_5.36.0-10ubuntu1 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpmix-dev_5.0.1-4 libpmix2_5.0.1-4 libpng16-16_1.6.40-3 libproc2-0_2:4.0.4-2ubuntu1 libpsl5_0.21.2-1build1 libpsm-infinipath1_3.3+20.604758e7-6.3 libpsm2-2_11.2.185-2 libpython3-dev_3.12.1-0ubuntu1 libpython3-stdlib_3.12.1-0ubuntu1 libpython3.12_3.12.1-2 libpython3.12-dev_3.12.1-2 libpython3.12-minimal_3.12.1-2 libpython3.12-stdlib_3.12.1-2 libquadmath0_13.2.0-10ubuntu1 librbio4_1:7.5.1+dfsg-1 librdmacm1_48.0-1 libreadline8_8.2-3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2ubuntu1 libselinux1_3.5-1build2 libsemanage-common_3.5-1build1 libsemanage2_3.5-1build1 libsepol2_3.5-2 libsframe1_2.41.90.20240115-1ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libspex2_1:7.5.1+dfsg-1 libspqr4_1:7.5.1+dfsg-1 libsqlite3-0_3.44.2-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.6-2 libssl3_3.0.10-1ubuntu3 libstdc++-13-dev_13.2.0-10ubuntu1 libstdc++6_13.2.0-10ubuntu1 libsub-override-perl_0.10-1 libsuitesparse-dev_1:7.5.1+dfsg-1 libsuitesparse-mongoose3_1:7.5.1+dfsg-1 libsuitesparseconfig7_1:7.5.1+dfsg-1 libsuperlu-dev_6.0.1+dfsg1-1 libsuperlu6_6.0.1+dfsg1-1 libsystemd-shared_255.2-3ubuntu1 libsystemd0_255.2-3ubuntu1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build1 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtool_2.4.7-7 libtsan2_13.2.0-10ubuntu1 libubsan1_13.2.0-10ubuntu1 libuchardet0_0.0.8-1 libucx0_1.15.0-1 libudev1_255.2-3ubuntu1 libumfpack6_1:7.5.1+dfsg-1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libuv1_1.46.0-3 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1build5 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxml2_2.9.14+dfsg-1.3build3 libxnvctrl0_510.47.03-0ubuntu1 libxxhash0_0.8.2-2 libyaml-0-2_0.2.5-1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.6.0-14.14 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_45 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.2-6ubuntu1 mpi-default-dev_1.15 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1 openmpi-bin_4.1.6-5ubuntu1 openmpi-common_4.1.6-5ubuntu1 openssh-client_1:9.4p1-1ubuntu2 openssl_3.0.10-1ubuntu3 optipng_0.7.7-3 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-10ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkg-config_1.8.1-2 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-2 pybind11-dev_2.11.1-2 pybuild-plugin-pyproject_6.20231223 python-babel-localedata_2.10.3-3build1 python3_3.12.1-0ubuntu1 python3-alabaster_0.7.12-1 python3-babel_2.10.3-3build1 python3-build_0.10.0-1 python3-certifi_2023.11.17-1 python3-chardet_5.2.0+dfsg-1 python3-dev_3.12.1-0ubuntu1 python3-distutils_3.11.5-1 python3-docutils_0.20.1+dfsg-3 python3-idna_3.3-2 python3-imagesize_1.4.1-1 python3-installer_0.7.0+dfsg1-2 python3-jinja2_3.1.2-1 python3-lib2to3_3.11.5-1 python3-markupsafe_2.1.3-1build1 python3-minimal_3.12.1-0ubuntu1 python3-packaging_23.2-1 python3-pkg-resources_68.1.2-2 python3-pybind11_2.11.1-2 python3-pygments_2.15.1+dfsg-1 python3-pyproject-hooks_1.0.0-2 python3-requests_2.31.0+dfsg-1ubuntu1 python3-roman_3.3-3 python3-setuptools_68.1.2-2 python3-snowballstemmer_2.2.0-4 python3-sphinx_7.2.6-3 python3-sphinx-rtd-theme_2.0.0+dfsg-1 python3-sphinxcontrib.jquery_4.1-5 python3-toml_0.10.2-1 python3-tz_2023.3.post1-2 python3-urllib3_2.0.7-1 python3-wheel_0.42.0-1 python3-yaml_6.0.1-2 python3.12_3.12.1-2 python3.12-dev_3.12.1-2 python3.12-minimal_3.12.1-2 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sgml-base_1.31 sphinx-common_7.2.6-3 sphinx-rtd-theme-common_2.0.0+dfsg-1 swig_4.1.0-0.3 swig4.0_4.1.0-0.3 systemd_255.2-3ubuntu1 systemd-dev_255.2-3ubuntu1 systemd-sysv_255.2-3ubuntu1 sysvinit-utils_3.08-3ubuntu1 tar_1.35+dfsg-3 tzdata_2023d-1ubuntu2 ubuntu-keyring_2023.11.28.1 usrmerge_38ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xml-core_0.19 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: apbs Binary: apbs, python3-apbslib, libapbs-dev, libapbs3, apbs-data, apbs-doc, libfetk-dev, libfetk1.9 Architecture: any all Version: 3.4.1-5build5 Maintainer: Ubuntu Developers Uploaders: Michael Banck Homepage: http://www.poissonboltzmann.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/apbs Vcs-Git: https://salsa.debian.org/debichem-team/apbs.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev Build-Depends-Indep: libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml Package-List: apbs deb science optional arch=any apbs-data deb science optional arch=all apbs-doc deb science optional arch=all libapbs-dev deb libdevel optional arch=any libapbs3 deb libs optional arch=any libfetk-dev deb libdevel optional arch=any libfetk1.9 deb libs optional arch=any python3-apbslib deb python optional arch=any Checksums-Sha1: 584fd36dc1424cb22fd8846f1cf2c7ead60ce0c6 85806314 apbs_3.4.1.orig.tar.gz 81bc54c4edbbc84f99b0e5632b757207a2556967 20305776 apbs_3.4.1-5build5.debian.tar.xz Checksums-Sha256: 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2 85806314 apbs_3.4.1.orig.tar.gz f4dd15bcf97fcb4d1f903bacc574a8dde158dfc6226a103516dead35b4bca0eb 20305776 apbs_3.4.1-5build5.debian.tar.xz Files: 5d2af7c3592f8c410a5df39887361520 85806314 apbs_3.4.1.orig.tar.gz e49396706c404b9a38190a966e7d4551 20305776 apbs_3.4.1-5build5.debian.tar.xz Original-Maintainer: Debichem Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmWqxfoACgkQr8/sjmac 4cKNIA/7B08ovSFROpLeN9nzFcj/f3VflUMypqmQj5nHig0EmYkN6dPTWqFuaKeT KuCk5eJLtzo0b0fhtVa+INWfXrwS7zHRm6RY6FAwrH8qnTcm1znHxCcHTvAfdrwU YmWGGRLHd8fxzVkRT/ohXkPYAkA1OrC3U4bsvKwd3e3Y9y8Sag0zsrt2itT579RS Mxs22wxt9vmxtEi2QEl8P01LksrFVCstY4IK4VPtrsrRR4Rb+ahNfzLlMHyLGB/M 5zX4y/Gfbco71sssmdoaj6Db3LlEHn1rLvr9rT8bkzqJdph6rbT7nfqy1z83NxhW m1npm6IwhZyXT0sSdmFApO/tMckrh9VEvuYTxqFPoTgkGgLAr6kwFrUngVqdQoSF 9LD+wx73dtUMWreQcs0JFB4DsX+jrepW7p9QV+ySbwmnVo3pz+3+W1phBzJ3ikln 4skBKxBDchGd/ZqGLx28P2PFM6f4L/Cbj7Mo7OVtLWmXp4tO+2Leph+pbDhScJoe pFp96qH/gttJfuAUn60SLrdy0WoC3XGna4zieYCMIuWhuvn7e36gKtnVwGO+7yQI FE93bluMOIjFOO2saHmBO97HVquEfvC3Z4Gq0QT3HpwSKL2YygL4cMKjutfFVdlQ bBJpaiV43ue1nsKref4gd3MuV9U9bIiAOO2w4FhikVqX4mu7n48= =Fi87 -----END PGP SIGNATURE----- gpgv: Signature made Fri Jan 19 18:56:58 2024 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-5build5.dsc: no acceptable signature found dpkg-source: info: extracting apbs in /<> dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-5build5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying cmake.patch dpkg-source: info: applying docs.patch dpkg-source: info: applying open-U-obsolete.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27660350 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27660350 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27660350 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-5build5 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build dh build --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None \ -DAPBS_STATIC_BUILD=Off \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETCHCONTENT_SOURCE_DIR_FETK=/<>/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DAPBS_STATIC_BUILD=Off -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETCHCONTENT_SOURCE_DIR_FETK=/<>/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Install prefix: /usr -- -- APBS Static build: Off -- Building shared libs: ON -- Find-library suffixes: .so;.so;.a -- -- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2 -- FETK set_basic_vars_and_paths: FALSE, FETK -- Setting project paths -- Install prefix: /usr -- FETK static build: OFF -- Building shared libs: ON -- Find-library suffixes: .so;.so;.so;.a Configuring build for PUNC -- FETK set_basic_vars_and_paths: FALSE, punc -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- Will build vf2c -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T - Success -- Performing Test SUPERLU_HAS_CLEAN_ENUMS -- Performing Test SUPERLU_HAS_CLEAN_ENUMS - Success -- Performing Test SUPERLU_HAS_GLOBALLU_T -- Performing Test SUPERLU_HAS_GLOBALLU_T - Success -- Found SuperLU: /usr/include/superlu (found version "5.0") -- Found ARPACK: libraries at /usr/lib/x86_64-linux-gnu/libarpack.so -- Will build CGCODE -- Building vf2c -- Type: EXTERNAL_HEADERS -- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h -- Type: INTERNAL_HEADERS -- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h -- Type: SOURCES -- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c -- Building cgcode -- Type: INTERNAL_HEADERS -- Items: vcgcode.h -- Type: SOURCES -- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c -- Type: INTERNAL_HEADERS -- Items: /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/punccf.h -- Type: SOURCES -- Items: punc_base.c -- Type: EXTERNAL_HEADERS -- Items: punc/punc.h;punc/punc_base.h -- Type: INTERNAL_HEADERS -- Items: punc_base_p.h Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src/gamercf.h -- Type: SOURCES -- Items: gamer_base.c -- Type: EXTERNAL_HEADERS -- Items: gamer/gamer.h;gamer/gamer_base.h -- Type: INTERNAL_HEADERS -- Items: gamer_base_p.h -- Type: SOURCES -- Items: triangle.c -- Type: EXTERNAL_HEADERS -- Items: gamer/triangle.h -- Type: INTERNAL_HEADERS -- Items: triangle_p.h -- Type: SOURCES -- Items: predicates.cpp;tetgen.cpp -- Type: EXTERNAL_HEADERS -- Items: gamer/tetgen.h -- Type: INTERNAL_HEADERS -- Items: tetgen_p.h -- Type: SOURCES -- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C -- Type: EXTERNAL_HEADERS -- Items: gamer/biom.h -- Type: INTERNAL_HEADERS -- Items: MarchingCube.h;PDB2Volume.h Configuring build for MC -- FETK set_basic_vars_and_paths: FALSE, mc -- Found UMFPACK: /usr/include/suitesparse -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.a -- Adding librt: /usr/lib/x86_64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- Found SuiteSparse: TRUE (found version "..") -- Type: INTERNAL_HEADERS -- Items: /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src/mccf.h -- Type: SOURCES -- Items: mc_base.c -- Type: EXTERNAL_HEADERS -- Items: mc/mc_base.h;mc/mc.h -- Type: INTERNAL_HEADERS -- Items: mc_base_p.h -- Type: SOURCES -- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c -- Type: EXTERNAL_HEADERS -- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h -- Type: INTERNAL_HEADERS -- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h -- Type: SOURCES -- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c -- Type: EXTERNAL_HEADERS -- Items: mc/whb.h -- Type: INTERNAL_HEADERS -- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h -- Type: SOURCES -- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c -- Type: EXTERNAL_HEADERS -- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h -- Type: INTERNAL_HEADERS -- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h -- Type: SOURCES -- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c -- Type: EXTERNAL_HEADERS -- Items: mc/gem.h;mc/vel.h;mc/ves.h -- Type: INTERNAL_HEADERS -- Items: gem_p.h;vel_p.h;ves_p.h -- Type: SOURCES -- Items: pde.c -- Type: EXTERNAL_HEADERS -- Items: mc/pde.h -- Type: INTERNAL_HEADERS -- Items: pde_p.h -- Type: SOURCES -- Items: am.c;lsolv.c;nsolv.c -- Type: EXTERNAL_HEADERS -- Items: mc/am.h;mc/nam.h -- Type: INTERNAL_HEADERS -- Items: am_p.h;nam_p.h -- Type: SOURCES -- Items: dyn.c;svio.c -- Type: EXTERNAL_HEADERS -- Items: mc/dyn.h -- Type: INTERNAL_HEADERS -- Items: dyn_p.h;svio_p.h -- Type: SOURCES -- Items: mcsh.c -- Type: EXTERNAL_HEADERS -- Items: mc/mcsh.h -- Type: INTERNAL_HEADERS -- Items: mcsh_p.h -- ############################################################# -- ** PROJECT NAME: APBS -- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver -- ** PROJECT URL: http://www.poissonboltzmann.org/ -- ** VERSION_DATA: 3.4.1 -- ** CURRENT_TIME: 2024-01-19T18:56:34 -- ** CURRENT_YEAR: 2024 -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found Intl: built in to C library -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.a -- Adding librt: /usr/lib/x86_64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- UMFPack libraries: /usr/lib/x86_64-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Building of iAPBS interface disabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_fem -- With source files vcsm.c;vfetk.c;vpee.c -- With external header files vcsm.h;vfetk.h;vpee.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic -- Added apbs_fem -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig4.0 (found version "4.1.0") -- Found Python3: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.12 -- ***** Python3 library path is: /usr/lib/x86_64-linux-gnu/libpython3.12.so -- ***** Python3 library dir is: /usr/lib/x86_64-linux-gnu CMake Warning at /usr/lib/cmake/pybind11/pybind11Tools.cmake:24 (message): Set PYBIND11_PYTHON_VERSION to search for a specific version, not PYTHON_VERSION (which is an output). Assuming that is what you meant to do and continuing anyway. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) CMake Warning (dev) at /usr/lib/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "3.6") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.12.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.11.1") -- LIBS mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- ******* TESTING ADDED ***************** -- Found Python3: /usr/bin/python3 (found suitable exact version "3.12.1") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t born -- ******* FOUND TEST CASE actin, actin-dimer-auto -- TEST actin-dimer-auto_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t actin-dimer-auto -- ******* FOUND TEST CASE alkanes, alkanes -- TEST alkanes_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t FKBP -- ******* FOUND TEST CASE hca, hca-bind -- TEST hca-bind_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t ionize -- ******* FOUND TEST CASE ion, ion-pmf -- TEST ion-pmf_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t ion-pmf -- ******* FOUND TEST CASE pka, pka-lig -- TEST pka-lig_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t pka-lig -- ******* FOUND TEST CASE point, point-pmf -- TEST point-pmf_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t solv -- Configuring done (9.0s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depend make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src/cgcode /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake "--color=" cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/python /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/gamer/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src/vf2c /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake "--color=" Dependee "/<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Dependee "/<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target apbslib_swig_compilation make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o -MF CMakeFiles/gamer.dir/base/gamer_base.c.o.d -o CMakeFiles/gamer.dir/base/gamer_base.c.o -c /<>/debian/external_deps/fetk/gamer/src/base/gamer_base.c [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o -MF CMakeFiles/cgcode.dir/scgdrv.c.o.d -o CMakeFiles/cgcode.dir/scgdrv.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c [ 1%] Swig compile apbslib.i for python cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /<>/obj-x86_64-linux-gnu/tools/python /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir [ 1%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o -MF CMakeFiles/vf2c.dir/f77vers.c.o.d -o CMakeFiles/vf2c.dir/f77vers.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/f77vers.c cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E touch /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /<>/obj-x86_64-linux-gnu/tools/python -interface _apbslib -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/python3.12 -I/<>/tools/python -o /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /<>/tools/python/apbslib.i cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o -MF CMakeFiles/gamer.dir/triangle/triangle.c.o.d -o CMakeFiles/gamer.dir/triangle/triangle.c.o -c /<>/debian/external_deps/fetk/gamer/src/triangle/triangle.c [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o -MF CMakeFiles/vf2c.dir/i77vers.c.o.d -o CMakeFiles/vf2c.dir/i77vers.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i77vers.c [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o -MF CMakeFiles/vf2c.dir/s_rnge.c.o.d -o CMakeFiles/vf2c.dir/s_rnge.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o -MF CMakeFiles/cgcode.dir/scg.c.o.d -o CMakeFiles/cgcode.dir/scg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scg.c [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o -MF CMakeFiles/vf2c.dir/abort_.c.o.d -o CMakeFiles/vf2c.dir/abort_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/abort_.c [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o -MF CMakeFiles/vf2c.dir/exit_.c.o.d -o CMakeFiles/vf2c.dir/exit_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/exit_.c [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o -MF CMakeFiles/cgcode.dir/scr.c.o.d -o CMakeFiles/cgcode.dir/scr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scr.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o -MF CMakeFiles/vf2c.dir/getarg_.c.o.d -o CMakeFiles/vf2c.dir/getarg_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/getarg_.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o -MF CMakeFiles/vf2c.dir/iargc_.c.o.d -o CMakeFiles/vf2c.dir/iargc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/iargc_.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o -MF CMakeFiles/cgcode.dir/scrind.c.o.d -o CMakeFiles/cgcode.dir/scrind.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scrind.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o -MF CMakeFiles/vf2c.dir/getenv_.c.o.d -o CMakeFiles/vf2c.dir/getenv_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/getenv_.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o -MF CMakeFiles/vf2c.dir/signal_.c.o.d -o CMakeFiles/vf2c.dir/signal_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/signal_.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o [ 5%] Built target apbslib_swig_compilation cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o -MF CMakeFiles/vf2c.dir/s_stop.c.o.d -o CMakeFiles/vf2c.dir/s_stop.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o -MF CMakeFiles/cgcode.dir/spcg.c.o.d -o CMakeFiles/cgcode.dir/spcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcg.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o -MF CMakeFiles/cgcode.dir/scgnr.c.o.d -o CMakeFiles/cgcode.dir/scgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgnr.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o -MF CMakeFiles/vf2c.dir/s_paus.c.o.d -o CMakeFiles/vf2c.dir/s_paus.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o -MF CMakeFiles/cgcode.dir/scgne.c.o.d -o CMakeFiles/cgcode.dir/scgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgne.c cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o -MF CMakeFiles/cgcode.dir/spcgnr.c.o.d -o CMakeFiles/cgcode.dir/spcgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o -MF CMakeFiles/vf2c.dir/cabs.c.o.d -o CMakeFiles/vf2c.dir/cabs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o -MF CMakeFiles/vf2c.dir/derf_.c.o.d -o CMakeFiles/vf2c.dir/derf_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/derf_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o -MF CMakeFiles/cgcode.dir/spcgne.c.o.d -o CMakeFiles/cgcode.dir/spcgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcgne.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o -MF CMakeFiles/cgcode.dir/sppcg.c.o.d -o CMakeFiles/cgcode.dir/sppcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sppcg.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o -MF CMakeFiles/vf2c.dir/erf_.c.o.d -o CMakeFiles/vf2c.dir/erf_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o -MF CMakeFiles/vf2c.dir/erfc_.c.o.d -o CMakeFiles/vf2c.dir/erfc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/erfc_.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o -MF CMakeFiles/cgcode.dir/spcgca.c.o.d -o CMakeFiles/cgcode.dir/spcgca.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o -MF CMakeFiles/vf2c.dir/sig_die.c.o.d -o CMakeFiles/vf2c.dir/sig_die.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o -MF CMakeFiles/cgcode.dir/sdpchb.c.o.d -o CMakeFiles/cgcode.dir/sdpchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o -MF CMakeFiles/vf2c.dir/uninit.c.o.d -o CMakeFiles/vf2c.dir/uninit.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/uninit.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o -MF CMakeFiles/cgcode.dir/scbfix.c.o.d -o CMakeFiles/cgcode.dir/scbfix.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o -MF CMakeFiles/cgcode.dir/sckchb.c.o.d -o CMakeFiles/cgcode.dir/sckchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o -MF CMakeFiles/vf2c.dir/pow_ci.c.o.d -o CMakeFiles/vf2c.dir/pow_ci.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o -MF CMakeFiles/vf2c.dir/pow_dd.c.o.d -o CMakeFiles/vf2c.dir/pow_dd.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 11%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -MF CMakeFiles/gamer.dir/tetgen/predicates.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -c /<>/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o -MF CMakeFiles/cgcode.dir/scgchk.c.o.d -o CMakeFiles/cgcode.dir/scgchk.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o -MF CMakeFiles/cgcode.dir/sonest.c.o.d -o CMakeFiles/cgcode.dir/sonest.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sonest.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o -MF CMakeFiles/vf2c.dir/pow_hh.c.o.d -o CMakeFiles/vf2c.dir/pow_hh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o -MF CMakeFiles/cgcode.dir/msstop.c.o.d -o CMakeFiles/cgcode.dir/msstop.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o -MF CMakeFiles/vf2c.dir/pow_ii.c.o.d -o CMakeFiles/vf2c.dir/pow_ii.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o -MF CMakeFiles/vf2c.dir/pow_ri.c.o.d -o CMakeFiles/vf2c.dir/pow_ri.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o -MF CMakeFiles/cgcode.dir/r1mach.c.o.d -o CMakeFiles/cgcode.dir/r1mach.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/r1mach.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o -MF CMakeFiles/vf2c.dir/pow_zi.c.o.d -o CMakeFiles/vf2c.dir/pow_zi.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o -MF CMakeFiles/cgcode.dir/sratqr.c.o.d -o CMakeFiles/cgcode.dir/sratqr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o -MF CMakeFiles/vf2c.dir/pow_zz.c.o.d -o CMakeFiles/vf2c.dir/pow_zz.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o -MF CMakeFiles/vf2c.dir/c_abs.c.o.d -o CMakeFiles/vf2c.dir/c_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_abs.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o -MF CMakeFiles/vf2c.dir/c_cos.c.o.d -o CMakeFiles/vf2c.dir/c_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o -MF CMakeFiles/vf2c.dir/c_div.c.o.d -o CMakeFiles/vf2c.dir/c_div.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o -MF CMakeFiles/cgcode.dir/dcgdrv.c.o.d -o CMakeFiles/cgcode.dir/dcgdrv.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o -MF CMakeFiles/vf2c.dir/c_exp.c.o.d -o CMakeFiles/vf2c.dir/c_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_exp.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o -MF CMakeFiles/cgcode.dir/dcg.c.o.d -o CMakeFiles/cgcode.dir/dcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o -MF CMakeFiles/vf2c.dir/c_log.c.o.d -o CMakeFiles/vf2c.dir/c_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o -MF CMakeFiles/vf2c.dir/c_sin.c.o.d -o CMakeFiles/vf2c.dir/c_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o -MF CMakeFiles/cgcode.dir/dcr.c.o.d -o CMakeFiles/cgcode.dir/dcr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o -MF CMakeFiles/vf2c.dir/c_sqrt.c.o.d -o CMakeFiles/vf2c.dir/c_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o -MF CMakeFiles/vf2c.dir/z_abs.c.o.d -o CMakeFiles/vf2c.dir/z_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o -MF CMakeFiles/vf2c.dir/z_cos.c.o.d -o CMakeFiles/vf2c.dir/z_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o -MF CMakeFiles/cgcode.dir/dcrind.c.o.d -o CMakeFiles/cgcode.dir/dcrind.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcrind.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o -MF CMakeFiles/vf2c.dir/z_div.c.o.d -o CMakeFiles/vf2c.dir/z_div.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_div.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o -MF CMakeFiles/vf2c.dir/z_exp.c.o.d -o CMakeFiles/vf2c.dir/z_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o -MF CMakeFiles/vf2c.dir/z_log.c.o.d -o CMakeFiles/vf2c.dir/z_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_log.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o -MF CMakeFiles/cgcode.dir/dpcg.c.o.d -o CMakeFiles/cgcode.dir/dpcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o -MF CMakeFiles/cgcode.dir/dcgnr.c.o.d -o CMakeFiles/cgcode.dir/dcgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o -MF CMakeFiles/vf2c.dir/z_sqrt.c.o.d -o CMakeFiles/vf2c.dir/z_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o -MF CMakeFiles/vf2c.dir/r_abs.c.o.d -o CMakeFiles/vf2c.dir/r_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o -MF CMakeFiles/vf2c.dir/r_acos.c.o.d -o CMakeFiles/vf2c.dir/r_acos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o -MF CMakeFiles/cgcode.dir/dcgne.c.o.d -o CMakeFiles/cgcode.dir/dcgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgne.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o -MF CMakeFiles/vf2c.dir/r_asin.c.o.d -o CMakeFiles/vf2c.dir/r_asin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_asin.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o -MF CMakeFiles/vf2c.dir/r_atan.c.o.d -o CMakeFiles/vf2c.dir/r_atan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o -MF CMakeFiles/cgcode.dir/dpcgnr.c.o.d -o CMakeFiles/cgcode.dir/dpcgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o -MF CMakeFiles/vf2c.dir/r_atn2.c.o.d -o CMakeFiles/vf2c.dir/r_atn2.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o -MF CMakeFiles/vf2c.dir/r_cnjg.c.o.d -o CMakeFiles/vf2c.dir/r_cnjg.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o -MF CMakeFiles/vf2c.dir/r_cos.c.o.d -o CMakeFiles/vf2c.dir/r_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_cos.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o -MF CMakeFiles/cgcode.dir/dpcgne.c.o.d -o CMakeFiles/cgcode.dir/dpcgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o -MF CMakeFiles/vf2c.dir/r_cosh.c.o.d -o CMakeFiles/vf2c.dir/r_cosh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o -MF CMakeFiles/vf2c.dir/r_dim.c.o.d -o CMakeFiles/vf2c.dir/r_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_dim.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o -MF CMakeFiles/cgcode.dir/dppcg.c.o.d -o CMakeFiles/cgcode.dir/dppcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dppcg.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o -MF CMakeFiles/vf2c.dir/r_exp.c.o.d -o CMakeFiles/vf2c.dir/r_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_exp.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o -MF CMakeFiles/vf2c.dir/r_imag.c.o.d -o CMakeFiles/vf2c.dir/r_imag.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o -MF CMakeFiles/vf2c.dir/r_int.c.o.d -o CMakeFiles/vf2c.dir/r_int.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_int.c [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o [ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o -MF CMakeFiles/cgcode.dir/dpcgca.c.o.d -o CMakeFiles/cgcode.dir/dpcgca.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o -MF CMakeFiles/vf2c.dir/r_lg10.c.o.d -o CMakeFiles/vf2c.dir/r_lg10.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o -MF CMakeFiles/vf2c.dir/r_log.c.o.d -o CMakeFiles/vf2c.dir/r_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_log.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o -MF CMakeFiles/vf2c.dir/r_mod.c.o.d -o CMakeFiles/vf2c.dir/r_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_mod.c [ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o -MF CMakeFiles/cgcode.dir/ddpchb.c.o.d -o CMakeFiles/cgcode.dir/ddpchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o -MF CMakeFiles/vf2c.dir/r_nint.c.o.d -o CMakeFiles/vf2c.dir/r_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o -MF CMakeFiles/vf2c.dir/r_sign.c.o.d -o CMakeFiles/vf2c.dir/r_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sign.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o -MF CMakeFiles/vf2c.dir/r_sin.c.o.d -o CMakeFiles/vf2c.dir/r_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sin.c [ 27%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o -MF CMakeFiles/cgcode.dir/dcbfix.c.o.d -o CMakeFiles/cgcode.dir/dcbfix.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o -MF CMakeFiles/vf2c.dir/r_sinh.c.o.d -o CMakeFiles/vf2c.dir/r_sinh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 27%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o -MF CMakeFiles/vf2c.dir/r_sqrt.c.o.d -o CMakeFiles/vf2c.dir/r_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o -MF CMakeFiles/cgcode.dir/dcgchk.c.o.d -o CMakeFiles/cgcode.dir/dcgchk.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o -MF CMakeFiles/vf2c.dir/r_tan.c.o.d -o CMakeFiles/vf2c.dir/r_tan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_tan.c [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o -MF CMakeFiles/cgcode.dir/donest.c.o.d -o CMakeFiles/cgcode.dir/donest.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o -MF CMakeFiles/vf2c.dir/r_tanh.c.o.d -o CMakeFiles/vf2c.dir/r_tanh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o -MF CMakeFiles/cgcode.dir/mdstop.c.o.d -o CMakeFiles/cgcode.dir/mdstop.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o -MF CMakeFiles/vf2c.dir/d_abs.c.o.d -o CMakeFiles/vf2c.dir/d_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o -MF CMakeFiles/cgcode.dir/d1mach.c.o.d -o CMakeFiles/cgcode.dir/d1mach.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/d1mach.c cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o -MF CMakeFiles/vf2c.dir/d_acos.c.o.d -o CMakeFiles/vf2c.dir/d_acos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o -MF CMakeFiles/cgcode.dir/dratqr.c.o.d -o CMakeFiles/cgcode.dir/dratqr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o -MF CMakeFiles/vf2c.dir/d_asin.c.o.d -o CMakeFiles/vf2c.dir/d_asin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_asin.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o -MF CMakeFiles/vf2c.dir/d_atan.c.o.d -o CMakeFiles/vf2c.dir/d_atan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o -MF CMakeFiles/vf2c.dir/d_atn2.c.o.d -o CMakeFiles/vf2c.dir/d_atn2.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 31%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o -MF CMakeFiles/cgcode.dir/depsln.c.o.d -o CMakeFiles/cgcode.dir/depsln.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o -MF CMakeFiles/vf2c.dir/d_cnjg.c.o.d -o CMakeFiles/vf2c.dir/d_cnjg.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 31%] Linking C shared library libcgcode.so cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o -MF CMakeFiles/vf2c.dir/d_cos.c.o.d -o CMakeFiles/vf2c.dir/d_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_cos.c /usr/src/apbs-3.4.1-5build5/debian/external_deps/fetk/punc/src/cgcode/donest.c:34:33: warning: type of ‘sratqr_’ does not match original declaration [-Wlto-type-mismatch] /usr/src/apbs-3.4.1-5build5/debian/external_deps/fetk/punc/src/cgcode/sratqr.c:12:22: note: ‘sratqr_’ was previously declared here /usr/src/apbs-3.4.1-5build5/debian/external_deps/fetk/punc/src/cgcode/sratqr.c:12:22: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o -MF CMakeFiles/vf2c.dir/d_cosh.c.o.d -o CMakeFiles/vf2c.dir/d_cosh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o -MF CMakeFiles/vf2c.dir/d_dim.c.o.d -o CMakeFiles/vf2c.dir/d_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_dim.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o -MF CMakeFiles/vf2c.dir/d_exp.c.o.d -o CMakeFiles/vf2c.dir/d_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o -MF CMakeFiles/vf2c.dir/d_imag.c.o.d -o CMakeFiles/vf2c.dir/d_imag.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_imag.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o -MF CMakeFiles/vf2c.dir/d_int.c.o.d -o CMakeFiles/vf2c.dir/d_int.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 33%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -MF CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -c /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o -MF CMakeFiles/vf2c.dir/d_lg10.c.o.d -o CMakeFiles/vf2c.dir/d_lg10.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o -MF CMakeFiles/vf2c.dir/d_log.c.o.d -o CMakeFiles/vf2c.dir/d_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o -MF CMakeFiles/vf2c.dir/d_mod.c.o.d -o CMakeFiles/vf2c.dir/d_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o -MF CMakeFiles/vf2c.dir/d_nint.c.o.d -o CMakeFiles/vf2c.dir/d_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_nint.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o -MF CMakeFiles/vf2c.dir/d_prod.c.o.d -o CMakeFiles/vf2c.dir/d_prod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o -MF CMakeFiles/vf2c.dir/d_sign.c.o.d -o CMakeFiles/vf2c.dir/d_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o -MF CMakeFiles/vf2c.dir/d_sin.c.o.d -o CMakeFiles/vf2c.dir/d_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sin.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o -MF CMakeFiles/vf2c.dir/d_sinh.c.o.d -o CMakeFiles/vf2c.dir/d_sinh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o -MF CMakeFiles/vf2c.dir/d_sqrt.c.o.d -o CMakeFiles/vf2c.dir/d_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 37%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -MF CMakeFiles/gamer.dir/biom/CorrectNormals.C.o.d -o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘void tetgenmesh::constrainedfacets()’: /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20804:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20804 | equatptlist = new list("point *"); | ^~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20809:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20809 | horizptlist = new list("point *"); | ^~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20810:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20810 | belowptlist = new list("point *"); | ^~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20811:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20811 | aboveptlist = new list("point *"); | ^~~~~~~~~ [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o -MF CMakeFiles/vf2c.dir/d_tan.c.o.d -o CMakeFiles/vf2c.dir/d_tan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_tan.c /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘long int tetgenmesh::reconstructmesh()’: /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:24383:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 24383 | markerlist = new list("int"); | ^~~~~ [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o -MF CMakeFiles/vf2c.dir/d_tanh.c.o.d -o CMakeFiles/vf2c.dir/d_tanh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o -MF CMakeFiles/vf2c.dir/i_abs.c.o.d -o CMakeFiles/vf2c.dir/i_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o -MF CMakeFiles/vf2c.dir/i_dim.c.o.d -o CMakeFiles/vf2c.dir/i_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_dim.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o -MF CMakeFiles/vf2c.dir/i_dnnt.c.o.d -o CMakeFiles/vf2c.dir/i_dnnt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o -MF CMakeFiles/vf2c.dir/i_indx.c.o.d -o CMakeFiles/vf2c.dir/i_indx.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_indx.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o -MF CMakeFiles/vf2c.dir/i_len.c.o.d -o CMakeFiles/vf2c.dir/i_len.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o -MF CMakeFiles/vf2c.dir/i_mod.c.o.d -o CMakeFiles/vf2c.dir/i_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o -MF CMakeFiles/vf2c.dir/i_nint.c.o.d -o CMakeFiles/vf2c.dir/i_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_nint.c [ 39%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -MF CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o.d -o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o -MF CMakeFiles/vf2c.dir/i_sign.c.o.d -o CMakeFiles/vf2c.dir/i_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_sign.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o -MF CMakeFiles/vf2c.dir/lbitbits.c.o.d -o CMakeFiles/vf2c.dir/lbitbits.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o -MF CMakeFiles/vf2c.dir/lbitshft.c.o.d -o CMakeFiles/vf2c.dir/lbitshft.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o -MF CMakeFiles/vf2c.dir/h_abs.c.o.d -o CMakeFiles/vf2c.dir/h_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o -MF CMakeFiles/vf2c.dir/h_dim.c.o.d -o CMakeFiles/vf2c.dir/h_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_dim.c cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_symlink_library libcgcode.so.1.9.3 libcgcode.so.1.9 libcgcode.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o -MF CMakeFiles/vf2c.dir/h_dnnt.c.o.d -o CMakeFiles/vf2c.dir/h_dnnt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 41%] Built target cgcode [ 41%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o -MF CMakeFiles/gamer.dir/biom/MarchingCube.C.o.d -o CMakeFiles/gamer.dir/biom/MarchingCube.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o -MF CMakeFiles/vf2c.dir/h_indx.c.o.d -o CMakeFiles/vf2c.dir/h_indx.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_indx.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o -MF CMakeFiles/vf2c.dir/h_len.c.o.d -o CMakeFiles/vf2c.dir/h_len.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o -MF CMakeFiles/vf2c.dir/h_mod.c.o.d -o CMakeFiles/vf2c.dir/h_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 43%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o -MF CMakeFiles/vf2c.dir/h_nint.c.o.d -o CMakeFiles/vf2c.dir/h_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o -MF CMakeFiles/vf2c.dir/h_sign.c.o.d -o CMakeFiles/vf2c.dir/h_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o -MF CMakeFiles/vf2c.dir/l_ge.c.o.d -o CMakeFiles/vf2c.dir/l_ge.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o -MF CMakeFiles/vf2c.dir/l_gt.c.o.d -o CMakeFiles/vf2c.dir/l_gt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o -MF CMakeFiles/vf2c.dir/l_le.c.o.d -o CMakeFiles/vf2c.dir/l_le.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o -MF CMakeFiles/vf2c.dir/l_lt.c.o.d -o CMakeFiles/vf2c.dir/l_lt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_lt.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o -MF CMakeFiles/vf2c.dir/hl_ge.c.o.d -o CMakeFiles/vf2c.dir/hl_ge.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o -MF CMakeFiles/vf2c.dir/hl_gt.c.o.d -o CMakeFiles/vf2c.dir/hl_gt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o -MF CMakeFiles/vf2c.dir/hl_le.c.o.d -o CMakeFiles/vf2c.dir/hl_le.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_le.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o -MF CMakeFiles/vf2c.dir/hl_lt.c.o.d -o CMakeFiles/vf2c.dir/hl_lt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o -MF CMakeFiles/vf2c.dir/ef1asc_.c.o.d -o CMakeFiles/vf2c.dir/ef1asc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o -MF CMakeFiles/vf2c.dir/ef1cmc_.c.o.d -o CMakeFiles/vf2c.dir/ef1cmc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o -MF CMakeFiles/vf2c.dir/f77_aloc.c.o.d -o CMakeFiles/vf2c.dir/f77_aloc.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o -MF CMakeFiles/vf2c.dir/s_cat.c.o.d -o CMakeFiles/vf2c.dir/s_cat.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_cat.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o -MF CMakeFiles/vf2c.dir/s_cmp.c.o.d -o CMakeFiles/vf2c.dir/s_cmp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o -MF CMakeFiles/vf2c.dir/s_copy.c.o.d -o CMakeFiles/vf2c.dir/s_copy.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_copy.c [ 47%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Volume.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o -MF CMakeFiles/vf2c.dir/dtime_.c.o.d -o CMakeFiles/vf2c.dir/dtime_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/dtime_.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o -MF CMakeFiles/vf2c.dir/etime_.c.o.d -o CMakeFiles/vf2c.dir/etime_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o -MF CMakeFiles/vf2c.dir/backspac.c.o.d -o CMakeFiles/vf2c.dir/backspac.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/backspac.c [ 48%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o -MF CMakeFiles/gamer.dir/biom/ReadLattice.C.o.d -o CMakeFiles/gamer.dir/biom/ReadLattice.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C /<>/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function ‘f_back’: /<>/debian/external_deps/fetk/punc/src/vf2c/backspac.c:47:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 47 | fread((char *)&n,sizeof(uiolen),1,f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o -MF CMakeFiles/vf2c.dir/close.c.o.d -o CMakeFiles/vf2c.dir/close.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/close.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o -MF CMakeFiles/vf2c.dir/dfe.c.o.d -o CMakeFiles/vf2c.dir/dfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/dfe.c /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function ‘float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)’: /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:85:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(fp,"%d\n",&m); | ~~~~~~^~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:88:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fscanf(fp,"%f %f %f %f\n",&x,&y,&z,&radius); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o -MF CMakeFiles/vf2c.dir/dolio.c.o.d -o CMakeFiles/vf2c.dir/dolio.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/dolio.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o -MF CMakeFiles/vf2c.dir/due.c.o.d -o CMakeFiles/vf2c.dir/due.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/due.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o -MF CMakeFiles/vf2c.dir/endfile.c.o.d -o CMakeFiles/vf2c.dir/endfile.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/endfile.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o -MF CMakeFiles/vf2c.dir/err.c.o.d -o CMakeFiles/vf2c.dir/err.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/err.c [ 50%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o -MF CMakeFiles/gamer.dir/biom/ReadPDB.C.o.d -o CMakeFiles/gamer.dir/biom/ReadPDB.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 51%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -MF CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o.d -o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o -MF CMakeFiles/vf2c.dir/fmt.c.o.d -o CMakeFiles/vf2c.dir/fmt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/fmt.c /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘SurfaceMesh* SurfaceMesh_readOFF(char*)’: /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:401:14: warning: too many arguments for format [-Wformat-extra-args] 401 | printf("Read error. Expected 3 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:494:14: warning: too many arguments for format [-Wformat-extra-args] 494 | printf("Read error. Expected 4 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)’: /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:754:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 754 | in.save_nodes("plc"); | ^~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:755:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 755 | in.save_poly("plc"); | ^~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:761:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 761 | out.save_nodes("result"); | ^~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:762:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 762 | out.save_elements("result"); | ^~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:763:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 763 | out.save_faces("result"); | ^~~~~~~~ [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o -MF CMakeFiles/vf2c.dir/fmtlib.c.o.d -o CMakeFiles/vf2c.dir/fmtlib.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o -MF CMakeFiles/vf2c.dir/ftell_.c.o.d -o CMakeFiles/vf2c.dir/ftell_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ftell_.c [ 52%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -MF CMakeFiles/gamer.dir/biom/RegionGrowing.C.o.d -o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o -MF CMakeFiles/vf2c.dir/iio.c.o.d -o CMakeFiles/vf2c.dir/iio.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/iio.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o -MF CMakeFiles/vf2c.dir/ilnw.c.o.d -o CMakeFiles/vf2c.dir/ilnw.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ilnw.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o -MF CMakeFiles/vf2c.dir/inquire.c.o.d -o CMakeFiles/vf2c.dir/inquire.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/inquire.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o -MF CMakeFiles/vf2c.dir/lread.c.o.d -o CMakeFiles/vf2c.dir/lread.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lread.c [ 53%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -MF CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o.d -o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 54%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o -MF CMakeFiles/gamer.dir/biom/SurfExtract.C.o.d -o CMakeFiles/gamer.dir/biom/SurfExtract.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o -MF CMakeFiles/vf2c.dir/lwrite.c.o.d -o CMakeFiles/vf2c.dir/lwrite.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o -MF CMakeFiles/vf2c.dir/open.c.o.d -o CMakeFiles/vf2c.dir/open.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/open.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o -MF CMakeFiles/vf2c.dir/rdfmt.c.o.d -o CMakeFiles/vf2c.dir/rdfmt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c [ 55%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o -MF CMakeFiles/gamer.dir/biom/SurfRefine.C.o.d -o CMakeFiles/gamer.dir/biom/SurfRefine.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 55%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -MF CMakeFiles/gamer.dir/biom/SurfSmooth.C.o.d -o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o -MF CMakeFiles/vf2c.dir/rewind.c.o.d -o CMakeFiles/vf2c.dir/rewind.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rewind.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o -MF CMakeFiles/vf2c.dir/rsfe.c.o.d -o CMakeFiles/vf2c.dir/rsfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o -MF CMakeFiles/vf2c.dir/rsli.c.o.d -o CMakeFiles/vf2c.dir/rsli.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rsli.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o -MF CMakeFiles/vf2c.dir/rsne.c.o.d -o CMakeFiles/vf2c.dir/rsne.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o -MF CMakeFiles/vf2c.dir/sfe.c.o.d -o CMakeFiles/vf2c.dir/sfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/sfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o -MF CMakeFiles/vf2c.dir/sue.c.o.d -o CMakeFiles/vf2c.dir/sue.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o -MF CMakeFiles/vf2c.dir/typesize.c.o.d -o CMakeFiles/vf2c.dir/typesize.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/typesize.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o -MF CMakeFiles/vf2c.dir/uio.c.o.d -o CMakeFiles/vf2c.dir/uio.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o -MF CMakeFiles/vf2c.dir/util.c.o.d -o CMakeFiles/vf2c.dir/util.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/util.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o -MF CMakeFiles/vf2c.dir/wref.c.o.d -o CMakeFiles/vf2c.dir/wref.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o -MF CMakeFiles/vf2c.dir/wrtfmt.c.o.d -o CMakeFiles/vf2c.dir/wrtfmt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wrtfmt.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o -MF CMakeFiles/vf2c.dir/wsfe.c.o.d -o CMakeFiles/vf2c.dir/wsfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o -MF CMakeFiles/vf2c.dir/wsle.c.o.d -o CMakeFiles/vf2c.dir/wsle.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wsle.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o -MF CMakeFiles/vf2c.dir/wsne.c.o.d -o CMakeFiles/vf2c.dir/wsne.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o -MF CMakeFiles/vf2c.dir/xwsne.c.o.d -o CMakeFiles/vf2c.dir/xwsne.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o -MF CMakeFiles/vf2c.dir/main.c.o.d -o CMakeFiles/vf2c.dir/main.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/main.c /<>/debian/external_deps/fetk/punc/src/vf2c/main.c:115:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 115 | main(int argc, char **argv) | ^~~~ [ 60%] Linking C shared library libvf2c.so cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_link_script CMakeFiles/vf2c.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o CMakeFiles/vf2c.dir/z_abs.c.o CMakeFiles/vf2c.dir/z_cos.c.o CMakeFiles/vf2c.dir/z_div.c.o CMakeFiles/vf2c.dir/z_exp.c.o CMakeFiles/vf2c.dir/z_log.c.o CMakeFiles/vf2c.dir/z_sin.c.o CMakeFiles/vf2c.dir/z_sqrt.c.o CMakeFiles/vf2c.dir/r_abs.c.o CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o CMakeFiles/vf2c.dir/d_int.c.o CMakeFiles/vf2c.dir/d_lg10.c.o CMakeFiles/vf2c.dir/d_log.c.o CMakeFiles/vf2c.dir/d_mod.c.o CMakeFiles/vf2c.dir/d_nint.c.o CMakeFiles/vf2c.dir/d_prod.c.o CMakeFiles/vf2c.dir/d_sign.c.o CMakeFiles/vf2c.dir/d_sin.c.o CMakeFiles/vf2c.dir/d_sinh.c.o CMakeFiles/vf2c.dir/d_sqrt.c.o CMakeFiles/vf2c.dir/d_tan.c.o CMakeFiles/vf2c.dir/d_tanh.c.o CMakeFiles/vf2c.dir/i_abs.c.o CMakeFiles/vf2c.dir/i_dim.c.o CMakeFiles/vf2c.dir/i_dnnt.c.o CMakeFiles/vf2c.dir/i_indx.c.o CMakeFiles/vf2c.dir/i_len.c.o CMakeFiles/vf2c.dir/i_mod.c.o CMakeFiles/vf2c.dir/i_nint.c.o CMakeFiles/vf2c.dir/i_sign.c.o CMakeFiles/vf2c.dir/lbitbits.c.o CMakeFiles/vf2c.dir/lbitshft.c.o CMakeFiles/vf2c.dir/h_abs.c.o CMakeFiles/vf2c.dir/h_dim.c.o CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_symlink_library libvf2c.so.1.9.3 libvf2c.so.1.9 libvf2c.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 60%] Built target vf2c make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o -MF CMakeFiles/punc.dir/base/punc_base.c.o.d -o CMakeFiles/punc.dir/base/punc_base.c.o -c /<>/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/punc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_symlink_library libpunc.so.1.9.3 libpunc.so.1.9 libpunc.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 60%] Built target punc make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/mc/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o -MF CMakeFiles/mc.dir/bam/bmat.c.o.d -o CMakeFiles/mc.dir/bam/bmat.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/bmat.c [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o -MF CMakeFiles/mc.dir/bam/bsolv.c.o.d -o CMakeFiles/mc.dir/bam/bsolv.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o -MF CMakeFiles/mc.dir/base/mc_base.c.o.d -o CMakeFiles/mc.dir/base/mc_base.c.o -c /<>/debian/external_deps/fetk/mc/src/base/mc_base.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o -MF CMakeFiles/mc.dir/bam/bvec.c.o.d -o CMakeFiles/mc.dir/bam/bvec.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/bvec.c /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 922 | sprintf(rn,"Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /<>/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function ‘sprintf’, inlined from ‘Bvec_bcg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 919 | sprintf(rn,"--->Bvec_bcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_bcg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_galerkin’: /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /<>/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function ‘sprintf’, inlined from ‘Bmat_galerkin’ at /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 31 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:28: warning: ‘%s’ directive writing up to 79 bytes into a region of size 73 [-Wformat-overflow=] 631 | sprintf(rn,"Bvec_cg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 87 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 628 | sprintf(rn,"--->Bvec_cg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o -MF CMakeFiles/mc.dir/bam/mat.c.o.d -o CMakeFiles/mc.dir/bam/mat.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/mat.c /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 1422 | sprintf(rn,"Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cgnr’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 1419 | sprintf(rn,"--->Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cgnr’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o -MF CMakeFiles/mc.dir/bam/matcopy.c.o.d -o CMakeFiles/mc.dir/bam/matcopy.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/matcopy.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o -MF CMakeFiles/mc.dir/bam/matln.c.o.d -o CMakeFiles/mc.dir/bam/matln.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/matln.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o -MF CMakeFiles/mc.dir/bam/mtool.c.o.d -o CMakeFiles/mc.dir/bam/mtool.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/mtool.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o -MF CMakeFiles/mc.dir/bam/slu.c.o.d -o CMakeFiles/mc.dir/bam/slu.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/slu.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o -MF CMakeFiles/mc.dir/bam/vec.c.o.d -o CMakeFiles/mc.dir/bam/vec.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/vec.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o -MF CMakeFiles/mc.dir/bam/vec3.c.o.d -o CMakeFiles/mc.dir/bam/vec3.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/vec3.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o -MF CMakeFiles/mc.dir/bam/zslu.c.o.d -o CMakeFiles/mc.dir/bam/zslu.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/zslu.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o -MF CMakeFiles/mc.dir/whb/whb.c.o.d -o CMakeFiles/mc.dir/whb/whb.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/whb.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o -MF CMakeFiles/mc.dir/whb/bvechb.c.o.d -o CMakeFiles/mc.dir/whb/bvechb.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 267 | sprintf(rn,"Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /<>/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function ‘sprintf’, inlined from ‘Bvec_hcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 264 | sprintf(rn,"--->Bvec_hcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o -MF CMakeFiles/mc.dir/whb/rcmat.c.o.d -o CMakeFiles/mc.dir/whb/rcmat.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/rcmat.c /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 474 | sprintf(rn,"Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 471 | sprintf(rn,"--->Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function ‘Bvec_ctorPoint’: /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:28: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~ /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483646] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /<>/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function ‘sprintf’, inlined from ‘Bvec_ctorPoint’ at /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 21 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o -MF CMakeFiles/mc.dir/whb/brcmat.c.o.d -o CMakeFiles/mc.dir/whb/brcmat.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/brcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o -MF CMakeFiles/mc.dir/whb/subopt.c.o.d -o CMakeFiles/mc.dir/whb/subopt.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/subopt.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o -MF CMakeFiles/mc.dir/aprx/aprx.c.o.d -o CMakeFiles/mc.dir/aprx/aprx.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/aprx.c /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:495:31: warning: ‘%s’ directive writing up to 79 bytes into a region of size 70 [-Wformat-overflow=] 495 | sprintf(rn,"Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /<>/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function ‘sprintf’, inlined from ‘Bvec_sfpcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 11 and 90 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:492:35: warning: ‘%s’ directive writing up to 79 bytes into a region of size 66 [-Wformat-overflow=] 492 | sprintf(rn,"--->Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 15 and 94 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:776:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 776 | sprintf(rn,"Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:773:36: warning: ‘%s’ directive writing up to 79 bytes into a region of size 65 [-Wformat-overflow=] 773 | sprintf(rn,"--->Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 16 and 95 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o -MF CMakeFiles/mc.dir/aprx/assem.c.o.d -o CMakeFiles/mc.dir/aprx/assem.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/assem.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o -MF CMakeFiles/mc.dir/aprx/bnode.c.o.d -o CMakeFiles/mc.dir/aprx/bnode.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/bnode.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o -MF CMakeFiles/mc.dir/aprx/estim.c.o.d -o CMakeFiles/mc.dir/aprx/estim.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/estim.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o -MF CMakeFiles/mc.dir/aprx/eval.c.o.d -o CMakeFiles/mc.dir/aprx/eval.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/eval.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o -MF CMakeFiles/mc.dir/aprx/io.c.o.d -o CMakeFiles/mc.dir/aprx/io.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/io.c /<>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:368:40: warning: ‘__sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 368 | sprintf(filename, "f%dz.dat", block); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /<>/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:366:40: warning: ‘__sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 366 | sprintf(filename, "f%dy.dat", block); | ^ In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:364:40: warning: ‘__sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 364 | sprintf(filename, "f%dx.dat", block); | ^ In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o -MF CMakeFiles/mc.dir/aprx/node.c.o.d -o CMakeFiles/mc.dir/aprx/node.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/node.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o -MF CMakeFiles/mc.dir/aprx/parti.c.o.d -o CMakeFiles/mc.dir/aprx/parti.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/parti.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o -MF CMakeFiles/mc.dir/aprx/re.c.o.d -o CMakeFiles/mc.dir/aprx/re.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/re.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o -MF CMakeFiles/mc.dir/gem/vel.c.o.d -o CMakeFiles/mc.dir/gem/vel.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/vel.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o -MF CMakeFiles/mc.dir/gem/ves.c.o.d -o CMakeFiles/mc.dir/gem/ves.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/ves.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o -MF CMakeFiles/mc.dir/gem/gem.c.o.d -o CMakeFiles/mc.dir/gem/gem.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gem.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o -MF CMakeFiles/mc.dir/gem/gemchk.c.o.d -o CMakeFiles/mc.dir/gem/gemchk.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemchk.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o -MF CMakeFiles/mc.dir/gem/gemdisp.c.o.d -o CMakeFiles/mc.dir/gem/gemdisp.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o -MF CMakeFiles/mc.dir/gem/gemg.c.o.d -o CMakeFiles/mc.dir/gem/gemg.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemg.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o -MF CMakeFiles/mc.dir/gem/gemgen.c.o.d -o CMakeFiles/mc.dir/gem/gemgen.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function ‘Gem_delaunay’: /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type ‘double *[4]’ In file included from /<>/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type ‘double *[4]’ /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type ‘double *[4]’ /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o -MF CMakeFiles/mc.dir/gem/gemio.c.o.d -o CMakeFiles/mc.dir/gem/gemio.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemio.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o -MF CMakeFiles/mc.dir/gem/gemref.c.o.d -o CMakeFiles/mc.dir/gem/gemref.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemref.c /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:33: warning: ‘__sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 1656 | sprintf(str1,"TETRAHEDRA"); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /<>/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:33: warning: ‘TETRAHEDRON’ directive writing 11 bytes into a region of size 10 [-Wformat-overflow=] 1657 | sprintf(str2,"TETRAHEDRON"); | ~~~~~~~~~~^ In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o -MF CMakeFiles/mc.dir/gem/gemunref.c.o.d -o CMakeFiles/mc.dir/gem/gemunref.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemcube.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /<>/debian/external_deps/fetk/mc/src/pde/pde.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /<>/debian/external_deps/fetk/mc/src/nam/am.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /<>/debian/external_deps/fetk/mc/src/nam/lsolv.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /<>/debian/external_deps/fetk/mc/src/nam/nsolv.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /<>/debian/external_deps/fetk/mc/src/dyn/dyn.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o -MF CMakeFiles/mc.dir/dyn/svio.c.o.d -o CMakeFiles/mc.dir/dyn/svio.c.o -c /<>/debian/external_deps/fetk/mc/src/dyn/svio.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o -MF CMakeFiles/mc.dir/mcsh/mcsh.c.o.d -o CMakeFiles/mc.dir/mcsh/mcsh.c.o -c /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function ‘MCsh_builtIn’: /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 765 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 766 | sock, | ~~~~~ 767 | defKey, | ~~~~~~~ 768 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 769 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 771 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | defX, | ~~~~~ 773 | "GV"); | ~~~~~ /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type ‘double *[4]’ In file included from /<>/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /<>/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /<>/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /<>/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 810 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 811 | sock, | ~~~~~ 812 | defKey, | ~~~~~~~ 813 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 816 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 | defX, | ~~~~~ 818 | "MATH"); | ~~~~~~~ /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type ‘double *[4]’ /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/mc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 [ 73%] Linking CXX shared library libgamer.so cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /usr/src/apbs-3.4.1-5build5/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘__builtin___sprintf_chk’ writing 11 bytes into a region of size 10 overflows the destination [-Wstringop-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^ In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /usr/src/apbs-3.4.1-5build5/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘__builtin___sprintf_chk’ writing 12 bytes into a region of size 10 overflows the destination [-Wstringop-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^ cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_symlink_library libmc.so.1.9.3 libmc.so.1.9 libmc.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/generic /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/generic /<>/obj-x86_64-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/pmgc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/pmgc /<>/obj-x86_64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 73%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /<>/src/generic/nosh.c cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /<>/src/generic/mgparm.c [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /<>/src/pmgc/buildAd.c [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /<>/src/pmgc/buildBd.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF CMakeFiles/apbs_generic.dir/femparm.c.o.d -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /<>/src/generic/femparm.c [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /<>/src/pmgc/buildGd.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /<>/src/generic/pbamparm.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /<>/src/generic/pbsamparm.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /<>/src/generic/pbeparm.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /<>/src/generic/bemparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /<>/src/generic/geoflowparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /<>/src/generic/apolparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF CMakeFiles/apbs_generic.dir/vacc.c.o.d -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /<>/src/generic/vacc.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF CMakeFiles/apbs_generic.dir/valist.c.o.d -o CMakeFiles/apbs_generic.dir/valist.c.o -c /<>/src/generic/valist.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF CMakeFiles/apbs_generic.dir/vatom.c.o.d -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /<>/src/generic/vatom.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /<>/src/generic/vpbe.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /<>/src/generic/vcap.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -MF CMakeFiles/apbs_generic.dir/vclist.c.o.d -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /<>/src/generic/vclist.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /<>/src/generic/vstring.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF CMakeFiles/apbs_generic.dir/vparam.c.o.d -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /<>/src/generic/vparam.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /<>/src/generic/vgreen.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /<>/src/pmgc/buildPd.c [ 81%] Linking C shared library libapbs_generic.so cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so cd /<>/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_symlink_library libgamer.so.1.9.3 libgamer.so.1.9 libgamer.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 81%] Built target gamer [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /<>/src/pmgc/cgd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /<>/src/pmgc/gsd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /<>/src/pmgc/matvecd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /<>/src/pmgc/mgcsd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /<>/src/pmgc/mgdrvd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /<>/src/pmgc/mgsubd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /<>/src/pmgc/mikpckd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /<>/src/pmgc/mlinpckd.c cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library libapbs_generic.so.3 libapbs_generic.so.3 libapbs_generic.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 83%] Built target apbs_generic [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /<>/src/pmgc/mypdec.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /<>/src/pmgc/newtond.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /<>/src/pmgc/newdrvd.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /<>/src/pmgc/powerd.c cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /<>/src/pmgc/smoothd.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /<>/src/pmgc/mgfasd.c make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/fem /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/fem /<>/obj-x86_64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /<>/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o -MF CMakeFiles/apbs_fem.dir/vcsm.c.o.d -o CMakeFiles/apbs_fem.dir/vcsm.c.o -c /<>/src/fem/vcsm.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /<>/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o -MF CMakeFiles/apbs_fem.dir/vfetk.c.o.d -o CMakeFiles/apbs_fem.dir/vfetk.c.o -c /<>/src/fem/vfetk.c /<>/src/fem/vfetk.c: In function ‘Vfetk_PDE_ctor2’: /<>/src/fem/vfetk.c:1211:24: warning: assignment to ‘void (*)(struct sPDE *, int, int, double *, double *, double (*)[3])’ from incompatible pointer type ‘void (*)(PDE *, int, int, double *, double *)’ {aka ‘void (*)(struct sPDE *, int, int, double *, double *)’} [-Wincompatible-pointer-types] 1211 | thee->u_T = Vfetk_PDE_u_T; | ^ [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /<>/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o -MF CMakeFiles/apbs_fem.dir/vpee.c.o.d -o CMakeFiles/apbs_fem.dir/vpee.c.o -c /<>/src/fem/vpee.c [ 86%] Linking C shared library libapbs_pmgc.so cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1073:28: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1073 | sprintf(ptrfmt,"(%dI%d)",nptrline,numZdigits+1); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/src/fem/vfetk.h:67, from /<>/src/fem/vfetk.c:57: In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1073:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1074:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~ /<>/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1074:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1075:28: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1075 | sprintf(indfmt,"(%dI%d)",nindline,nrowdigits+1); | ^ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1075:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1076:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~ /<>/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1076:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 86%] Linking C shared library libapbs_fem.so cd /<>/obj-x86_64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-x86_64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_symlink_library libapbs_fem.so.3 libapbs_fem.so.3 libapbs_fem.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 86%] Built target apbs_fem cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library libapbs_pmgc.so.3 libapbs_pmgc.so.3 libapbs_pmgc.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 86%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/mg /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/mg /<>/obj-x86_64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /<>/src/mg/vpmg.c cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /<>/src/mg/vmgrid.c cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /<>/src/mg/vgrid.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF CMakeFiles/apbs_mg.dir/vopot.c.o.d -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /<>/src/mg/vopot.c /<>/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /<>/src/mg/vgrid.c:853:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /<>/src/mg/vpmgp.c /<>/src/mg/vgrid.c:831:7: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/src/mg/vgrid.h:67, from /<>/src/mg/vgrid.c:57: /usr/include/stdio.h:183:12: note: in a call to function ‘fclose’ declared ‘nonnull’ 183 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 87%] Linking C shared library libapbs_mg.so cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 87%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF CMakeFiles/apbs_routines.dir/routines.c.o.d -o CMakeFiles/apbs_routines.dir/routines.c.o -c /<>/src/routines.c /<>/src/routines.c: In function ‘initAPOL’: /<>/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5046 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/routines.c:5046:20: note: referencing argument 2 of type ‘char[1024]’ /<>/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /<>/src/routines.c:5046:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /<>/src/generic/apolparm.h:73, from /<>/src/generic/nosh.h:73, from /<>/src/apbs.h:70, from /<>/src/routines.h:64, from /<>/src/routines.c:54: /<>/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /<>/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5048 | atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/routines.c:5048:24: note: referencing argument 2 of type ‘char[1024]’ /<>/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /<>/src/routines.c:5048:24: note: referencing argument 3 of type ‘char[1024]’ /<>/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writematMG’: /<>/src/routines.c:2020:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2020 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/src/apbs.h:67: In function ‘sprintf’, inlined from ‘writematMG’ at /<>/src/routines.c:2020:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2919:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2919 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2919:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2963:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2963 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2963:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2954:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2954 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2954:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2937:34: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2937 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2937:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2930:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2930 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2930:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2944:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2944 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2944:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2909:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2909 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2909:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataFE’: /<>/src/routines.c:4887:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4887 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /<>/src/routines.c:4887:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataFE’: /<>/src/routines.c:4893:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4893 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /<>/src/routines.c:4893:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataFE’: /<>/src/routines.c:4880:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4880 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /<>/src/routines.c:4880:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 88%] Linking C shared library libapbs_routines.so cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake "--color=" cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build [ 88%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -MF CMakeFiles/smooth.dir/smooth.c.o.d -o CMakeFiles/smooth.dir/smooth.c.o -c /<>/tools/mesh/smooth.c make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -MF CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /<>/tools/mesh/mgmesh.c [ 89%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -MF CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /<>/tools/mesh/dxmath.c [ 89%] Building C object src/CMakeFiles/apbs.dir/main.c.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /<>/src/main.c /<>/src/main.c: In function ‘main’: /<>/src/main.c:319:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /<>/src/main.c:319:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ [ 89%] Linking C executable ../bin/mgmesh cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 89%] Linking C executable ../bin/dxmath cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 89%] Linking C executable ../bin/smooth cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 89%] Linking C executable apbs cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/apbs.dir/main.c.o -o apbs -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp libapbs_routines.so.3 mg/libapbs_mg.so.3 pmgc/libapbs_pmgc.so.3 fem/libapbs_fem.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 89%] Built target mgmesh make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 90%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o -MF CMakeFiles/mergedx.dir/mergedx.c.o.d -o CMakeFiles/mergedx.dir/mergedx.c.o -c /<>/tools/mesh/mergedx.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 90%] Built target dxmath make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 90%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o -MF CMakeFiles/mergedx2.dir/mergedx2.c.o.d -o CMakeFiles/mergedx2.dir/mergedx2.c.o -c /<>/tools/mesh/mergedx2.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 90%] Built target smooth make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/value.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 91%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/value.dir/value.c.o -MF CMakeFiles/value.dir/value.c.o.d -o CMakeFiles/value.dir/value.c.o -c /<>/tools/mesh/value.c [ 91%] Linking C executable ../bin/value cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 91%] Built target apbs [ 91%] Linking C executable ../bin/mergedx /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/value.dir/value.c.o -o ../bin/value ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 91%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /<>/tools/mesh/multivalue.c [ 92%] Linking C executable ../bin/multivalue cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/mergedx2 cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 92%] Built target value make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 92%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -MF CMakeFiles/benchmark.dir/benchmark.c.o.d -o CMakeFiles/benchmark.dir/benchmark.c.o -c /<>/tools/mesh/benchmark.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 92%] Built target multivalue make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake "--color=" [ 93%] Linking C executable ../bin/benchmark cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 93%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /<>/tools/mesh/similarity.c [ 93%] Built target mergedx make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 93%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /<>/tools/mesh/analysis.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 93%] Built target benchmark make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake "--color=" [ 94%] Linking C executable ../bin/similarity cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 95%] Linking C executable ../bin/analysis cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1 [ 95%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /<>/tools/mesh/dx2mol.c /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/analysis.dir/analysis.c.o -o ../bin/analysis ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 95%] Built target mergedx2 make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 95%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /<>/tools/mesh/dx2uhbd.c [ 95%] Linking C executable ../bin/dx2mol cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 96%] Linking C executable ../bin/dx2uhbd cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 96%] Built target analysis make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 96%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /<>/tools/mesh/del2dx.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 96%] Built target dx2uhbd make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' /<>/tools/mesh/del2dx.c: In function ‘main’: /<>/tools/mesh/del2dx.c:76:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:89:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:97:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:103:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:106:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 96%] Built target similarity make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake "--color=" [ 97%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /<>/tools/mesh/tensor2dx.c [ 97%] Built target dx2mol make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/manip /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/manip /<>/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build [ 97%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /<>/tools/mesh/uhbd_asc2bin.c [ 98%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF CMakeFiles/coulomb.dir/coulomb.c.o.d -o CMakeFiles/coulomb.dir/coulomb.c.o -c /<>/tools/manip/coulomb.c [ 99%] Linking C executable ../bin/del2dx cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /<>/tools/mesh/tensor2dx.c: In function ‘main’: /<>/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /<>/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Linking C executable ../bin/tensor2dx cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 [ 99%] Linking C executable ../bin/uhbd_asc2bin cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp [ 99%] Linking C executable ../bin/coulomb cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 99%] Built target del2dx make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/manip /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/manip /<>/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 99%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/born.dir/born.c.o -MF CMakeFiles/born.dir/born.c.o.d -o CMakeFiles/born.dir/born.c.o -c /<>/tools/manip/born.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 99%] Built target tensor2dx make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/python /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 99%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/python3.12 -I/<>/tools/python -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 99%] Built target uhbd_asc2bin make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python-pybind /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/python-pybind /<>/obj-x86_64-linux-gnu/tools/python-pybind/CMakeFiles/apbs_pybind.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o -MF CMakeFiles/apbs_pybind.dir/module.cpp.o.d -o CMakeFiles/apbs_pybind.dir/module.cpp.o -c /<>/tools/python-pybind/module.cpp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 99%] Built target coulomb [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -c /<>/tools/python-pybind/bind_nosh.cpp [ 99%] Linking C executable ../bin/born cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/born.dir/born.c.o -o ../bin/born ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 99%] Built target born [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -c /<>/tools/python-pybind/bind_vatom.cpp [100%] Linking C shared library _apbslib.so cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,_apbslib.so -o _apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target _apbslib [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -c /<>/tools/python-pybind/bind_valist.cpp [100%] Linking CXX shared module apbs.cpython-312-x86_64-linux-gnu.so cd /<>/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pybind.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-312-x86_64-linux-gnu.so CMakeFiles/apbs_pybind.dir/module.cpp.o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/<>' PYTHONPATH=/<>/obj-x86_64-linux-gnu/tools/python sphinx-build -b html docs /<>/obj-x86_64-linux-gnu/docs/_build/html # HTML generator Running Sphinx v7.2.6 WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: api/index.rst, background.rst, formats/apbs-xml-parm.rst, formats/flat-parm.rst, formats/harwell.rst, formats/index.rst, formats/mcsf.rst, formats/opendx.rst, formats/pdb.rst, formats/pqr.rst, ..., using/input/old/generic/sdens.rst, using/input/old/generic/srad.rst, using/input/old/generic/swin.rst, using/input/old/generic/temp.rst, using/input/old/index.rst, using/input/old/print.rst, using/input/old/read.rst, using/tests.rst, using/tools.rst, using/units.rst WARNING: Failed to import apbs.input_file.calculate.finite_element. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.process. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.generic. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.read. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.nonpolar.Nonpolar. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.finite_difference. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.boundary_element. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file. Possible hints: * AttributeError: module 'apbs' has no attribute 'input_file' * ModuleNotFoundError: No module named 'pyparsing' loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 127 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 1%] api/index reading sources... [ 2%] background reading sources... [ 2%] formats/apbs-xml-parm reading sources... [ 3%] formats/flat-parm reading sources... [ 4%] formats/harwell reading sources... [ 5%] formats/index reading sources... [ 6%] formats/mcsf reading sources... [ 6%] formats/opendx reading sources... [ 7%] formats/pdb reading sources... [ 8%] formats/pqr reading sources... [ 9%] formats/uhbd reading sources... [ 9%] formats/xml-struct reading sources... [ 10%] getting/index reading sources... [ 11%] getting/source reading sources... [ 12%] help reading sources... [ 13%] index reading sources... [ 13%] reading reading sources... [ 14%] releases reading sources... [ 15%] supporting reading sources... [ 16%] todo reading sources... [ 17%] using/examples/binding-energies reading sources... [ 17%] using/examples/salt-linkage reading sources... [ 18%] using/examples/solvation-energies reading sources... [ 19%] using/examples/visualization-pymol reading sources... [ 20%] using/examples/visualization-unitymol reading sources... [ 20%] using/index reading sources... [ 21%] using/input/new/calculate/boundary_element reading sources... [ 22%] using/input/new/calculate/finite_difference reading sources... [ 23%] using/input/new/calculate/finite_element reading sources... [ 24%] using/input/new/calculate/index reading sources... [ 24%] using/input/new/calculate/nonpolar reading sources... [ 25%] using/input/new/index reading sources... [ 26%] using/input/new/process reading sources... [ 27%] using/input/new/process_api reading sources... [ 28%] using/input/new/read reading sources... [ 28%] using/input/old/apolar/dpos reading sources... [ 29%] using/input/old/apolar/gamma reading sources... [ 30%] using/input/old/apolar/index reading sources... [ 31%] using/input/old/apolar/press reading sources... [ 31%] using/input/old/apolar/srfm reading sources... [ 32%] using/input/old/elec/3dmap reading sources... [ 33%] using/input/old/elec/akeyPRE reading sources... [ 34%] using/input/old/elec/akeySOLVE reading sources... [ 35%] using/input/old/elec/async reading sources... [ 35%] using/input/old/elec/bcfl reading sources... [ 36%] using/input/old/elec/cgcent reading sources... [ 37%] using/input/old/elec/cglen reading sources... [ 38%] using/input/old/elec/chgm reading sources... [ 39%] using/input/old/elec/diff reading sources... [ 39%] using/input/old/elec/dime reading sources... [ 40%] using/input/old/elec/domainLength reading sources... [ 41%] using/input/old/elec/dx reading sources... [ 42%] using/input/old/elec/ekey reading sources... [ 43%] using/input/old/elec/etol reading sources... [ 43%] using/input/old/elec/exp reading sources... [ 44%] using/input/old/elec/fe-manual reading sources... [ 45%] using/input/old/elec/fgcent reading sources... [ 46%] using/input/old/elec/fglen reading sources... [ 46%] using/input/old/elec/gamma-geoflow reading sources... [ 47%] using/input/old/elec/gcent reading sources... [ 48%] using/input/old/elec/geoflow-auto reading sources... [ 49%] using/input/old/elec/glen reading sources... [ 50%] using/input/old/elec/grid2d reading sources... [ 50%] using/input/old/elec/gridpts reading sources... [ 51%] using/input/old/elec/imat reading sources... [ 52%] using/input/old/elec/index reading sources... [ 53%] using/input/old/elec/ion reading sources... [ 54%] using/input/old/elec/lpbe reading sources... [ 54%] using/input/old/elec/lrpbe reading sources... [ 55%] using/input/old/elec/mac reading sources... [ 56%] using/input/old/elec/maxsolve reading sources... [ 57%] using/input/old/elec/maxvert reading sources... [ 57%] using/input/old/elec/mesh reading sources... [ 58%] using/input/old/elec/mg-auto reading sources... [ 59%] using/input/old/elec/mg-dummy reading sources... [ 60%] using/input/old/elec/mg-manual reading sources... [ 61%] using/input/old/elec/mg-para reading sources... [ 61%] using/input/old/elec/nlev reading sources... [ 62%] using/input/old/elec/npbe reading sources... [ 63%] using/input/old/elec/nrpbe reading sources... [ 64%] using/input/old/elec/ntraj reading sources... [ 65%] using/input/old/elec/ofrac reading sources... [ 65%] using/input/old/elec/outdata reading sources... [ 66%] using/input/old/elec/pbam-auto reading sources... [ 67%] using/input/old/elec/pbc reading sources... [ 68%] using/input/old/elec/pbsam-auto reading sources... [ 69%] using/input/old/elec/pdie reading sources... [ 69%] using/input/old/elec/pdime reading sources... [ 70%] using/input/old/elec/press-geoflow reading sources... [ 71%] using/input/old/elec/pygbe reading sources... [ 72%] using/input/old/elec/randorient reading sources... [ 72%] using/input/old/elec/runname reading sources... [ 73%] using/input/old/elec/runtype reading sources... [ 74%] using/input/old/elec/salt reading sources... [ 75%] using/input/old/elec/sdie reading sources... [ 76%] using/input/old/elec/srfm reading sources... [ 76%] using/input/old/elec/surf reading sources... [ 77%] using/input/old/elec/tabi reading sources... [ 78%] using/input/old/elec/targetNum reading sources... [ 79%] using/input/old/elec/targetRes reading sources... [ 80%] using/input/old/elec/term reading sources... [ 80%] using/input/old/elec/termcombine reading sources... [ 81%] using/input/old/elec/tolsp reading sources... [ 82%] using/input/old/elec/tree_n0 reading sources... [ 83%] using/input/old/elec/tree_order reading sources... [ 83%] using/input/old/elec/units reading sources... [ 84%] using/input/old/elec/usemap reading sources... [ 85%] using/input/old/elec/usemesh reading sources... [ 86%] using/input/old/elec/vdwdisp reading sources... [ 87%] using/input/old/elec/write reading sources... [ 87%] using/input/old/elec/writemat reading sources... [ 88%] using/input/old/elec/xyz reading sources... [ 89%] using/input/old/generic/bconc reading sources... [ 90%] using/input/old/generic/calcenergy reading sources... [ 91%] using/input/old/generic/calcforce reading sources... [ 91%] using/input/old/generic/grid reading sources... [ 92%] using/input/old/generic/mol reading sources... [ 93%] using/input/old/generic/sdens reading sources... [ 94%] using/input/old/generic/srad reading sources... [ 94%] using/input/old/generic/swin reading sources... [ 95%] using/input/old/generic/temp reading sources... [ 96%] using/input/old/index reading sources... [ 97%] using/input/old/print reading sources... [ 98%] using/input/old/read reading sources... [ 98%] using/tests reading sources... [ 99%] using/tools reading sources... [100%] using/units /<>/docs/getting/index.rst:41: ERROR: Unexpected indentation. /<>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow". /<>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk". /<>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam". /<>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "tabi-pb". WARNING: autodoc: failed to import module 'input_file.calculate.boundary_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_difference' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.generic' from module 'apbs'; the following exception was raised: No module named 'pyparsing' /<>/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition. /<>/docs/using/input/new/calculate/index.rst:33: ERROR: Document may not end with a transition. WARNING: autodoc: failed to import module 'input_file.calculate.nonpolar.Nonpolar' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.process' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.read' from module 'apbs'; the following exception was raised: No module named 'pyparsing' looking for now-outdated files... none found pickling environment... done checking consistency... /<>/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 1%] api/index writing output... [ 2%] background writing output... [ 2%] formats/apbs-xml-parm writing output... [ 3%] formats/flat-parm writing output... [ 4%] formats/harwell writing output... [ 5%] formats/index writing output... [ 6%] formats/mcsf writing output... [ 6%] formats/opendx writing output... [ 7%] formats/pdb writing output... [ 8%] formats/pqr writing output... [ 9%] formats/uhbd writing output... [ 9%] formats/xml-struct writing output... [ 10%] getting/index writing output... [ 11%] getting/source writing output... [ 12%] help writing output... [ 13%] index writing output... [ 13%] reading writing output... [ 14%] releases writing output... [ 15%] supporting writing output... [ 16%] todo writing output... [ 17%] using/examples/binding-energies writing output... [ 17%] using/examples/salt-linkage writing output... [ 18%] using/examples/solvation-energies writing output... [ 19%] using/examples/visualization-pymol writing output... [ 20%] using/examples/visualization-unitymol writing output... [ 20%] using/index writing output... [ 21%] using/input/new/calculate/boundary_element writing output... [ 22%] using/input/new/calculate/finite_difference writing output... [ 23%] using/input/new/calculate/finite_element writing output... [ 24%] using/input/new/calculate/index writing output... [ 24%] using/input/new/calculate/nonpolar writing output... [ 25%] using/input/new/index writing output... [ 26%] using/input/new/process writing output... [ 27%] using/input/new/process_api writing output... [ 28%] using/input/new/read writing output... [ 28%] using/input/old/apolar/dpos writing output... [ 29%] using/input/old/apolar/gamma writing output... [ 30%] using/input/old/apolar/index writing output... [ 31%] using/input/old/apolar/press writing output... [ 31%] using/input/old/apolar/srfm writing output... [ 32%] using/input/old/elec/3dmap writing output... [ 33%] using/input/old/elec/akeyPRE writing output... [ 34%] using/input/old/elec/akeySOLVE writing output... [ 35%] using/input/old/elec/async writing output... [ 35%] using/input/old/elec/bcfl writing output... [ 36%] using/input/old/elec/cgcent writing output... [ 37%] using/input/old/elec/cglen writing output... [ 38%] using/input/old/elec/chgm writing output... [ 39%] using/input/old/elec/diff writing output... [ 39%] using/input/old/elec/dime writing output... [ 40%] using/input/old/elec/domainLength writing output... [ 41%] using/input/old/elec/dx writing output... [ 42%] using/input/old/elec/ekey writing output... [ 43%] using/input/old/elec/etol writing output... [ 43%] using/input/old/elec/exp writing output... [ 44%] using/input/old/elec/fe-manual writing output... [ 45%] using/input/old/elec/fgcent writing output... [ 46%] using/input/old/elec/fglen writing output... [ 46%] using/input/old/elec/gamma-geoflow writing output... [ 47%] using/input/old/elec/gcent writing output... [ 48%] using/input/old/elec/geoflow-auto writing output... [ 49%] using/input/old/elec/glen writing output... [ 50%] using/input/old/elec/grid2d writing output... [ 50%] using/input/old/elec/gridpts writing output... [ 51%] using/input/old/elec/imat writing output... [ 52%] using/input/old/elec/index writing output... [ 53%] using/input/old/elec/ion writing output... [ 54%] using/input/old/elec/lpbe writing output... [ 54%] using/input/old/elec/lrpbe writing output... [ 55%] using/input/old/elec/mac writing output... [ 56%] using/input/old/elec/maxsolve writing output... [ 57%] using/input/old/elec/maxvert writing output... [ 57%] using/input/old/elec/mesh writing output... [ 58%] using/input/old/elec/mg-auto writing output... [ 59%] using/input/old/elec/mg-dummy writing output... [ 60%] using/input/old/elec/mg-manual writing output... [ 61%] using/input/old/elec/mg-para writing output... [ 61%] using/input/old/elec/nlev writing output... [ 62%] using/input/old/elec/npbe writing output... [ 63%] using/input/old/elec/nrpbe writing output... [ 64%] using/input/old/elec/ntraj writing output... [ 65%] using/input/old/elec/ofrac writing output... [ 65%] using/input/old/elec/outdata writing output... [ 66%] using/input/old/elec/pbam-auto writing output... [ 67%] using/input/old/elec/pbc writing output... [ 68%] using/input/old/elec/pbsam-auto writing output... [ 69%] using/input/old/elec/pdie writing output... [ 69%] using/input/old/elec/pdime writing output... [ 70%] using/input/old/elec/press-geoflow writing output... [ 71%] using/input/old/elec/pygbe writing output... [ 72%] using/input/old/elec/randorient writing output... [ 72%] using/input/old/elec/runname writing output... [ 73%] using/input/old/elec/runtype writing output... [ 74%] using/input/old/elec/salt writing output... [ 75%] using/input/old/elec/sdie writing output... [ 76%] using/input/old/elec/srfm writing output... [ 76%] using/input/old/elec/surf writing output... [ 77%] using/input/old/elec/tabi writing output... [ 78%] using/input/old/elec/targetNum writing output... [ 79%] using/input/old/elec/targetRes writing output... [ 80%] using/input/old/elec/term writing output... [ 80%] using/input/old/elec/termcombine writing output... [ 81%] using/input/old/elec/tolsp writing output... [ 82%] using/input/old/elec/tree_n0 writing output... [ 83%] using/input/old/elec/tree_order writing output... [ 83%] using/input/old/elec/units writing output... [ 84%] using/input/old/elec/usemap writing output... [ 85%] using/input/old/elec/usemesh writing output... [ 86%] using/input/old/elec/vdwdisp writing output... [ 87%] using/input/old/elec/write writing output... [ 87%] using/input/old/elec/writemat writing output... [ 88%] using/input/old/elec/xyz writing output... [ 89%] using/input/old/generic/bconc writing output... [ 90%] using/input/old/generic/calcenergy writing output... [ 91%] using/input/old/generic/calcforce writing output... [ 91%] using/input/old/generic/grid writing output... [ 92%] using/input/old/generic/mol writing output... [ 93%] using/input/old/generic/sdens writing output... [ 94%] using/input/old/generic/srad writing output... [ 94%] using/input/old/generic/swin writing output... [ 95%] using/input/old/generic/temp writing output... [ 96%] using/input/old/index writing output... [ 97%] using/input/old/print writing output... [ 98%] using/input/old/read writing output... [ 98%] using/tests writing output... [ 99%] using/tools writing output... [100%] using/units generating indices... genindex py-modindex done highlighting module code... writing additional pages... search done copying images... [ 10%] media/pb-schematic.png copying images... [ 20%] media/apbs_bind_eng.png copying images... [ 30%] media/rna-qdens-pymol.jpg copying images... [ 40%] media/rna-qdens-vmd.jpg copying images... [ 50%] media/apbs_sol_eng.png copying images... [ 60%] media/fas2-iso-pymol.png copying images... [ 70%] media/fas2-surf-pymol.png copying images... [ 80%] media/1fas_VR.png copying images... [ 90%] media/UI.png copying images... [100%] media/AChE.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 28 warnings. The HTML pages are in obj-x86_64-linux-gnu/docs/_build/html. make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=cmake dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /<>/debian/tmp/usr/share/apbs/cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /<>/debian/tmp/usr/include/punc/punc.h -- Installing: /<>/debian/tmp/usr/include/punc/punc_base.h -- Installing: /<>/debian/tmp/usr/include/punc/punccf.h -- Installing: /<>/debian/tmp/usr/include/punc/punc_base_p.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libpunc.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libpunc.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libpunc.so -- Installing: /<>/debian/tmp/usr/include/punc/varpack.h -- Installing: /<>/debian/tmp/usr/include/punc/vblas.h -- Installing: /<>/debian/tmp/usr/include/punc/vcgcode.h -- Installing: /<>/debian/tmp/usr/include/punc/vlapack.h -- Installing: /<>/debian/tmp/usr/include/punc/vpmg.h -- Installing: /<>/debian/tmp/usr/include/punc/vf2c.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libvf2c.so -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libcgcode.so -- Installing: /<>/debian/tmp/usr/include/gamer/gamer.h -- Installing: /<>/debian/tmp/usr/include/gamer/gamer_base.h -- Installing: /<>/debian/tmp/usr/include/gamer/triangle.h -- Installing: /<>/debian/tmp/usr/include/gamer/tetgen.h -- Installing: /<>/debian/tmp/usr/include/gamer/biom.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libgamer.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libgamer.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libgamer.so -- Installing: /<>/debian/tmp/usr/include/mc/mc_base.h -- Installing: /<>/debian/tmp/usr/include/mc/mc.h -- Installing: /<>/debian/tmp/usr/include/mc/bam.h -- Installing: /<>/debian/tmp/usr/include/mc/bmat.h -- Installing: /<>/debian/tmp/usr/include/mc/bvec.h -- Installing: /<>/debian/tmp/usr/include/mc/mat.h -- Installing: /<>/debian/tmp/usr/include/mc/mtool.h -- Installing: /<>/debian/tmp/usr/include/mc/slu.h -- Installing: /<>/debian/tmp/usr/include/mc/vec.h -- Installing: /<>/debian/tmp/usr/include/mc/vec3.h -- Installing: /<>/debian/tmp/usr/include/mc/zslu.h -- Installing: /<>/debian/tmp/usr/include/mc/whb.h -- Installing: /<>/debian/tmp/usr/include/mc/aprx.h -- Installing: /<>/debian/tmp/usr/include/mc/bnode.h -- Installing: /<>/debian/tmp/usr/include/mc/node.h -- Installing: /<>/debian/tmp/usr/include/mc/re.h -- Installing: /<>/debian/tmp/usr/include/mc/gem.h -- Installing: /<>/debian/tmp/usr/include/mc/vel.h -- Installing: /<>/debian/tmp/usr/include/mc/ves.h -- Installing: /<>/debian/tmp/usr/include/mc/pde.h -- Installing: /<>/debian/tmp/usr/include/mc/am.h -- Installing: /<>/debian/tmp/usr/include/mc/nam.h -- Installing: /<>/debian/tmp/usr/include/mc/dyn.h -- Installing: /<>/debian/tmp/usr/include/mc/mcsh.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libmc.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libmc.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libmc.so -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_routines.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_routines.so -- Installing: /<>/debian/tmp/usr/include/apbs/apbs.h -- Installing: /<>/debian/tmp/usr/include/apbs/routines.h -- Installing: /<>/debian/tmp/usr/bin/apbs -- Installing: /<>/debian/tmp/usr/include/generic/nosh.h -- Installing: /<>/debian/tmp/usr/include/generic/mgparm.h -- Installing: /<>/debian/tmp/usr/include/generic/femparm.h -- Installing: /<>/debian/tmp/usr/include/generic/pbamparm.h -- Installing: /<>/debian/tmp/usr/include/generic/pbsamparm.h -- Installing: /<>/debian/tmp/usr/include/generic/pbeparm.h -- Installing: /<>/debian/tmp/usr/include/generic/bemparm.h -- Installing: /<>/debian/tmp/usr/include/generic/geoflowparm.h -- Installing: /<>/debian/tmp/usr/include/generic/apolparm.h -- Installing: /<>/debian/tmp/usr/include/generic/vacc.h -- Installing: /<>/debian/tmp/usr/include/generic/valist.h -- Installing: /<>/debian/tmp/usr/include/generic/vatom.h -- Installing: /<>/debian/tmp/usr/include/generic/vpbe.h -- Installing: /<>/debian/tmp/usr/include/generic/vcap.h -- Installing: /<>/debian/tmp/usr/include/generic/vclist.h -- Installing: /<>/debian/tmp/usr/include/generic/vstring.h -- Installing: /<>/debian/tmp/usr/include/generic/vparam.h -- Installing: /<>/debian/tmp/usr/include/generic/vgreen.h -- Installing: /<>/debian/tmp/usr/include/generic/vmatrix.h -- Installing: /<>/debian/tmp/usr/include/generic/vhal.h -- Installing: /<>/debian/tmp/usr/include/generic/vunit.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_generic.so -- Installing: /<>/debian/tmp/usr/include/pmgc/buildAd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/buildBd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/buildGd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/buildPd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/cgd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/gsd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/matvecd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgcsd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgdrvd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgsubd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mikpckd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mlinpckd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mypdec.h -- Installing: /<>/debian/tmp/usr/include/pmgc/newtond.h -- Installing: /<>/debian/tmp/usr/include/pmgc/newdrvd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/powerd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/smoothd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgfasd.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so -- Installing: /<>/debian/tmp/usr/include/mg/vgrid.h -- Installing: /<>/debian/tmp/usr/include/mg/vmgrid.h -- Installing: /<>/debian/tmp/usr/include/mg/vopot.h -- Installing: /<>/debian/tmp/usr/include/mg/vpmg.h -- Installing: /<>/debian/tmp/usr/include/mg/vpmgp.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_mg.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_mg.so -- Installing: /<>/debian/tmp/usr/include/fem/vcsm.h -- Installing: /<>/debian/tmp/usr/include/fem/vfetk.h -- Installing: /<>/debian/tmp/usr/include/fem/vpee.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_fem.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_fem.so -- Installing: /<>/debian/tmp/usr/lib/apbs.cpython-312-x86_64-linux-gnu.so -- Installing: /<>/debian/tmp/usr/share/apbs/examples -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/pmf.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/run_selected_examples.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/proton.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/postprocess.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/run_apdx_files.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/test.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs_dx.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNB.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/fas2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/mache.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/run_examples.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.param -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.config -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tests -- Installing: /<>/debian/tmp/usr/share/apbs/tests/test_cases.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_results.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_tester.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_logger.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/noinput.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/main.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_constants.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/module.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/release-data.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/getReleases.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/psize.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/coulomb.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/born.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/inputgen.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/value.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/smooth.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/similarity.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/analysis.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/value make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/<>' (cd tests; PATH=/<>/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/<>/debian/tmp/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/<>/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) TESTING WITH BINARY_NAME:apbs START_DIR:/<>/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001235 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/<>/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/<>/debian/tmp/usr/bin/apbs Testing all sections The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv ================================================================================ Running tests for born section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) *** PASSED *** Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) *** PASSED *** Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) *** PASSED *** Elapsed time: 0.968034 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] COMPUTED RESULT 960.7073836227 COMPUTED RESULT 2200.266567971 COMPUTED RESULT 4732.245131587 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.7735526282 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) *** PASSED *** Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) *** PASSED *** Elapsed time: 0.765572 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 2201.243880085 COMPUTED RESULT 4733.006258977 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.0124252387 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE0.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE1.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605696E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605696e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE2.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344954e+01 Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) *** PASSED *** Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) *** PASSED *** Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) *** PASSED *** Elapsed time: 3.643208 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] COMPUTED RESULT 960.7073836226 COMPUTED RESULT 3257.1427835731997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867463003 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE0.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE1.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE2.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328301e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734462084052e+01 Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) *** PASSED *** Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) *** PASSED *** Elapsed time: 3.291449 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.669498 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermediate energies in input file apbs-smol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 3258.1578983732998 COMPUTED RESULT 5942.108652589999 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -229.38714395599 Running tests for actin-dimer-auto section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058625E+02 kJ/mol Global net ELEC energy = 1.048683058625E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) *** PASSED *** Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) *** PASSED *** Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) *** PASSED *** Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) *** PASSED *** Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) *** PASSED *** Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) *** PASSED *** Testing computed result against expected result (1.048683058625e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 41.538062 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058625] EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] COMPUTED RESULT 152761.7850342 COMPUTED RESULT 291951.0754196 COMPUTED RESULT 152767.184488 COMPUTED RESULT 291546.8859278 COMPUTED RESULT 305631.7807611 COMPUTED RESULT 583602.8296532 COMPUTED RESULT 104.8683058625 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077691E+02 kJ/mol Global net ELEC energy = 1.095841077691E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) *** PASSED *** Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) *** PASSED *** Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) *** PASSED *** Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) *** PASSED *** Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) *** PASSED *** Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) *** PASSED *** Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 37.016434 seconds -------------------------------------------------------------------------------- Total elapsed time: 78.554496 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] COMPUTED RESULT 152863.2421825 COMPUTED RESULT 292061.866232 COMPUTED RESULT 152929.7900572 COMPUTED RESULT 291659.2202835 COMPUTED RESULT 305924.4262535 COMPUTED RESULT 583830.6706232 COMPUTED RESULT 109.5841077691 Running tests for alkanes section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'alkanes.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) *** PASSED *** Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) *** PASSED *** Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) *** PASSED *** Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) *** PASSED *** Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) *** PASSED *** Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) *** PASSED *** Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) *** PASSED *** Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) *** PASSED *** Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) *** PASSED *** Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) *** PASSED *** Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) *** PASSED *** Elapsed time: 9.957926 seconds -------------------------------------------------------------------------------- Total elapsed time: 9.957926 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in Checking for intermediate energies in input file alkanes.out EXPECTED COMPUTED: 11 EXPECTED EXPECTED: 11 COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01'] COMPUTED RESULT 14.39739455792 COMPUTED RESULT 12.08346456826 COMPUTED RESULT 13.54016672221 COMPUTED RESULT 9.363673200142 COMPUTED RESULT 9.422717598546 COMPUTED RESULT 16.40068943201 COMPUTED RESULT 13.23144287435 COMPUTED RESULT 7.894367190329 COMPUTED RESULT 14.49633815052 COMPUTED RESULT 14.47900211546 COMPUTED RESULT 11.92358496286 Running tests for FKBP section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7h-dmso-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086371E+01 kJ/mol Global net ELEC energy = 1.500810086371E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) *** PASSED *** Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) *** PASSED *** Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) *** PASSED *** Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 6.668427 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermediate energies in input file 1d7h-dmso-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086371] EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01'] COMPUTED RESULT 10608.99690259 COMPUTED RESULT 42765.23673491 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 39.61107503213 COMPUTED RESULT 712.1048606059 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10584.10584089 COMPUTED RESULT 42053.85249581 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3335.429017008 COMPUTED RESULT -21.80527370616 COMPUTED RESULT -3328.631844166 COMPUTED RESULT 15.00810086371 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7h-dmso-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192073E+01 kJ/mol Global net ELEC energy = 1.624454192073E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) *** PASSED *** Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) *** PASSED *** Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) *** PASSED *** Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 6.24172 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermediate energies in input file 1d7h-dmso-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192073] EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01'] COMPUTED RESULT 10749.48704824 COMPUTED RESULT 42894.87256481 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 37.19709905887 COMPUTED RESULT 712.5747080979 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10716.54753674 COMPUTED RESULT 42181.78203716 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3205.793187109 COMPUTED RESULT -21.33542621421 COMPUTED RESULT -3200.702302816 COMPUTED RESULT 16.24454192073 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7i-dss-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) *** PASSED *** Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) *** PASSED *** Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) *** PASSED *** Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 6.757093 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermediate energies in input file 1d7i-dss-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933668] EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01'] COMPUTED RESULT 9160.578033846 COMPUTED RESULT 39557.01871716 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 94.31133325426 COMPUTED RESULT 1677.348113184 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9040.108332204 COMPUTED RESULT 37877.47796627 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -3460.997931137 COMPUTED RESULT -20.52167100108 COMPUTED RESULT -3454.901259473 COMPUTED RESULT 14.42499933668 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) *** PASSED *** Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) *** PASSED *** Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) *** PASSED *** Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 6.294259 seconds -------------------------------------------------------------------------------- Total elapsed time: 25.961499 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file 1d7i-dss-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742844] EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01'] COMPUTED RESULT 9634.884642408 COMPUTED RESULT 40031.77540425 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 79.42232645345 COMPUTED RESULT 1677.798535473 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9507.068451372 COMPUTED RESULT 38350.75772299 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -2986.24124404 COMPUTED RESULT -20.07124871262 COMPUTED RESULT -2981.621502756 COMPUTED RESULT 15.45150742844 Running tests for hca-bind section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) *** PASSED *** Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) *** PASSED *** Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) *** PASSED *** Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) *** PASSED *** Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) *** PASSED *** Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) *** PASSED *** Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) *** PASSED *** Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) *** PASSED *** Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) *** PASSED *** Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 5.764227 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01'] COMPUTED RESULT 221.3600726771 COMPUTED RESULT 1825.764811255 COMPUTED RESULT 6458.471211905 COMPUTED RESULT 20936.06095527 COMPUTED RESULT 151543.3544464 COMPUTED RESULT 178636.9323561 COMPUTED RESULT 21053.22784838 COMPUTED RESULT 153330.4996252 COMPUTED RESULT 185042.9388099 COMPUTED RESULT -52.46475812665 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) *** PASSED *** Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) *** PASSED *** Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) *** PASSED *** Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) *** PASSED *** Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) *** PASSED *** Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) *** PASSED *** Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) *** PASSED *** Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) *** PASSED *** Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) *** PASSED *** Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 5.675447 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.439674 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01'] COMPUTED RESULT 188.4888131017 COMPUTED RESULT 1820.045922544 COMPUTED RESULT 6460.002606908 COMPUTED RESULT 21891.61497021 COMPUTED RESULT 152000.0494925 COMPUTED RESULT 179043.619158 COMPUTED RESULT 21958.42512312 COMPUTED RESULT 153777.1604355 COMPUTED RESULT 185449.5619747 COMPUTED RESULT -54.05979017066 Running tests for ionize section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) *** PASSED *** Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) *** PASSED *** Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) *** PASSED *** Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) *** PASSED *** Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) *** PASSED *** Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) *** PASSED *** Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) *** PASSED *** Elapsed time: 1.390626 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398] EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02'] COMPUTED RESULT 5823.898055191 COMPUTED RESULT 9793.274462353 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8219.846763777 COMPUTED RESULT 13927.41988698 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3862.359524598 COMPUTED RESULT 6288.15625161 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.67882018629 COMPUTED RESULT -199.7462636633 COMPUTED RESULT -297.4598403628 COMPUTED RESULT -474.5272838398 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) *** PASSED *** Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) *** PASSED *** Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) *** PASSED *** Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) *** PASSED *** Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) *** PASSED *** Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) *** PASSED *** Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 1.310139 seconds -------------------------------------------------------------------------------- Total elapsed time: 2.700765 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828] EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02'] COMPUTED RESULT 5824.172730822 COMPUTED RESULT 9793.622759239 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8221.328580569 COMPUTED RESULT 13928.67783119 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3863.066835285 COMPUTED RESULT 6289.649216644 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.33052329981 COMPUTED RESULT -198.4883194538 COMPUTED RESULT -295.9668753288 COMPUTED RESULT -472.1246714828 Running tests for ion-pmf section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'ion-pmf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.130e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.767e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) *** PASSED *** Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) *** PASSED *** Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) *** PASSED *** Elapsed time: 5.444832 seconds -------------------------------------------------------------------------------- Total elapsed time: 5.444832 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65308087297 Running tests for pka-lig section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) *** PASSED *** Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) *** PASSED *** Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) *** PASSED *** Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) *** PASSED *** Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) *** PASSED *** Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) *** PASSED *** Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 7.432215 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermediate energies in input file apbs-mol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] COMPUTED RESULT 2224.988750664 COMPUTED RESULT 10496.95084686 COMPUTED RESULT 181845.0789522 COMPUTED RESULT 300825.4338259 COMPUTED RESULT 184091.8409896 COMPUTED RESULT 311330.4681884 COMPUTED RESULT 8.08351564873 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) *** PASSED *** Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) *** PASSED *** Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) *** PASSED *** Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) *** PASSED *** Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) *** PASSED *** Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) *** PASSED *** Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 6.865508 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermediate energies in input file apbs-smol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] COMPUTED RESULT 2226.793167046 COMPUTED RESULT 10505.04485887 COMPUTED RESULT 182797.6621645 COMPUTED RESULT 301722.8546773 COMPUTED RESULT 185081.9075387 COMPUTED RESULT 312248.8625388 COMPUTED RESULT 20.96300255723 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) *** PASSED *** Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) *** PASSED *** Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) *** PASSED *** Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) *** PASSED *** Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) *** PASSED *** Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) *** PASSED *** Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 6.594987 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in Checking for intermediate energies in input file apbs-mol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] COMPUTED RESULT 2244.350164274 COMPUTED RESULT 10521.49475373 COMPUTED RESULT 186261.5690066 COMPUTED RESULT 305181.0884053 COMPUTED RESULT 188662.5455219 COMPUTED RESULT 315821.8439277 COMPUTED RESULT 119.2607686581 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) *** PASSED *** Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) *** PASSED *** Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) *** PASSED *** Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) *** PASSED *** Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) *** PASSED *** Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) *** PASSED *** Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 6.219421 seconds -------------------------------------------------------------------------------- Total elapsed time: 27.112131 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermediate energies in input file apbs-smol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] COMPUTED RESULT 2251.46678942 COMPUTED RESULT 10528.14502873 COMPUTED RESULT 186407.1689626 COMPUTED RESULT 305331.9953673 COMPUTED RESULT 188802.7142979 COMPUTED RESULT 315969.0177241 COMPUTED RESULT 108.8773280806 Running tests for point-pmf section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) *** PASSED *** Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) *** PASSED *** Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) *** PASSED *** Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) *** PASSED *** Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) *** PASSED *** Elapsed time: 0.269774 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermediate energies in input file complex-0_1.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027] EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 89.75920687031 COMPUTED RESULT 205.8277719334 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 89.7592 COMPUTED RESULT 205.828 COMPUTED RESULT 96.5336 COMPUTED RESULT 88.6151 COMPUTED RESULT 201.106 COMPUTED RESULT 18.30820799027 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) *** PASSED *** Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) *** PASSED *** Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 0.280582 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermediate energies in input file complex-0_2.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.90669408675] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 208.4282010393 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 208.428 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.656 COMPUTED RESULT 203.83 COMPUTED RESULT 8.90669408675 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) *** PASSED *** Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) *** PASSED *** Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) *** PASSED *** Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) *** PASSED *** Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) *** PASSED *** Elapsed time: 0.314013 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermediate energies in input file complex-0_3.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984] EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 133.7661883222 COMPUTED RESULT 237.436145212 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 133.766 COMPUTED RESULT 237.436 COMPUTED RESULT 96.5336 COMPUTED RESULT 132.672 COMPUTED RESULT 232.924 COMPUTED RESULT 5.909599816984 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_4.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) *** PASSED *** Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) *** PASSED *** Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) *** PASSED *** Elapsed time: 0.287179 seconds -------------------------------------------------------------------------------- Total elapsed time: 1.151548 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file complex-0_4.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 203.9516519 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 203.952 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.654 COMPUTED RESULT 199.493 COMPUTED RESULT 4.430144947418 Running tests for solv section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) *** PASSED *** Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) *** PASSED *** Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) *** PASSED *** Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) *** PASSED *** Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) *** PASSED *** Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) *** PASSED *** Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) *** PASSED *** Elapsed time: 0.409208 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] COMPUTED RESULT 1847.663548071 COMPUTED RESULT 1883.912182952 COMPUTED RESULT 2732.623683321 COMPUTED RESULT 3123.035854133 COMPUTED RESULT -36.24863488074 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) *** PASSED *** Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) *** PASSED *** Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) *** PASSED *** Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) *** PASSED *** Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) *** PASSED *** Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) *** PASSED *** Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) *** PASSED *** Elapsed time: 0.431226 seconds -------------------------------------------------------------------------------- Total elapsed time: 0.840434 seconds Test results have been logged -------------------------------------------------------------------------------- Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] COMPUTED RESULT 1847.86044002 COMPUTED RESULT 1885.436377745 COMPUTED RESULT 2734.040568569 COMPUTED RESULT 3125.279428954 COMPUTED RESULT -37.57593772493 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/<>' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_sphinxdoc -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_python3 -O--buildsystem=cmake I: dh_python3 fs:431: renaming _apbslib.so to _apbslib.cpython-312-x86_64-linux-gnu.so dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms-indep make[1]: Entering directory '/<>' dh_fixperms for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \ ion-pmf/runme.sh \ point-pmf/runme.sh \ protein-rna/postprocess.sh \ protein-rna/test.sh \ helix/Run_membrane-helix.sh \ protein-rna/run_apdx_files.sh; \ do \ chmod +x debian/apbs-data/usr/share/apbs/examples/${example}; \ done for script in amber2charmm.sh \ param/pdb2pqr/amber2uhbd.sh \ qcd2pqr.awk; \ do \ chmod a+x debian/apbs-data/usr/share/apbs/tools/conversion/${script}; \ done for example in bem-pKa/test_proteins \ pbsam-barn_bars; \ do \ chmod a-x debian/apbs-data/usr/share/apbs/examples/${example}/*.pqr; \ done make[1]: Leaving directory '/<>' dh_fixperms -O--buildsystem=cmake -Napbs-data -Napbs-doc dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 441486 new size 445918 dwz: debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 93098 new size 93735 dwz: debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 989135 new size 991383 dh_strip -a -O--buildsystem=cmake debugedit: debian/apbs/usr/bin/apbs: Unknown DWARF DW_FORM_0x1f20 278178369ea07ef9d6c102da38e8cee1cc8fa38c debugedit: debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3: Unknown DWARF DW_FORM_0x1f20 93bfb0384bef43a3227f64f8391486239fea09fc debugedit: debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_fem.so.3: Unknown DWARF DW_FORM_0x1f21 a49400fe318e45db914f74e67367d8de4523f636 debugedit: debian/apbs/usr/lib/apbs/tools/bin/born: Unknown DWARF DW_FORM_0x1f20 4e8bef8be1702d8f14aaa39009adea04ca427a50 debugedit: debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_routines.so.3: Unknown DWARF DW_FORM_0x1f20 36888c6c21fd35f8acaac3da70b047a9cf256340 debugedit: debian/apbs/usr/lib/apbs/tools/bin/similarity: Unknown DWARF DW_FORM_0x1f20 3a4f4e8a3c62d96ecf2300740bb2d9cd1672ef69 999dd56a647fef4a4c057051a1adaa7edb368338 debugedit: debian/apbs/usr/lib/apbs/tools/bin/dxmath: Unknown DWARF DW_FORM_0x1f21 d28504f42a983c0ea0fdb4a7f9af116e44c3d270 debugedit: debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_mg.so.3: Unknown DWARF DW_FORM_0x1f20 a33c1ea5fc1bcbc165ab32b0679102ae7f9422bc debugedit: debian/apbs/usr/lib/apbs/tools/bin/dx2mol: Unknown DWARF DW_FORM_0x1f20 5b16379417f665935b088f18d884a2f009b2c846 debugedit: debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_generic.so.3: Unknown DWARF DW_FORM_0x1f20 652dc1ee043c43b37a39e72c6c412fe56386609c debugedit: debian/apbs/usr/lib/apbs/tools/bin/coulomb: Unknown DWARF DW_FORM_0x1f20 57dd2689280c64d8357414d502c6e4386b37f58c debugedit: debian/apbs/usr/lib/apbs/tools/bin/tensor2dx: Unknown DWARF DW_FORM_0x1f20 bdc9bf995c8a826495fdb34540e229b355d0484e debugedit: debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3: Unknown DWARF DW_FORM_0x1f21 debugedit: debian/apbs/usr/lib/apbs/tools/bin/mergedx: Unknown DWARF DW_FORM_0x1f20 ccfa23cedad69283d6d01bb05dcd58923a422cc4 b2e7b9e9d0934c34d1680cd02c9c1cdfc1a2a9ca debugedit: debian/apbs/usr/lib/apbs/tools/bin/mgmesh: Unknown DWARF DW_FORM_0x1f20 902d6ec8300ab0a32c23ed31403c18674d59f7b9 debugedit: debian/apbs/usr/lib/apbs/tools/bin/multivalue: Unknown DWARF DW_FORM_0x1f20 68d8db99c8d5721292acfed6b66fa0ab2ebdd571 debugedit: debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin: Unknown DWARF DW_FORM_0x1f20 30362d638a0cfe347a7c36b1208da87cf1dc51ce debugedit: debian/apbs/usr/lib/apbs/tools/bin/smooth: Unknown DWARF DW_FORM_0x1f20 0622c61ce7d700340f1e266c01ea3038c5b70c8a debugedit: debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd: Unknown DWARF DW_FORM_0x1f20 d9703855a026a93f8a440dce8eefdf1c1d9cfd70 5e52ba5a878d1dc670d4b85aa811a903f9ac0e7c debugedit: debian/apbs/usr/lib/apbs/tools/bin/del2dx: Unknown DWARF DW_FORM_0x1f20 a7f33a87ff86abe98e2b682316e04ef41d22300f debugedit: debian/apbs/usr/lib/apbs/tools/bin/benchmark: Unknown DWARF DW_FORM_0x1f20 f008927baafda746345032133ac87d991cbada34 debugedit: debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libpunc.so.1.9.3: Unknown DWARF DW_FORM_0x1f21 12e2f4fec8bf6135b5666162df42c20e1555c997 debugedit: debian/apbs/usr/lib/apbs/tools/bin/analysis: Unknown DWARF DW_FORM_0x1f20 c0b1986364502dcb41508846cf23439aec58b7f4 d16414b61f1807023b4bdfb2d6331cbcdd43a70a debugedit: debian/apbs/usr/lib/apbs/tools/bin/mergedx2: Unknown DWARF DW_FORM_0x1f20 b114181e7039e884a7f165a49c87f3a366216d77 debugedit: debian/apbs/usr/lib/apbs/tools/bin/value: Unknown DWARF DW_FORM_0x1f20 59e8ff1f913014cf168fd62e3bf1831e5d463dea debugedit: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-312-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 6fdd736c3dc83f69c2a381f81b2d20e554720385 debugedit: debian/python3-apbslib/usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-312-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 0c9ec84e47c8b2b2abbe6f955e4898385d702898 dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol snrm2_ used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_di used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol daxpy_ used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol e_wsfe used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol s_stop used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dnrm2_ used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol saxpy_ used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol asin used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan2 used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tanh used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erf used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sincos used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sin used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol exp used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tan used by debian/libfetk1.9/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libarpack.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libgomp.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libsuitesparseconfig.so.7 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libspqr.so.4 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcgcode.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libvf2c.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libumfpack.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libccolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libapbs_fem.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libpunc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcholmod.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libcamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libmc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libsuperlu.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/born were not linked against libmpi.so.40 (they use none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libfetk-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package apbs-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-apbslib-dbgsym (in debian/.debhelper/python3-apbslib/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libfetk-dev (in debian/libfetk-dev); do_strip: , oemstrip: pkgstriptranslations: processing apbs (in debian/apbs); do_strip: , oemstrip: pkgstriptranslations: processing libapbs3-dbgsym (in debian/.debhelper/libapbs3/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libfetk-dev/DEBIAN/control, package libfetk-dev, directory debian/libfetk-dev INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgstripfiles: processing control file: debian/.debhelper/python3-apbslib/dbgsym-root/DEBIAN/control, package python3-apbslib-dbgsym, directory debian/.debhelper/python3-apbslib/dbgsym-root dpkg-deb: building package 'python3-apbslib-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-apbslib/python3-apbslib-dbgsym_3.4.1-5build5_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/libapbs3/dbgsym-root/DEBIAN/control, package libapbs3-dbgsym, directory debian/.debhelper/libapbs3/dbgsym-root dpkg-deb: building package 'libapbs3-dbgsym' in 'debian/.debhelper/scratch-space/build-libapbs3/libapbs3-dbgsym_3.4.1-5build5_amd64.deb'. pkgstripfiles: processing control file: debian/apbs/DEBIAN/control, package apbs, directory debian/apbs .. removing usr/share/doc/apbs/ChangeLog.md Skipping arch: any to arch: all dependency to apbs-data Searching for duplicated docs in dependency libapbs3... symlinking changelog.Debian.gz in apbs to file in libapbs3 Searching for duplicated docs in dependency libfetk1.9... pkgstripfiles: Running PNG optimization (using 4 cpus) for package apbs ... pkgstripfiles: No PNG files. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-5build5_amd64.deb'. Renaming libapbs3-dbgsym_3.4.1-5build5_amd64.deb to libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb Renaming python3-apbslib-dbgsym_3.4.1-5build5_amd64.deb to python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing apbs-data (in debian/apbs-data); do_strip: , oemstrip: INFO: pkgstriptranslations version 154 pkgstriptranslations: processing apbs-dbgsym (in debian/.debhelper/apbs/dbgsym-root); do_strip: , oemstrip: INFO: pkgstriptranslations version 154 pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstriptranslations: processing libapbs-dev (in debian/libapbs-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/apbs-data/DEBIAN/control, package apbs-data, directory debian/apbs-data INFO: pkgstripfiles: waiting for lock (apbs-data) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgstripfiles: processing control file: debian/.debhelper/apbs/dbgsym-root/DEBIAN/control, package apbs-dbgsym, directory debian/.debhelper/apbs/dbgsym-root dpkg-deb: building package 'apbs-dbgsym' in 'debian/.debhelper/scratch-space/build-apbs/apbs-dbgsym_3.4.1-5build5_amd64.deb'. pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com Renaming apbs-dbgsym_3.4.1-5build5_amd64.deb to apbs-dbgsym_3.4.1-5build5_amd64.ddeb pkgstripfiles: processing control file: debian/libapbs-dev/DEBIAN/control, package libapbs-dev, directory debian/libapbs-dev .. removing usr/share/doc/libapbs-dev/ChangeLog.md INFO: pkgstripfiles: waiting for lock (libapbs-dev) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-apbslib (in debian/python3-apbslib); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/python3-apbslib/DEBIAN/control, package python3-apbslib, directory debian/python3-apbslib Searching for duplicated docs in dependency libapbs3... symlinking changelog.Debian.gz in python3-apbslib to file in libapbs3 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-apbslib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-5build5_amd64.deb'. INFO: pkgstripfiles: waiting for lock (apbs-data) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... Searching for duplicated docs in dependency libapbs3... symlinking changelog.Debian.gz in libapbs-dev to file in libapbs3 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-5build5_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libapbs3 (in debian/libapbs3); do_strip: , oemstrip: INFO: pkgstripfiles: waiting for lock (apbs-data) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libapbs3/DEBIAN/control, package libapbs3, directory debian/libapbs3 Searching for duplicated docs in dependency libfetk1.9... symlinking changelog.Debian.gz in libapbs3 to file in libfetk1.9 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs3' in '../libapbs3_3.4.1-5build5_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package apbs-data ... pkgstripfiles: No PNG files. INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-5build5_all.deb'. INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing apbs-doc (in debian/apbs-doc); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/apbs-doc/DEBIAN/control, package apbs-doc, directory debian/apbs-doc pkgstripfiles: Disabled PNG optimization for -doc package apbs-doc (to save build time) dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-5build5_all.deb'. Searching for duplicated docs in dependency libfetk1.9... symlinking changelog.Debian.gz in libfetk-dev to file in libfetk1.9 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libfetk-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-5build5_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libfetk1.9 (in debian/libfetk1.9); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libfetk1.9/DEBIAN/control, package libfetk1.9, directory debian/libfetk1.9 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libfetk1.9 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libfetk1.9' in '../libfetk1.9_3.4.1-5build5_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libfetk1.9-dbgsym (in debian/.debhelper/libfetk1.9/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/libfetk1.9/dbgsym-root/DEBIAN/control, package libfetk1.9-dbgsym, directory debian/.debhelper/libfetk1.9/dbgsym-root dpkg-deb: building package 'libfetk1.9-dbgsym' in 'debian/.debhelper/scratch-space/build-libfetk1.9/libfetk1.9-dbgsym_3.4.1-5build5_amd64.deb'. Renaming libfetk1.9-dbgsym_3.4.1-5build5_amd64.deb to libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb dpkg-genbuildinfo --build=binary -O../apbs_3.4.1-5build5_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../apbs_3.4.1-5build5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-01-19T19:05:03Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ apbs_3.4.1-5build5_amd64.changes: --------------------------------- Format: 1.8 Date: Fri, 19 Jan 2024 18:56:34 +0000 Source: apbs Binary: apbs apbs-data apbs-doc libapbs-dev libapbs3 libfetk-dev libfetk1.9 python3-apbslib Built-For-Profiles: noudeb Architecture: all amd64 Version: 3.4.1-5build5 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: apbs - Adaptive Poisson Boltzmann Solver apbs-data - data files for APBS (Adaptive Poisson Boltzmann Solver) apbs-doc - Adaptive Poisson Boltzmann Solver libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs3 - Adaptive Poisson Boltzmann Solver libfetk-dev - FETK libraries for APBS (development headers) libfetk1.9 - FETK libraries for APBS (shared libraries) python3-apbslib - Adaptive Poisson Boltzmann Solver Changes: apbs (3.4.1-5build5) noble; urgency=medium . * No-change rebuild with Python 3.12 as default Checksums-Sha1: 47f824673966613f5008bd072005e52fb892d0b4 1763012 apbs-data_3.4.1-5build5_all.deb 36a0575d16dcb361a49c8a0c720c8a26748ccdb0 110704 apbs-dbgsym_3.4.1-5build5_amd64.ddeb be775d279520d2fd130424ef7c228863ccf4a76f 5847788 apbs-doc_3.4.1-5build5_all.deb 1d661b948e457c4d555bd2c72666b7a9c176e4d2 14430 apbs_3.4.1-5build5_amd64.buildinfo 5c96675fb05c496f16fa4b5991b5a8ab9c812a27 76886 apbs_3.4.1-5build5_amd64.deb fa1c555dc421314d76428fe1db189a2085b6929d 99448 libapbs-dev_3.4.1-5build5_amd64.deb c0ee57d24cf0a177f190d6be68357c9f2589f701 595812 libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb 94647ef82177a52e32d2cafb3240d09566b7e6ff 266426 libapbs3_3.4.1-5build5_amd64.deb 92f8066a522722ceeed0b9a55c858b21f89db1d4 144488 libfetk-dev_3.4.1-5build5_amd64.deb 9554c728c849ec46bfd55f449a7cc960868b7ce9 1818362 libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb ad088d01f15bcf784d52ee58f23098e77e7d414d 598072 libfetk1.9_3.4.1-5build5_amd64.deb 8cf2e1f2cbf817c9130a094da2f9c5058d027ce0 1890498 python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb 7e187968c26024a2c20be72d65f7ee227a5522a4 211282 python3-apbslib_3.4.1-5build5_amd64.deb Checksums-Sha256: 09a2346383cccb9843b369389780fe14262086aa93ed68841a718cd6fcf77de7 1763012 apbs-data_3.4.1-5build5_all.deb 89b0d3279117fb4548f99385d1380ce437711b6843d1abc2b4580d1743f65420 110704 apbs-dbgsym_3.4.1-5build5_amd64.ddeb 6afb6b7ae22f07265c7de92075616cd7d1cacd9d1878b1444876192a8be4e3bd 5847788 apbs-doc_3.4.1-5build5_all.deb 7f7cb4d10e23e834b43620edcff3433f1bfd2076449737f7e3e72d6c62aa9469 14430 apbs_3.4.1-5build5_amd64.buildinfo 88a3e4372766f5f48e1403ca0a342ccebff83e64c38926e130aedc640bbd0f7d 76886 apbs_3.4.1-5build5_amd64.deb 15cdb20e0b4a29acb941b21fe0273031c3b477d624842cd85ba09e7285323e3c 99448 libapbs-dev_3.4.1-5build5_amd64.deb 9162a264aaa9c6dd27e8d6730f05337cdb02ff4b2116ff6377d2fca06d5d41e5 595812 libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb 0309d18bc4b4621f86dd574a13d8b8d59d0e8c7e04b20e7f2da7f86984987ca1 266426 libapbs3_3.4.1-5build5_amd64.deb bd45e7603c1896f20c881ce1644ab4ea4dae40102a467297a05a7e5216b65947 144488 libfetk-dev_3.4.1-5build5_amd64.deb b6785b279b2fb29bc3d67651ac64f1d71fdad89be3b273abf91b9f18c09c123e 1818362 libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb e1cc63dc1bddaeb9a62fea677928875770312a0d2c16c5796bb7805049ce72cb 598072 libfetk1.9_3.4.1-5build5_amd64.deb f1178ddade7cb0529b59c49f69fdcbe052ff5fd5e76da87abbe5f6a99d1dc448 1890498 python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb 58a2895d5e267064934f05069ab033deb251038f6f49a29aa68b461145b44f9a 211282 python3-apbslib_3.4.1-5build5_amd64.deb Files: f2615f0b7bb5f217f56c08e401b5a191 1763012 science optional apbs-data_3.4.1-5build5_all.deb 5aabfd6ba2c5df42fa63a42d080902af 110704 debug optional apbs-dbgsym_3.4.1-5build5_amd64.ddeb 6e0f869c63f23f21bd658ab9760f2e4e 5847788 science optional apbs-doc_3.4.1-5build5_all.deb 5359d7ab3c448ff004f48e8828a51b04 14430 science optional apbs_3.4.1-5build5_amd64.buildinfo a1ecc57862d7930dc44f72f0b76ca49f 76886 science optional apbs_3.4.1-5build5_amd64.deb d585b5eaf223aa5f0a161c70d93a3e1e 99448 libdevel optional libapbs-dev_3.4.1-5build5_amd64.deb cc2bb75a1d0473132bd722b2f274ec3c 595812 debug optional libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb c333ccf17059db8c2a68bb0825526b6a 266426 libs optional libapbs3_3.4.1-5build5_amd64.deb bcb2ac329d52a31b7e4eea383adadf77 144488 libdevel optional libfetk-dev_3.4.1-5build5_amd64.deb 565da9825deb7a8ae23c3500476ec878 1818362 debug optional libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb 33c89b42de2f20e490de87701933d8e1 598072 libs optional libfetk1.9_3.4.1-5build5_amd64.deb e8bfdea8ead1241b6b195d28c1df2615 1890498 debug optional python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb bfecd1489f432235cc1d2e5d4da261ed 211282 python optional python3-apbslib_3.4.1-5build5_amd64.deb Original-Maintainer: Debichem Team /<>/apbs_3.4.1-5build5_amd64.changes.new could not be renamed to /<>/apbs_3.4.1-5build5_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: apbs Binary: apbs apbs-data apbs-dbgsym apbs-doc libapbs-dev libapbs3 libapbs3-dbgsym libfetk-dev libfetk1.9 libfetk1.9-dbgsym python3-apbslib python3-apbslib-dbgsym Architecture: all amd64 Version: 3.4.1-5build5 Checksums-Md5: f2615f0b7bb5f217f56c08e401b5a191 1763012 apbs-data_3.4.1-5build5_all.deb 5aabfd6ba2c5df42fa63a42d080902af 110704 apbs-dbgsym_3.4.1-5build5_amd64.ddeb 6e0f869c63f23f21bd658ab9760f2e4e 5847788 apbs-doc_3.4.1-5build5_all.deb a1ecc57862d7930dc44f72f0b76ca49f 76886 apbs_3.4.1-5build5_amd64.deb d585b5eaf223aa5f0a161c70d93a3e1e 99448 libapbs-dev_3.4.1-5build5_amd64.deb cc2bb75a1d0473132bd722b2f274ec3c 595812 libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb c333ccf17059db8c2a68bb0825526b6a 266426 libapbs3_3.4.1-5build5_amd64.deb bcb2ac329d52a31b7e4eea383adadf77 144488 libfetk-dev_3.4.1-5build5_amd64.deb 565da9825deb7a8ae23c3500476ec878 1818362 libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb 33c89b42de2f20e490de87701933d8e1 598072 libfetk1.9_3.4.1-5build5_amd64.deb e8bfdea8ead1241b6b195d28c1df2615 1890498 python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb bfecd1489f432235cc1d2e5d4da261ed 211282 python3-apbslib_3.4.1-5build5_amd64.deb Checksums-Sha1: 47f824673966613f5008bd072005e52fb892d0b4 1763012 apbs-data_3.4.1-5build5_all.deb 36a0575d16dcb361a49c8a0c720c8a26748ccdb0 110704 apbs-dbgsym_3.4.1-5build5_amd64.ddeb be775d279520d2fd130424ef7c228863ccf4a76f 5847788 apbs-doc_3.4.1-5build5_all.deb 5c96675fb05c496f16fa4b5991b5a8ab9c812a27 76886 apbs_3.4.1-5build5_amd64.deb fa1c555dc421314d76428fe1db189a2085b6929d 99448 libapbs-dev_3.4.1-5build5_amd64.deb c0ee57d24cf0a177f190d6be68357c9f2589f701 595812 libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb 94647ef82177a52e32d2cafb3240d09566b7e6ff 266426 libapbs3_3.4.1-5build5_amd64.deb 92f8066a522722ceeed0b9a55c858b21f89db1d4 144488 libfetk-dev_3.4.1-5build5_amd64.deb 9554c728c849ec46bfd55f449a7cc960868b7ce9 1818362 libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb ad088d01f15bcf784d52ee58f23098e77e7d414d 598072 libfetk1.9_3.4.1-5build5_amd64.deb 8cf2e1f2cbf817c9130a094da2f9c5058d027ce0 1890498 python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb 7e187968c26024a2c20be72d65f7ee227a5522a4 211282 python3-apbslib_3.4.1-5build5_amd64.deb Checksums-Sha256: 09a2346383cccb9843b369389780fe14262086aa93ed68841a718cd6fcf77de7 1763012 apbs-data_3.4.1-5build5_all.deb 89b0d3279117fb4548f99385d1380ce437711b6843d1abc2b4580d1743f65420 110704 apbs-dbgsym_3.4.1-5build5_amd64.ddeb 6afb6b7ae22f07265c7de92075616cd7d1cacd9d1878b1444876192a8be4e3bd 5847788 apbs-doc_3.4.1-5build5_all.deb 88a3e4372766f5f48e1403ca0a342ccebff83e64c38926e130aedc640bbd0f7d 76886 apbs_3.4.1-5build5_amd64.deb 15cdb20e0b4a29acb941b21fe0273031c3b477d624842cd85ba09e7285323e3c 99448 libapbs-dev_3.4.1-5build5_amd64.deb 9162a264aaa9c6dd27e8d6730f05337cdb02ff4b2116ff6377d2fca06d5d41e5 595812 libapbs3-dbgsym_3.4.1-5build5_amd64.ddeb 0309d18bc4b4621f86dd574a13d8b8d59d0e8c7e04b20e7f2da7f86984987ca1 266426 libapbs3_3.4.1-5build5_amd64.deb bd45e7603c1896f20c881ce1644ab4ea4dae40102a467297a05a7e5216b65947 144488 libfetk-dev_3.4.1-5build5_amd64.deb b6785b279b2fb29bc3d67651ac64f1d71fdad89be3b273abf91b9f18c09c123e 1818362 libfetk1.9-dbgsym_3.4.1-5build5_amd64.ddeb e1cc63dc1bddaeb9a62fea677928875770312a0d2c16c5796bb7805049ce72cb 598072 libfetk1.9_3.4.1-5build5_amd64.deb f1178ddade7cb0529b59c49f69fdcbe052ff5fd5e76da87abbe5f6a99d1dc448 1890498 python3-apbslib-dbgsym_3.4.1-5build5_amd64.ddeb 58a2895d5e267064934f05069ab033deb251038f6f49a29aa68b461145b44f9a 211282 python3-apbslib_3.4.1-5build5_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Fri, 19 Jan 2024 19:05:03 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137ubuntu1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.41.90.20240115-1ubuntu1), binutils-common (= 2.41.90.20240115-1ubuntu1), binutils-x86-64-linux-gnu (= 2.41.90.20240115-1ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), ca-certificates (= 20230311ubuntu1), cmake (= 3.28.1-1), cmake-data (= 3.28.1-1), coreutils (= 9.4-2ubuntu2), cpp (= 4:13.2.0-2ubuntu1), cpp-13 (= 13.2.0-10ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.83), debhelper (= 13.11.9ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20231223), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), docutils-common (= 0.20.1+dfsg-3), dpkg (= 1.22.2ubuntu2), dpkg-dev (= 1.22.2ubuntu2), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), fonts-font-awesome (= 5.0.10+really4.7.0~dfsg-4.1), fonts-lato (= 2.015-1), fonts-mathjax (= 2.7.9+dfsg-1), g++ (= 4:13.2.0-2ubuntu1), g++-13 (= 13.2.0-10ubuntu1), gcc (= 4:13.2.0-2ubuntu1), gcc-13 (= 13.2.0-10ubuntu1), gcc-13-base (= 13.2.0-10ubuntu1), gettext (= 0.21-14), gettext-base (= 0.21-14), gfortran-13 (= 13.2.0-10ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), ibverbs-providers (= 48.0-1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-4ubuntu1), libamd3 (= 1:7.5.1+dfsg-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.7.2-1ubuntu2), libarpack2 (= 3.9.1-1), libarpack2-dev (= 3.9.1-1), libasan8 (= 13.2.0-10ubuntu1), libatomic1 (= 13.2.0-10ubuntu1), libattr1 (= 1:2.5.1-5), libaudit-common (= 1:3.1.2-1), libaudit1 (= 1:3.1.2-1), libbinutils (= 2.41.90.20240115-1ubuntu1), libblas-dev (= 3.11.0-2build1), libblas3 (= 3.11.0-2build1), libblkid1 (= 2.39.2-6ubuntu1), libbrotli1 (= 1.1.0-2), libbsd0 (= 0.11.8-1), libbtf2 (= 1:7.5.1+dfsg-1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcamd3 (= 1:7.5.1+dfsg-1), libcap-ng0 (= 0.8.4-1), libcap2 (= 1:2.66-4ubuntu1), libcbor0.10 (= 0.10.2-1.1ubuntu1), libcc1-0 (= 13.2.0-10ubuntu1), libccolamd3 (= 1:7.5.1+dfsg-1), libcholmod5 (= 1:7.5.1+dfsg-1), libcolamd3 (= 1:7.5.1+dfsg-1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.41.90.20240115-1ubuntu1), libctf0 (= 2.41.90.20240115-1ubuntu1), libcurl4 (= 8.5.0-2ubuntu1), libcxsparse4 (= 1:7.5.1+dfsg-1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.11.9ubuntu1), libdpkg-perl (= 1.22.2ubuntu2), libdw1 (= 0.190-1), libedit2 (= 3.1-20230828-1), libelf1 (= 0.190-1), libevent-2.1-7 (= 2.1.12-stable-9), libevent-core-2.1-7 (= 2.1.12-stable-9), libevent-dev (= 2.1.12-stable-9), libevent-extra-2.1-7 (= 2.1.12-stable-9), libevent-openssl-2.1-7 (= 2.1.12-stable-9), libevent-pthreads-2.1-7 (= 2.1.12-stable-9), libexpat1 (= 2.5.0-2), libexpat1-dev (= 2.5.0-2), libfabric1 (= 1.17.0-3), libffi8 (= 3.4.4-2), libfido2-1 (= 1.14.0-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-10ubuntu1), libgcc-s1 (= 13.2.0-10ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran-13-dev (= 13.2.0-10ubuntu1), libgfortran5 (= 13.2.0-10ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu7), libgomp1 (= 13.2.0-10ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.41.90.20240115-1ubuntu1), libgssapi-krb5-2 (= 1.20.1-5build1), libhogweed6 (= 3.9.1-2), libhwasan0 (= 13.2.0-10ubuntu1), libhwloc-dev (= 2.10.0-1), libhwloc-plugins (= 2.10.0-1), libhwloc15 (= 2.10.0-1), libibverbs-dev (= 48.0-1), libibverbs1 (= 48.0-1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.4-1build1), libisl23 (= 0.26-3), libitm1 (= 13.2.0-10ubuntu1), libjansson4 (= 2.14-2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-mathjax (= 2.7.9+dfsg-1), libjs-sphinxdoc (= 7.2.6-3), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libklu2 (= 1:7.5.1+dfsg-1), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack-dev (= 3.11.0-2build1), liblapack3 (= 3.11.0-2build1), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu2), libldl3 (= 1:7.5.1+dfsg-1), liblsan0 (= 13.2.0-10ubuntu1), libltdl-dev (= 2.4.7-7), libltdl7 (= 2.4.7-7), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmaloc-dev (= 1.5-1), libmaloc1 (= 1.5-1), libmd0 (= 1.1.0-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libmunge2 (= 0.5.15-3ubuntu1), libncursesw6 (= 6.4+20240113-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.58.0-1), libnl-3-200 (= 3.7.0-0.3), libnl-3-dev (= 3.7.0-0.3), libnl-route-3-200 (= 3.7.0-0.3), libnl-route-3-dev (= 3.7.0-0.3), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnuma-dev (= 2.0.16-1), libnuma1 (= 2.0.16-1), libopenmpi-dev (= 4.1.6-5ubuntu1), libopenmpi3 (= 4.1.6-5ubuntu1), libp11-kit0 (= 0.25.3-2ubuntu2), libpam-modules (= 1.5.2-9.1ubuntu2), libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libparu0 (= 1:7.5.1+dfsg-1), libpciaccess0 (= 0.17-3), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.1-2), libpmix-dev (= 5.0.1-4), libpmix2 (= 5.0.1-4), libproc2-0 (= 2:4.0.4-2ubuntu1), libpsl5 (= 0.21.2-1build1), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2), libpython3-dev (= 3.12.1-0ubuntu1), libpython3-stdlib (= 3.12.1-0ubuntu1), libpython3.12 (= 3.12.1-2), libpython3.12-dev (= 3.12.1-2), libpython3.12-minimal (= 3.12.1-2), libpython3.12-stdlib (= 3.12.1-2), libquadmath0 (= 13.2.0-10ubuntu1), librbio4 (= 1:7.5.1+dfsg-1), librdmacm1 (= 48.0-1), libreadline8 (= 8.2-3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.4-2ubuntu1), libselinux1 (= 3.5-1build2), libsemanage-common (= 3.5-1build1), libsemanage2 (= 3.5-1build1), libsepol2 (= 3.5-2), libsframe1 (= 2.41.90.20240115-1ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libspex2 (= 1:7.5.1+dfsg-1), libspqr4 (= 1:7.5.1+dfsg-1), libsqlite3-0 (= 3.44.2-1), libssh-4 (= 0.10.6-2), libssl3 (= 3.0.10-1ubuntu3), libstdc++-13-dev (= 13.2.0-10ubuntu1), libstdc++6 (= 13.2.0-10ubuntu1), libsub-override-perl (= 0.10-1), libsuitesparse-dev (= 1:7.5.1+dfsg-1), libsuitesparse-mongoose3 (= 1:7.5.1+dfsg-1), libsuitesparseconfig7 (= 1:7.5.1+dfsg-1), libsuperlu-dev (= 6.0.1+dfsg1-1), libsuperlu6 (= 6.0.1+dfsg1-1), libsystemd0 (= 255.2-3ubuntu1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-10ubuntu1), libubsan1 (= 13.2.0-10ubuntu1), libuchardet0 (= 0.0.8-1), libucx0 (= 1.15.0-1), libudev1 (= 255.2-3ubuntu1), libumfpack6 (= 1:7.5.1+dfsg-1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libuv1 (= 1.46.0-3), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxml2 (= 2.9.14+dfsg-1.3build3), libxnvctrl0 (= 510.47.03-0ubuntu1), libyaml-0-2 (= 0.2.5-1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 45), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20231126-1), media-types (= 10.1.0), mpi-default-dev (= 1.15), ncurses-base (= 6.4+20240113-1), ncurses-bin (= 6.4+20240113-1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1), openmpi-bin (= 4.1.6-5ubuntu1), openmpi-common (= 4.1.6-5ubuntu1), openssh-client (= 1:9.4p1-1ubuntu2), openssl (= 3.0.10-1ubuntu3), passwd (= 1:4.13+dfsg1-3ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-2ubuntu1), pybind11-dev (= 2.11.1-2), pybuild-plugin-pyproject (= 6.20231223), python-babel-localedata (= 2.10.3-3build1), python3 (= 3.12.1-0ubuntu1), python3-alabaster (= 0.7.12-1), python3-babel (= 2.10.3-3build1), python3-build (= 0.10.0-1), python3-certifi (= 2023.11.17-1), python3-chardet (= 5.2.0+dfsg-1), python3-dev (= 3.12.1-0ubuntu1), python3-distutils (= 3.11.5-1), python3-docutils (= 0.20.1+dfsg-3), python3-idna (= 3.3-2), python3-imagesize (= 1.4.1-1), python3-installer (= 0.7.0+dfsg1-2), python3-jinja2 (= 3.1.2-1), python3-lib2to3 (= 3.11.5-1), python3-markupsafe (= 2.1.3-1build1), python3-minimal (= 3.12.1-0ubuntu1), python3-packaging (= 23.2-1), python3-pkg-resources (= 68.1.2-2), python3-pybind11 (= 2.11.1-2), python3-pygments (= 2.15.1+dfsg-1), python3-pyproject-hooks (= 1.0.0-2), python3-requests (= 2.31.0+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-setuptools (= 68.1.2-2), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 7.2.6-3), python3-sphinx-rtd-theme (= 2.0.0+dfsg-1), python3-sphinxcontrib.jquery (= 4.1-5), python3-toml (= 0.10.2-1), python3-tz (= 2023.3.post1-2), python3-urllib3 (= 2.0.7-1), python3-wheel (= 0.42.0-1), python3-yaml (= 6.0.1-2), python3.12 (= 3.12.1-2), python3.12-dev (= 3.12.1-2), python3.12-minimal (= 3.12.1-2), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.20), sgml-base (= 1.31), sphinx-common (= 7.2.6-3), sphinx-rtd-theme-common (= 2.0.0+dfsg-1), swig (= 4.1.0-0.3), swig4.0 (= 4.1.0-0.3), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.35+dfsg-3), tzdata (= 2023d-1ubuntu2), util-linux (= 2.39.2-6ubuntu1), xml-core (= 0.19), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1705690594" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ apbs-data_3.4.1-5build5_all.deb ------------------------------- new Debian package, version 2.0. size 1763012 bytes: control archive=8449 bytes. 783 bytes, 20 lines control 25574 bytes, 312 lines md5sums Package: apbs-data Source: apbs Version: 3.4.1-5build5 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 15880 Breaks: apbs (<= 1.4-2) Section: science Priority: optional Multi-Arch: foreign Homepage: http://www.poissonboltzmann.org/ Description: data files for APBS (Adaptive Poisson Boltzmann Solver) APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains all data files for apbs package to reduce the redundancy between architectures in Debian. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/FKBP/ -rw-r--r-- root/root 118791 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -rw-r--r-- root/root 5249 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -rw-r--r-- root/root 5262 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/FKBP/1d7h-dmso/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/ -rw-r--r-- root/root 103106 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -rw-r--r-- root/root 13309 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -rw-r--r-- root/root 183314 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -rw-r--r-- root/root 183314 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -rw-r--r-- root/root 628 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -rwxr-xr-x root/root 181 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -rw-r--r-- root/root 118073 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-min.pqr -rw-r--r-- root/root 119067 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -rw-r--r-- root/root 5236 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -rw-r--r-- root/root 5248 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss-smol.in drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/FKBP/1d7i-dss/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/ -rw-r--r-- root/root 103106 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -rw-r--r-- root/root 13305 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -rw-r--r-- root/root 183310 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -rw-r--r-- root/root 868 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -rw-r--r-- root/root 118073 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-min.pqr -rw-r--r-- root/root 4384 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/README.md -rw-r--r-- root/root 718 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/dmso-min.pqr -rw-r--r-- root/root 994 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/dss-min.pqr -rw-r--r-- root/root 4276 2022-04-29 18:53 ./usr/share/apbs/examples/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/actin-dimer/ -rw-r--r-- root/root 5879 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/actin-dimer/UHBD/ -rw-r--r-- root/root 27551 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -rw-r--r-- root/root 24783 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -rw-r--r-- root/root 2156 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -rw-r--r-- root/root 393759 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb -rw-r--r-- root/root 393759 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb -rw-r--r-- root/root 920 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/single.inp -rw-r--r-- root/root 1971182 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot -rw-r--r-- root/root 1639 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -rw-r--r-- root/root 1738 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -rw-r--r-- root/root 1740 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -rw-r--r-- root/root 799272 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/complex.pqr -rw-r--r-- root/root 1808 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/mesh.m -rw-r--r-- root/root 399636 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/mol1.pqr -rw-r--r-- root/root 399636 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/mol2.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/alkanes/ -rw-r--r-- root/root 1221 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/2-methylbutane.pdb -rw-r--r-- root/root 12664 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/README.md -rw-r--r-- root/root 2976 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/alkanes.in -rw-r--r-- root/root 285 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/apbs-forces.in -rw-r--r-- root/root 1019 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/butane.pdb -rw-r--r-- root/root 1249 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/cyclohexane.pdb -rw-r--r-- root/root 894 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/cyclopentane.pdb -rw-r--r-- root/root 553 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/ethane.pdb -rw-r--r-- root/root 5233 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/force.result -rw-r--r-- root/root 1340 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/hexane.pdb -rw-r--r-- root/root 1007 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/isobutane.pdb -rw-r--r-- root/root 355 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/methane.pdb -rw-r--r-- root/root 781 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/mol.pdb -rw-r--r-- root/root 1208 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/neopentane.pdb -rw-r--r-- root/root 620 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/parm.dat -rw-r--r-- root/root 1143 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/pentane.pdb -rw-r--r-- root/root 781 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/propane.pdb drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/bem-binding-energy/ -rw-r--r-- root/root 879 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/1d30.in -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -rw-r--r-- root/root 889 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -rw-r--r-- root/root 1024 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/ -rw-r--r-- root/root 43640 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr -rw-r--r-- root/root 41504 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr -rw-r--r-- root/root 2137 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/bem-pKa/ -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -rw-r--r-- root/root 891 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -rw-r--r-- root/root 891 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -rw-r--r-- root/root 875 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/ASH66.in -rw-r--r-- root/root 881 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/ASP66.in -rw-r--r-- root/root 1036 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/bem-pKa/test_proteins/ -rw-r--r-- root/root 137270 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -rw-r--r-- root/root 137200 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -rw-r--r-- root/root 137455 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -rw-r--r-- root/root 137385 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -rw-r--r-- root/root 910 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -rw-r--r-- root/root 840 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/bem/ -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -rw-r--r-- root/root 879 2022-04-29 18:53 ./usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -rw-r--r-- root/root 878 2022-04-29 18:53 ./usr/share/apbs/examples/bem/451c_order1.in -rw-r--r-- root/root 878 2022-04-29 18:53 ./usr/share/apbs/examples/bem/451c_order5.in -rw-r--r-- root/root 1381 2022-04-29 18:53 ./usr/share/apbs/examples/bem/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/bem/test_proteins/ -rw-r--r-- root/root 153780 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/1a63.pqr -rw-r--r-- root/root 38306 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -rw-r--r-- root/root 42524 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -rw-r--r-- root/root 90105 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/451c.pqr -rw-r--r-- root/root 40 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/oneb.pqr -rw-r--r-- root/root 80 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/twob.pqr -rw-r--r-- root/root 82 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/twob2.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/born/ -rw-r--r-- root/root 4410 2022-04-29 18:53 ./usr/share/apbs/examples/born/README.md -rw-r--r-- root/root 719 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-apolar.in -rw-r--r-- root/root 1386 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-forces.in -rw-r--r-- root/root 1151 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-auto.in -rw-r--r-- root/root 1047 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -rw-r--r-- root/root 1160 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-fem.in -rw-r--r-- root/root 1130 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-parallel.in -rw-r--r-- root/root 1126 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-smol-auto.in -rw-r--r-- root/root 668 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-smol-fem.in -rw-r--r-- root/root 1132 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-smol-parallel.in -rw-r--r-- root/root 350 2022-04-29 18:53 ./usr/share/apbs/examples/born/apolarforces -rw-r--r-- root/root 66 2022-04-29 18:53 ./usr/share/apbs/examples/born/ion.pqr -rw-r--r-- root/root 1836 2022-04-29 18:53 ./usr/share/apbs/examples/born/mesh.m -rw-r--r-- root/root 524 2022-04-29 18:53 ./usr/share/apbs/examples/born/parm.dat -rw-r--r-- root/root 643 2022-04-29 18:53 ./usr/share/apbs/examples/born/pmf.dat -rw-r--r-- root/root 266 2022-04-29 18:53 ./usr/share/apbs/examples/born/polarforces drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/geoflow/ -rw-r--r-- root/root 686 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/1a63.in -rw-r--r-- root/root 153780 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/1a63.pqr -rw-r--r-- root/root 1130 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/README.md -rw-r--r-- root/root 910 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/gly.pdb -rw-r--r-- root/root 1613 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/gly.pqr -rw-r--r-- root/root 668 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/glycerol.in -rw-r--r-- root/root 695 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/imidazole.in -rw-r--r-- root/root 532 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/imidazole_zap.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/hca-bind/ -rw-r--r-- root/root 3483 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/hca-bind/UHBD/ -rw-r--r-- root/root 0 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -rw-r--r-- root/root 13931 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp -rw-r--r-- root/root 260500 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -rw-r--r-- root/root 13811 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -rw-r--r-- root/root 255148 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf.log -rw-r--r-- root/root 153885 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd -rw-r--r-- root/root 0 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -rw-r--r-- root/root 1118 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -rw-r--r-- root/root 640151 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -rw-r--r-- root/root 1215 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/acet.pqr -rw-r--r-- root/root 1776 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/apbs-mol.in -rw-r--r-- root/root 1779 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/apbs-smol.in -rw-r--r-- root/root 168329 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/complex.pqr -rw-r--r-- root/root 167114 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/hca.pqr -rw-r--r-- root/root 1808 2022-04-29 18:53 ./usr/share/apbs/examples/hca-bind/mesh.m drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/helix/ -rw-r--r-- root/root 2286 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -rw-r--r-- root/root 2241 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Apbs_dummy.in -rw-r--r-- root/root 3337 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -rw-r--r-- root/root 22699 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Membrane-helix-0.pqr -rw-r--r-- root/root 22699 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Membrane-helix-12.pqr -rw-r--r-- root/root 22699 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Membrane-helix-16.pqr -rw-r--r-- root/root 22699 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Membrane-helix-4.pqr -rw-r--r-- root/root 22699 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Membrane-helix-8.pqr -rwxr-xr-x root/root 3164 2022-04-29 18:53 ./usr/share/apbs/examples/helix/Run_membrane-helix.sh -rw-r--r-- root/root 24960 2022-04-29 18:53 ./usr/share/apbs/examples/helix/draw_membrane2.c drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/ion-pmf/ -rw-r--r-- root/root 25824 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/README.md -rw-r--r-- root/root 642 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/apolarforces -rw-r--r-- root/root 1214 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/complex.in -rw-r--r-- root/root 1214 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/ion-pmf.in -rw-r--r-- root/root 136 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -rw-r--r-- root/root 526 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/parm.dat -rw-r--r-- root/root 616 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/polarforces -rwxr-xr-x root/root 913 2022-04-29 18:53 ./usr/share/apbs/examples/ion-pmf/runme.sh drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/ion-protein/ -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/491.pqr -rw-r--r-- root/root 3285 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/ion-protein/UHBD/ -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/UHBD/491.pdb -rw-r--r-- root/root 25542 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -rw-r--r-- root/root 2280 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/UHBD/small491.inp -rw-r--r-- root/root 25511 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/UHBD/small491.log -rw-r--r-- root/root 17353 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/UHBD/small491.pdb -rw-r--r-- root/root 1467 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -rw-r--r-- root/root 1464 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -rw-r--r-- root/root 1470 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -rw-r--r-- root/root 1467 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -rw-r--r-- root/root 17677 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/complex.pqr -rw-r--r-- root/root 17610 2022-04-29 18:53 ./usr/share/apbs/examples/ion-protein/small491.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/ionize/ -rw-r--r-- root/root 3082 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/ionize/UHBD/ -rw-r--r-- root/root 923 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/UHBD/elec.dat.exam -rw-r--r-- root/root 12851 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/UHBD/elec.inp.exam -rw-r--r-- root/root 41212 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam -rw-r--r-- root/root 540 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam -rw-r--r-- root/root 552 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/acetate.pqr -rw-r--r-- root/root 552 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/acetic-acid.pqr -rw-r--r-- root/root 3129 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/apbs-mol.in -rw-r--r-- root/root 3135 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/apbs-smol.in -rw-r--r-- root/root 69 2022-04-29 18:53 ./usr/share/apbs/examples/ionize/proton.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/misc/ -rw-r--r-- root/root 500 2022-04-29 18:53 ./usr/share/apbs/examples/misc/README.md -rw-r--r-- root/root 1094120 2022-04-29 18:53 ./usr/share/apbs/examples/misc/achbp.pqr -rw-r--r-- root/root 794 2022-04-29 18:53 ./usr/share/apbs/examples/misc/apbs-PDB.in -rw-r--r-- root/root 756 2022-04-29 18:53 ./usr/share/apbs/examples/misc/apbs.in -rw-r--r-- root/root 61608 2022-04-29 18:53 ./usr/share/apbs/examples/misc/fas2.pqr -rw-r--r-- root/root 562972 2022-04-29 18:53 ./usr/share/apbs/examples/misc/mache.pqr -rw-r--r-- root/root 69290 2022-04-29 18:53 ./usr/share/apbs/examples/misc/param.dat drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pbam/ -rw-r--r-- root/root 899 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/1a63.in -rw-r--r-- root/root 153780 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/1a63.pqr -rw-r--r-- root/root 1015 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/README.md -rw-r--r-- root/root 13 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/neg_1.xyz -rw-r--r-- root/root 13 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/neg_2.xyz -rw-r--r-- root/root 13 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/neg_3.xyz -rw-r--r-- root/root 210 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/neg_charge.pqr -rw-r--r-- root/root 15 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/pos_1.xyz -rw-r--r-- root/root 14 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/pos_2.xyz -rw-r--r-- root/root 13 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/pos_3.xyz -rw-r--r-- root/root 210 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/pos_charge.pqr -rw-r--r-- root/root 974 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/toy_dynamics.in -rw-r--r-- root/root 831 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/toy_electrostatic.in -rw-r--r-- root/root 711 2022-04-29 18:53 ./usr/share/apbs/examples/pbam/toy_energyforce.in drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pbsam-barn_bars/ -rw-r--r-- root/root 1471 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in -rw-r--r-- root/root 128020 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr -rw-r--r-- root/root 103822 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pbsam-gly/ -rw-r--r-- root/root 821 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/README.md -rw-r--r-- root/root 2204 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly.pqr -rw-r--r-- root/root 51474 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly.vert -rw-r--r-- root/root 2448 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -rw-r--r-- root/root 2448 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr -rw-r--r-- root/root 1196 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -rw-r--r-- root/root 942 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -rw-r--r-- root/root 839 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/gly_energyforce.in drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pbsam-gly/msms/ -rw-r--r-- root/root 881 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -rw-r--r-- root/root 2204 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -rw-r--r-- root/root 14 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -rw-r--r-- root/root 16 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz -rw-r--r-- root/root 19 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz -rw-r--r-- root/root 16 2022-04-29 18:53 ./usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pka-lig/ -rw-r--r-- root/root 3957 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pka-lig/UHBD/ -rw-r--r-- root/root 906 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/README -rw-r--r-- root/root 246527 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out -rw-r--r-- root/root 249732 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out -rw-r--r-- root/root 13753 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -rw-r--r-- root/root 246005 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out -rw-r--r-- root/root 249210 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out -rw-r--r-- root/root 13231 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out -rw-r--r-- root/root 2685 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/apbs-mol-surf.in -rw-r--r-- root/root 2719 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in -rw-r--r-- root/root 2691 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/apbs-smol-surf.in -rw-r--r-- root/root 2725 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in -rw-r--r-- root/root 232789 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -rw-r--r-- root/root 235985 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -rw-r--r-- root/root 3196 2022-04-29 18:53 ./usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/point-pmf/ -rw-r--r-- root/root 1422 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/README.md -rw-r--r-- root/root 1255 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/apbs.in -rw-r--r-- root/root 1259 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_1.in -rw-r--r-- root/root 134 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_1.pqr -rw-r--r-- root/root 1259 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_2.in -rw-r--r-- root/root 134 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_2.pqr -rw-r--r-- root/root 1259 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_3.in -rw-r--r-- root/root 134 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_3.pqr -rw-r--r-- root/root 1259 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_4.in -rw-r--r-- root/root 134 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/complex-0_4.pqr -rw-r--r-- root/root 998 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/energy.dat -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/mol0.pqr -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/mol1.pqr -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/mol2.pqr -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/mol3.pqr -rw-r--r-- root/root 67 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/mol4.pqr -rw-r--r-- root/root 1255 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/point-pmf-0.in -rwxr-xr-x root/root 593 2022-04-29 18:53 ./usr/share/apbs/examples/point-pmf/runme.sh drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/protein-rna/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/protein-rna/PDB/ -rw-r--r-- root/root 50320 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb -rw-r--r-- root/root 81019 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb -rw-r--r-- root/root 30799 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb -rw-r--r-- root/root 4276 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/README.md -rw-r--r-- root/root 883 2024-01-19 18:56 ./usr/share/apbs/examples/protein-rna/apbs_dx.py -rw-r--r-- root/root 91 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/dxmath.txt -rw-r--r-- root/root 2415 2024-01-19 18:56 ./usr/share/apbs/examples/protein-rna/fit.py -rw-r--r-- root/root 43517 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr -rw-r--r-- root/root 70047 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/model_outNB.pqr -rw-r--r-- root/root 26715 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/model_outNpep.pqr -rwxr-xr-x root/root 988 2024-01-19 18:56 ./usr/share/apbs/examples/protein-rna/postprocess.sh -rwxr-xr-x root/root 281 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/run_apdx_files.sh -rw-r--r-- root/root 1637 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/template.txt -rwxr-xr-x root/root 1277 2022-04-29 18:53 ./usr/share/apbs/examples/protein-rna/test.sh drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pygbe/ -rw-r--r-- root/root 103 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys.in drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pygbe/lys/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/pygbe/lys/geometry/ -rw-r--r-- root/root 446338 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1.face -rw-r--r-- root/root 576080 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1.vert -rw-r--r-- root/root 2046 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.face -rw-r--r-- root/root 2800 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.vert -rw-r--r-- root/root 9672 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.face -rw-r--r-- root/root 12640 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.vert -rw-r--r-- root/root 2170 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.face -rw-r--r-- root/root 2960 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.vert -rw-r--r-- root/root 475044 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.face -rw-r--r-- root/root 613120 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert -rw-r--r-- root/root 1258 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/lys.config -rw-r--r-- root/root 228 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/lys.param -rw-r--r-- root/root 92618 2022-04-29 18:53 ./usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr -rwxr-xr-x root/root 677 2022-04-29 18:53 ./usr/share/apbs/examples/run_examples.sh -rwxr-xr-x root/root 4826 2022-04-29 18:53 ./usr/share/apbs/examples/run_selected_examples.sh drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/solv/ -rw-r--r-- root/root 3868 2022-04-29 18:53 ./usr/share/apbs/examples/solv/README.md drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/examples/solv/UHBD/ -rw-r--r-- root/root 808 2022-04-29 18:53 ./usr/share/apbs/examples/solv/UHBD/solv.dat.exam -rw-r--r-- root/root 4225 2022-04-29 18:53 ./usr/share/apbs/examples/solv/UHBD/solv.inp.exam -rw-r--r-- root/root 21026 2022-04-29 18:53 ./usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam -rw-r--r-- root/root 2277 2022-04-29 18:53 ./usr/share/apbs/examples/solv/apbs-mol.in -rw-r--r-- root/root 2275 2022-04-29 18:53 ./usr/share/apbs/examples/solv/apbs-smol.in -rw-r--r-- root/root 216 2022-04-29 18:53 ./usr/share/apbs/examples/solv/methanol.pqr -rw-r--r-- root/root 144 2022-04-29 18:53 ./usr/share/apbs/examples/solv/methoxide.pqr drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tests/ -rw-r--r-- root/root 143 2022-04-29 18:53 ./usr/share/apbs/tests/README.md -rw-r--r-- root/root 7804 2024-01-19 18:56 ./usr/share/apbs/tests/apbs_check_forces.py -rw-r--r-- root/root 2698 2024-01-19 18:56 ./usr/share/apbs/tests/apbs_check_intermediate_energies.py -rw-r--r-- root/root 2408 2024-01-19 18:56 ./usr/share/apbs/tests/apbs_check_results.py -rw-r--r-- root/root 735 2024-01-19 18:56 ./usr/share/apbs/tests/apbs_logger.py -rw-r--r-- root/root 14689 2024-01-19 18:56 ./usr/share/apbs/tests/apbs_tester.py -rw-r--r-- root/root 10277 2024-01-19 18:56 ./usr/share/apbs/tests/test_cases.cfg drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/ -rw-r--r-- root/root 230 2022-04-29 18:53 ./usr/share/apbs/tools/CMakeLists.txt -rw-r--r-- root/root 117 2022-04-29 18:53 ./usr/share/apbs/tools/README.md lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/bin -> ../../../lib/apbs/tools/bin drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/conversion/ -rw-r--r-- root/root 7068 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -rwxr-xr-x root/root 1372 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/amber2charmm.sh drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/conversion/param/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/conversion/param/pdb2pqr/ -rw-r--r-- root/root 29675 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -rwxr-xr-x root/root 2793 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -rw-r--r-- root/root 898 2024-01-19 18:56 ./usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat -rw-r--r-- root/root 21312 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/conversion/param/vparam/ -rw-r--r-- root/root 100020 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat -rw-r--r-- root/root 321168 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml -rwxr-xr-x root/root 793 2022-04-29 18:53 ./usr/share/apbs/tools/conversion/qcd2pqr.awk drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/manip/ -rw-r--r-- root/root 298 2022-04-29 18:53 ./usr/share/apbs/tools/manip/CMakeLists.txt -rw-r--r-- root/root 7583 2022-04-29 18:53 ./usr/share/apbs/tools/manip/born.c -rw-r--r-- root/root 6187 2022-04-29 18:53 ./usr/share/apbs/tools/manip/coulomb.c -rw-r--r-- root/root 15873 2024-01-19 18:56 ./usr/share/apbs/tools/manip/inputgen.py -rw-r--r-- root/root 18315 2022-04-29 18:53 ./usr/share/apbs/tools/manip/psize.py drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/visualization/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/visualization/opendx/ -rw-r--r-- root/root 3173 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/multipot.cfg -rw-r--r-- root/root 34706 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/multipot.net -rw-r--r-- root/root 5931 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/pot.cfg -rw-r--r-- root/root 471 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/pot.cm -rw-r--r-- root/root 30467 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/pot.net -rw-r--r-- root/root 5462 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/potacc.cfg -rw-r--r-- root/root 538 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/potacc.cm -rw-r--r-- root/root 31293 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/potacc.net -rw-r--r-- root/root 2549 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/surface.cfg -rw-r--r-- root/root 21114 2022-04-29 18:53 ./usr/share/apbs/tools/visualization/opendx/surface.net drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs-data/ -rw-r--r-- root/root 3602 2024-01-19 18:56 ./usr/share/doc/apbs-data/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/apbs-data/copyright apbs-doc_3.4.1-5build5_all.deb ------------------------------ new Debian package, version 2.0. size 5847788 bytes: control archive=7993 bytes. 1499 bytes, 33 lines control 26004 bytes, 279 lines md5sums Package: apbs-doc Source: apbs Version: 3.4.1-5build5 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 7585 Depends: libjs-mathjax, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 7.2.2), sphinx-rtd-theme-common (>= 2.0.0+dfsg) Recommends: apbs Suggests: python3-apbslib Section: science Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . This package contains the apbs documentation. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc-base/ -rw-r--r-- root/root 243 2023-01-10 18:37 ./usr/share/doc-base/apbs-doc.apbs drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs-doc/ -rw-r--r-- root/root 3602 2024-01-19 18:56 ./usr/share/doc/apbs-doc/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/apbs-doc/copyright drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_images/ -rw-r--r-- root/root 2194551 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/1fas_VR.png -rw-r--r-- root/root 2499424 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/AChE.png -rw-r--r-- root/root 313620 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/UI.png -rw-r--r-- root/root 41457 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/apbs_bind_eng.png -rw-r--r-- root/root 40630 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/apbs_sol_eng.png -rw-r--r-- root/root 86861 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/fas2-iso-pymol.png -rw-r--r-- root/root 117556 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/fas2-surf-pymol.png -rw-r--r-- root/root 202010 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/pb-schematic.png -rw-r--r-- root/root 168607 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/rna-qdens-pymol.jpg -rw-r--r-- root/root 61266 2022-04-29 18:53 ./usr/share/doc/apbs/html/_images/rna-qdens-vmd.jpg drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/api/ -rw-r--r-- root/root 583 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/api/index.rst.txt -rw-r--r-- root/root 15763 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/background.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/formats/ -rw-r--r-- root/root 1159 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/apbs-xml-parm.rst.txt -rw-r--r-- root/root 883 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/flat-parm.rst.txt -rw-r--r-- root/root 370 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/harwell.rst.txt -rw-r--r-- root/root 522 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/index.rst.txt -rw-r--r-- root/root 130 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/mcsf.rst.txt -rw-r--r-- root/root 2462 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/opendx.rst.txt -rw-r--r-- root/root 225 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/pdb.rst.txt -rw-r--r-- root/root 2139 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/pqr.rst.txt -rw-r--r-- root/root 1190 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/uhbd.rst.txt -rw-r--r-- root/root 1350 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/formats/xml-struct.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/getting/ -rw-r--r-- root/root 3640 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/getting/index.rst.txt -rw-r--r-- root/root 7341 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/getting/source.rst.txt -rw-r--r-- root/root 743 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/help.rst.txt -rw-r--r-- root/root 2055 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/index.rst.txt -rw-r--r-- root/root 7266 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/reading.rst.txt -rw-r--r-- root/root 51294 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/releases.rst.txt -rw-r--r-- root/root 2297 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/supporting.rst.txt -rw-r--r-- root/root 95 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/todo.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/examples/ -rw-r--r-- root/root 4101 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/examples/binding-energies.rst.txt -rw-r--r-- root/root 8757 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/examples/salt-linkage.rst.txt -rw-r--r-- root/root 8753 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/examples/solvation-energies.rst.txt -rw-r--r-- root/root 4877 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/examples/visualization-pymol.rst.txt -rw-r--r-- root/root 6814 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/examples/visualization-unitymol.rst.txt -rw-r--r-- root/root 4225 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/index.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/new/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/new/calculate/ -rw-r--r-- root/root 672 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/calculate/boundary_element.rst.txt -rw-r--r-- root/root 520 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/calculate/finite_difference.rst.txt -rw-r--r-- root/root 530 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/calculate/finite_element.rst.txt -rw-r--r-- root/root 872 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/calculate/index.rst.txt -rw-r--r-- root/root 342 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/calculate/nonpolar.rst.txt -rw-r--r-- root/root 801 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/index.rst.txt -rw-r--r-- root/root 642 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/process.rst.txt -rw-r--r-- root/root 211 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/process_api.rst.txt -rw-r--r-- root/root 1172 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/new/read.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/old/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/old/apolar/ -rw-r--r-- root/root 962 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/apolar/dpos.rst.txt -rw-r--r-- root/root 782 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/apolar/gamma.rst.txt -rw-r--r-- root/root 3608 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/apolar/index.rst.txt -rw-r--r-- root/root 845 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/apolar/press.rst.txt -rw-r--r-- root/root 609 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/apolar/srfm.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/ -rw-r--r-- root/root 588 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/3dmap.rst.txt -rw-r--r-- root/root 671 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/akeyPRE.rst.txt -rw-r--r-- root/root 533 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/akeySOLVE.rst.txt -rw-r--r-- root/root 985 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/async.rst.txt -rw-r--r-- root/root 2758 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/bcfl.rst.txt -rw-r--r-- root/root 787 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/cgcent.rst.txt -rw-r--r-- root/root 772 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/cglen.rst.txt -rw-r--r-- root/root 1547 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/chgm.rst.txt -rw-r--r-- root/root 1101 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/diff.rst.txt -rw-r--r-- root/root 1441 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/dime.rst.txt -rw-r--r-- root/root 678 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/domainLength.rst.txt -rw-r--r-- root/root 524 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/dx.rst.txt -rw-r--r-- root/root 645 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/ekey.rst.txt -rw-r--r-- root/root 1192 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/etol.rst.txt -rw-r--r-- root/root 790 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/exp.rst.txt -rw-r--r-- root/root 1701 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/fe-manual.rst.txt -rw-r--r-- root/root 961 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/fgcent.rst.txt -rw-r--r-- root/root 665 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/fglen.rst.txt -rw-r--r-- root/root 835 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/gamma-geoflow.rst.txt -rw-r--r-- root/root 896 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/gcent.rst.txt -rw-r--r-- root/root 2431 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/geoflow-auto.rst.txt -rw-r--r-- root/root 553 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/glen.rst.txt -rw-r--r-- root/root 848 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/grid2d.rst.txt -rw-r--r-- root/root 505 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/gridpts.rst.txt -rw-r--r-- root/root 800 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/imat.rst.txt -rw-r--r-- root/root 2238 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/index.rst.txt -rw-r--r-- root/root 1228 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/ion.rst.txt -rw-r--r-- root/root 615 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/lpbe.rst.txt -rw-r--r-- root/root 1071 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/lrpbe.rst.txt -rw-r--r-- root/root 946 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/mac.rst.txt -rw-r--r-- root/root 515 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/maxsolve.rst.txt -rw-r--r-- root/root 560 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/maxvert.rst.txt -rw-r--r-- root/root 735 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/mesh.rst.txt -rw-r--r-- root/root 2696 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/mg-auto.rst.txt -rw-r--r-- root/root 974 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/mg-dummy.rst.txt -rw-r--r-- root/root 1227 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/mg-manual.rst.txt -rw-r--r-- root/root 916 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/mg-para.rst.txt -rw-r--r-- root/root 550 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/nlev.rst.txt -rw-r--r-- root/root 621 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/npbe.rst.txt -rw-r--r-- root/root 1153 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/nrpbe.rst.txt -rw-r--r-- root/root 323 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/ntraj.rst.txt -rw-r--r-- root/root 1853 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/ofrac.rst.txt -rw-r--r-- root/root 689 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/outdata.rst.txt -rw-r--r-- root/root 2770 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/pbam-auto.rst.txt -rw-r--r-- root/root 959 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/pbc.rst.txt -rw-r--r-- root/root 5252 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/pbsam-auto.rst.txt -rw-r--r-- root/root 1073 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/pdie.rst.txt -rw-r--r-- root/root 1310 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/pdime.rst.txt -rw-r--r-- root/root 904 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/press-geoflow.rst.txt -rw-r--r-- root/root 333 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/pygbe.rst.txt -rw-r--r-- root/root 251 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/randorient.rst.txt -rw-r--r-- root/root 311 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/runname.rst.txt -rw-r--r-- root/root 1438 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/runtype.rst.txt -rw-r--r-- root/root 559 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/salt.rst.txt -rw-r--r-- root/root 994 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/sdie.rst.txt -rw-r--r-- root/root 3228 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/srfm.rst.txt -rw-r--r-- root/root 539 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/surf.rst.txt -rw-r--r-- root/root 4819 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/tabi.rst.txt -rw-r--r-- root/root 523 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/targetNum.rst.txt -rw-r--r-- root/root 665 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/targetRes.rst.txt -rw-r--r-- root/root 2079 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/term.rst.txt -rw-r--r-- root/root 551 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/termcombine.rst.txt -rw-r--r-- root/root 424 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/tolsp.rst.txt -rw-r--r-- root/root 536 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/tree_n0.rst.txt -rw-r--r-- root/root 551 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/tree_order.rst.txt -rw-r--r-- root/root 590 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/units.rst.txt -rw-r--r-- root/root 2338 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/usemap.rst.txt -rw-r--r-- root/root 613 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/usemesh.rst.txt -rw-r--r-- root/root 330 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/vdwdisp.rst.txt -rw-r--r-- root/root 5132 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/write.rst.txt -rw-r--r-- root/root 596 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/writemat.rst.txt -rw-r--r-- root/root 789 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/elec/xyz.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/ -rw-r--r-- root/root 689 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/bconc.rst.txt -rw-r--r-- root/root 1223 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/calcenergy.rst.txt -rw-r--r-- root/root 1605 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/calcforce.rst.txt -rw-r--r-- root/root 587 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/grid.rst.txt -rw-r--r-- root/root 1088 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/mol.rst.txt -rw-r--r-- root/root 1084 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/sdens.rst.txt -rw-r--r-- root/root 1178 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/srad.rst.txt -rw-r--r-- root/root 956 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/swin.rst.txt -rw-r--r-- root/root 851 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/generic/temp.rst.txt -rw-r--r-- root/root 2431 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/index.rst.txt -rw-r--r-- root/root 2159 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/print.rst.txt -rw-r--r-- root/root 5464 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/input/old/read.rst.txt -rw-r--r-- root/root 2539 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/tests.rst.txt -rw-r--r-- root/root 3607 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/tools.rst.txt -rw-r--r-- root/root 3083 2022-04-29 18:53 ./usr/share/doc/apbs/html/_sources/using/units.rst.txt drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/ -rw-r--r-- root/root 4289 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/_sphinx_javascript_frameworks_compat.js -rw-r--r-- root/root 15094 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/basic.css drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/css/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/css/badge_only.css -> ../../../../../sphinx_rtd_theme/static/css/badge_only.css lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/css/theme.css -> ../../../../../sphinx_rtd_theme/static/css/theme.css lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/doctools.js -> ../../../../javascript/sphinxdoc/1.0/doctools.js -rw-r--r-- root/root 328 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/documentation_options.js -rw-r--r-- root/root 286 2023-12-19 10:34 ./usr/share/doc/apbs/html/_static/file.png drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-Bold.ttf -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-Bold.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-BoldItalic.ttf -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-BoldItalic.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-Italic.ttf -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-Italic.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-Regular.ttf -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/Lato-Regular.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/RobotoSlab-Bold.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/RobotoSlab-Regular.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/fontawesome-webfont.eot -> ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/fontawesome-webfont.svg -> ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/fontawesome-webfont.ttf -> ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/fontawesome-webfont.woff -> ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/fonts/fontawesome-webfont.woff2 -> ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/jquery.js -> ../../../../javascript/jquery/jquery.min.js drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/js/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/js/theme.js -> ../../../../../sphinx_rtd_theme/static/js/theme.js lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/language_data.js -> ../../../../javascript/sphinxdoc/1.0/language_data.js -rw-r--r-- root/root 90 2023-12-19 10:34 ./usr/share/doc/apbs/html/_static/minus.png -rw-r--r-- root/root 90 2023-12-19 10:34 ./usr/share/doc/apbs/html/_static/plus.png -rw-r--r-- root/root 4819 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/pygments.css lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/api/ -rw-r--r-- root/root 6080 2024-01-19 18:56 ./usr/share/doc/apbs/html/api/index.html -rw-r--r-- root/root 28713 2024-01-19 18:56 ./usr/share/doc/apbs/html/background.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/ -rw-r--r-- root/root 8949 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/apbs-xml-parm.html -rw-r--r-- root/root 7799 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/flat-parm.html -rw-r--r-- root/root 6366 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/harwell.html -rw-r--r-- root/root 8541 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/index.html -rw-r--r-- root/root 6158 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/mcsf.html -rw-r--r-- root/root 15265 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/opendx.html -rw-r--r-- root/root 6372 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/pdb.html -rw-r--r-- root/root 9506 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/pqr.html -rw-r--r-- root/root 14219 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/uhbd.html -rw-r--r-- root/root 8785 2024-01-19 18:56 ./usr/share/doc/apbs/html/formats/xml-struct.html -rw-r--r-- root/root 4820 2024-01-19 18:56 ./usr/share/doc/apbs/html/genindex.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/getting/ -rw-r--r-- root/root 12257 2024-01-19 18:56 ./usr/share/doc/apbs/html/getting/index.html -rw-r--r-- root/root 22247 2024-01-19 18:56 ./usr/share/doc/apbs/html/getting/source.html -rw-r--r-- root/root 6608 2024-01-19 18:56 ./usr/share/doc/apbs/html/help.html -rw-r--r-- root/root 17011 2024-01-19 18:56 ./usr/share/doc/apbs/html/index.html -rw-r--r-- root/root 3327 2024-01-19 18:56 ./usr/share/doc/apbs/html/objects.inv -rw-r--r-- root/root 4726 2024-01-19 18:56 ./usr/share/doc/apbs/html/py-modindex.html -rw-r--r-- root/root 17227 2024-01-19 18:56 ./usr/share/doc/apbs/html/reading.html -rw-r--r-- root/root 85111 2024-01-19 18:56 ./usr/share/doc/apbs/html/releases.html -rw-r--r-- root/root 4587 2024-01-19 18:56 ./usr/share/doc/apbs/html/search.html -rw-r--r-- root/root 118051 2024-01-19 18:56 ./usr/share/doc/apbs/html/searchindex.js -rw-r--r-- root/root 8986 2024-01-19 18:56 ./usr/share/doc/apbs/html/supporting.html -rw-r--r-- root/root 4886 2024-01-19 18:56 ./usr/share/doc/apbs/html/todo.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/examples/ -rw-r--r-- root/root 12867 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/examples/binding-energies.html -rw-r--r-- root/root 25499 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/examples/salt-linkage.html -rw-r--r-- root/root 23001 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/examples/solvation-energies.html -rw-r--r-- root/root 13759 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/examples/visualization-pymol.html -rw-r--r-- root/root 17205 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/examples/visualization-unitymol.html -rw-r--r-- root/root 20850 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/index.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/calculate/ -rw-r--r-- root/root 8039 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/calculate/boundary_element.html -rw-r--r-- root/root 7893 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/calculate/finite_difference.html -rw-r--r-- root/root 7838 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/calculate/finite_element.html -rw-r--r-- root/root 8935 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/calculate/index.html -rw-r--r-- root/root 7773 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/calculate/nonpolar.html -rw-r--r-- root/root 9603 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/index.html -rw-r--r-- root/root 8692 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/process.html -rw-r--r-- root/root 7546 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/process_api.html -rw-r--r-- root/root 9804 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/new/read.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/apolar/ -rw-r--r-- root/root 9129 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/apolar/dpos.html -rw-r--r-- root/root 8459 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/apolar/gamma.html -rw-r--r-- root/root 14114 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/apolar/index.html -rw-r--r-- root/root 8423 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/apolar/press.html -rw-r--r-- root/root 8561 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/apolar/srfm.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/ -rw-r--r-- root/root 7913 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/3dmap.html -rw-r--r-- root/root 8731 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/akeyPRE.html -rw-r--r-- root/root 8589 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/akeySOLVE.html -rw-r--r-- root/root 9104 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/async.html -rw-r--r-- root/root 11487 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/bcfl.html -rw-r--r-- root/root 9430 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/cgcent.html -rw-r--r-- root/root 9009 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/cglen.html -rw-r--r-- root/root 10302 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/chgm.html -rw-r--r-- root/root 9238 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/diff.html -rw-r--r-- root/root 10257 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/dime.html -rw-r--r-- root/root 8691 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/domainLength.html -rw-r--r-- root/root 7842 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/dx.html -rw-r--r-- root/root 8837 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/ekey.html -rw-r--r-- root/root 9695 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/etol.html -rw-r--r-- root/root 8601 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/exp.html -rw-r--r-- root/root 11746 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/fe-manual.html -rw-r--r-- root/root 9141 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/fgcent.html -rw-r--r-- root/root 8825 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/fglen.html -rw-r--r-- root/root 8381 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/gamma-geoflow.html -rw-r--r-- root/root 9396 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/gcent.html -rw-r--r-- root/root 11244 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/geoflow-auto.html -rw-r--r-- root/root 8586 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/glen.html -rw-r--r-- root/root 8676 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/grid2d.html -rw-r--r-- root/root 7841 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/gridpts.html -rw-r--r-- root/root 8560 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/imat.html -rw-r--r-- root/root 12981 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/index.html -rw-r--r-- root/root 9817 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/ion.html -rw-r--r-- root/root 8713 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/lpbe.html -rw-r--r-- root/root 9185 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/lrpbe.html -rw-r--r-- root/root 9021 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/mac.html -rw-r--r-- root/root 8452 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/maxsolve.html -rw-r--r-- root/root 8554 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/maxvert.html -rw-r--r-- root/root 8944 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/mesh.html -rw-r--r-- root/root 13118 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/mg-auto.html -rw-r--r-- root/root 10080 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/mg-dummy.html -rw-r--r-- root/root 11224 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/mg-manual.html -rw-r--r-- root/root 10885 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/mg-para.html -rw-r--r-- root/root 8648 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/nlev.html -rw-r--r-- root/root 8731 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/npbe.html -rw-r--r-- root/root 9328 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/nrpbe.html -rw-r--r-- root/root 7840 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/ntraj.html -rw-r--r-- root/root 11302 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/ofrac.html -rw-r--r-- root/root 8175 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/outdata.html -rw-r--r-- root/root 12382 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/pbam-auto.html -rw-r--r-- root/root 8547 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/pbc.html -rw-r--r-- root/root 16899 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/pbsam-auto.html -rw-r--r-- root/root 9300 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/pdie.html -rw-r--r-- root/root 10057 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/pdime.html -rw-r--r-- root/root 8319 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/press-geoflow.html -rw-r--r-- root/root 4847 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/pygbe.html -rw-r--r-- root/root 7565 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/randorient.html -rw-r--r-- root/root 7768 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/runname.html -rw-r--r-- root/root 9742 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/runtype.html -rw-r--r-- root/root 7898 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/salt.html -rw-r--r-- root/root 9228 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/sdie.html -rw-r--r-- root/root 12000 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/srfm.html -rw-r--r-- root/root 7954 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/surf.html -rw-r--r-- root/root 15287 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/tabi.html -rw-r--r-- root/root 8319 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/targetNum.html -rw-r--r-- root/root 8767 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/targetRes.html -rw-r--r-- root/root 11516 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/term.html -rw-r--r-- root/root 8435 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/termcombine.html -rw-r--r-- root/root 7659 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/tolsp.html -rw-r--r-- root/root 8414 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/tree_n0.html -rw-r--r-- root/root 8420 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/tree_order.html -rw-r--r-- root/root 8294 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/units.html -rw-r--r-- root/root 12847 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/usemap.html -rw-r--r-- root/root 8455 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/usemesh.html -rw-r--r-- root/root 7931 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/vdwdisp.html -rw-r--r-- root/root 17506 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/write.html -rw-r--r-- root/root 8917 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/writemat.html -rw-r--r-- root/root 8341 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/elec/xyz.html drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/ -rw-r--r-- root/root 8668 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/bconc.html -rw-r--r-- root/root 10002 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/calcenergy.html -rw-r--r-- root/root 10966 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/calcforce.html -rw-r--r-- root/root 8647 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/grid.html -rw-r--r-- root/root 9461 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/mol.html -rw-r--r-- root/root 9419 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/sdens.html -rw-r--r-- root/root 9667 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/srad.html -rw-r--r-- root/root 9099 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/swin.html -rw-r--r-- root/root 9020 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/generic/temp.html -rw-r--r-- root/root 11876 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/index.html -rw-r--r-- root/root 13914 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/print.html -rw-r--r-- root/root 20863 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/input/old/read.html -rw-r--r-- root/root 11239 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/tests.html -rw-r--r-- root/root 16054 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/tools.html -rw-r--r-- root/root 13672 2024-01-19 18:56 ./usr/share/doc/apbs/html/using/units.html apbs_3.4.1-5build5_amd64.deb ---------------------------- new Debian package, version 2.0. size 76886 bytes: control archive=1739 bytes. 1829 bytes, 30 lines control 1479 bytes, 23 lines md5sums Package: apbs Version: 3.4.1-5build5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 386 Depends: apbs-data (= 3.4.1-5build5), libapbs3 (= 3.4.1-5build5), libjs-mathjax, libamd3 (>= 1:7.0.1), libarpack2 (>= 2.1), libblas3 | libblas.so.3, libc6 (>= 2.34), libcamd3 (>= 1:7.0.1), libccolamd3 (>= 1:7.0.1), libcholmod5 (>= 1:7.3.1), libcolamd3 (>= 1:7.0.1), libfetk1.9 (>= 3.4.1), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi3 (>= 4.1.6), libspqr4 (>= 1:7.5.1+dfsg), libstdc++6 (>= 4.1.1), libsuitesparseconfig7 (>= 1:7.0.1), libsuperlu6 (>= 6.0.1+dfsg1), libumfpack6 (>= 1:7.0.1) Section: science Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . This package contains the apbs program and utilities. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/bin/ -rwxr-xr-x root/root 35120 2024-01-19 18:56 ./usr/bin/apbs drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/apbs/tools/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/ -rwxr-xr-x root/root 18736 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/analysis -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/benchmark -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/born -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/coulomb -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/del2dx -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/dx2mol -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/dx2uhbd -rwxr-xr-x root/root 22832 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/dxmath -rwxr-xr-x root/root 22832 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/mergedx -rwxr-xr-x root/root 26928 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/mergedx2 -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/mgmesh -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/multivalue -rwxr-xr-x root/root 26928 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/similarity -rwxr-xr-x root/root 18736 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/smooth -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/tensor2dx -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/uhbd_asc2bin -rwxr-xr-x root/root 14640 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/value drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/ -rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/apbs/README -rw-r--r-- root/root 294 2021-01-10 13:57 ./usr/share/doc/apbs/README.test lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/changelog.Debian.gz -> ../libapbs3/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/apbs/copyright -rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/apbs/releases.rst.gz drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/man/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/man/man1/ -rw-r--r-- root/root 835 2024-01-19 18:56 ./usr/share/man/man1/apbs.1.gz libapbs-dev_3.4.1-5build5_amd64.deb ----------------------------------- new Debian package, version 2.0. size 99448 bytes: control archive=2154 bytes. 752 bytes, 20 lines control 3873 bytes, 58 lines md5sums Package: libapbs-dev Source: apbs Version: 3.4.1-5build5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 713 Depends: libapbs3 (= 3.4.1-5build5) Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the development headers to build against libapbs_* shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/ -rw-r--r-- root/root 3281 2022-04-29 18:53 ./usr/include/apbs/apbs.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/fem/ -rw-r--r-- root/root 11331 2022-04-29 18:53 ./usr/include/apbs/fem/vcsm.h -rw-r--r-- root/root 37852 2022-04-29 18:53 ./usr/include/apbs/fem/vfetk.h -rw-r--r-- root/root 10184 2022-04-29 18:53 ./usr/include/apbs/fem/vpee.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/generic/ -rw-r--r-- root/root 8229 2022-04-29 18:53 ./usr/include/apbs/generic/apolparm.h -rw-r--r-- root/root 6395 2022-04-29 18:53 ./usr/include/apbs/generic/bemparm.h -rw-r--r-- root/root 8873 2022-04-29 18:53 ./usr/include/apbs/generic/femparm.h -rw-r--r-- root/root 6121 2022-04-29 18:53 ./usr/include/apbs/generic/geoflowparm.h -rw-r--r-- root/root 12602 2022-04-29 18:53 ./usr/include/apbs/generic/mgparm.h -rw-r--r-- root/root 21080 2022-04-29 18:53 ./usr/include/apbs/generic/nosh.h -rw-r--r-- root/root 10919 2022-04-29 18:53 ./usr/include/apbs/generic/pbamparm.h -rw-r--r-- root/root 11096 2022-04-29 18:53 ./usr/include/apbs/generic/pbeparm.h -rw-r--r-- root/root 7321 2022-04-29 18:53 ./usr/include/apbs/generic/pbsamparm.h -rw-r--r-- root/root 23163 2022-04-29 18:53 ./usr/include/apbs/generic/vacc.h -rw-r--r-- root/root 8494 2022-04-29 18:53 ./usr/include/apbs/generic/valist.h -rw-r--r-- root/root 10351 2022-04-29 18:53 ./usr/include/apbs/generic/vatom.h -rw-r--r-- root/root 5946 2022-04-29 18:53 ./usr/include/apbs/generic/vcap.h -rw-r--r-- root/root 9280 2022-04-29 18:53 ./usr/include/apbs/generic/vclist.h -rw-r--r-- root/root 12789 2022-04-29 18:53 ./usr/include/apbs/generic/vgreen.h -rw-r--r-- root/root 38131 2022-04-29 18:53 ./usr/include/apbs/generic/vhal.h -rw-r--r-- root/root 3084 2022-04-29 18:53 ./usr/include/apbs/generic/vmatrix.h -rw-r--r-- root/root 12145 2022-04-29 18:53 ./usr/include/apbs/generic/vparam.h -rw-r--r-- root/root 19880 2022-04-29 18:53 ./usr/include/apbs/generic/vpbe.h -rw-r--r-- root/root 5171 2022-04-29 18:53 ./usr/include/apbs/generic/vstring.h -rw-r--r-- root/root 3958 2022-04-29 18:53 ./usr/include/apbs/generic/vunit.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/mg/ -rw-r--r-- root/root 14945 2022-04-29 18:53 ./usr/include/apbs/mg/vgrid.h -rw-r--r-- root/root 6887 2022-04-29 18:53 ./usr/include/apbs/mg/vmgrid.h -rw-r--r-- root/root 6160 2022-04-29 18:53 ./usr/include/apbs/mg/vopot.h -rw-r--r-- root/root 52888 2022-04-29 18:53 ./usr/include/apbs/mg/vpmg.h -rw-r--r-- root/root 11010 2022-04-29 18:53 ./usr/include/apbs/mg/vpmgp.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/pmgc/ -rw-r--r-- root/root 12319 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildAd.h -rw-r--r-- root/root 5305 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildBd.h -rw-r--r-- root/root 16972 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildGd.h -rw-r--r-- root/root 10038 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildPd.h -rw-r--r-- root/root 3475 2022-04-29 18:53 ./usr/include/apbs/pmgc/cgd.h -rw-r--r-- root/root 5776 2022-04-29 18:53 ./usr/include/apbs/pmgc/gsd.h -rw-r--r-- root/root 19097 2022-04-29 18:53 ./usr/include/apbs/pmgc/matvecd.h -rw-r--r-- root/root 5762 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgcsd.h -rw-r--r-- root/root 9284 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgdrvd.h -rw-r--r-- root/root 7729 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgfasd.h -rw-r--r-- root/root 14987 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgsubd.h -rw-r--r-- root/root 12104 2022-04-29 18:53 ./usr/include/apbs/pmgc/mikpckd.h -rw-r--r-- root/root 4008 2022-04-29 18:53 ./usr/include/apbs/pmgc/mlinpckd.h -rw-r--r-- root/root 7781 2022-04-29 18:53 ./usr/include/apbs/pmgc/mypdec.h -rw-r--r-- root/root 5950 2022-04-29 18:53 ./usr/include/apbs/pmgc/newdrvd.h -rw-r--r-- root/root 6700 2022-04-29 18:53 ./usr/include/apbs/pmgc/newtond.h -rw-r--r-- root/root 8220 2022-04-29 18:53 ./usr/include/apbs/pmgc/powerd.h -rw-r--r-- root/root 4685 2022-04-29 18:53 ./usr/include/apbs/pmgc/smoothd.h -rw-r--r-- root/root 33482 2022-04-29 18:53 ./usr/include/apbs/routines.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_fem.so -> libapbs_fem.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_generic.so -> libapbs_generic.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_mg.so -> libapbs_mg.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_pmgc.so -> libapbs_pmgc.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_routines.so -> libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/cmake/ -rw-r--r-- root/root 949 2023-01-10 18:37 ./usr/share/apbs/cmake/FindAMD.cmake -rw-r--r-- root/root 2501 2023-01-10 18:37 ./usr/share/apbs/cmake/FindARPACK.cmake -rw-r--r-- root/root 22563 2023-01-10 18:37 ./usr/share/apbs/cmake/FindLAPACK.cmake -rw-r--r-- root/root 23393 2023-01-10 18:37 ./usr/share/apbs/cmake/FindSuiteSparse.cmake -rw-r--r-- root/root 2578 2023-01-10 18:37 ./usr/share/apbs/cmake/FindSuperLU.cmake -rw-r--r-- root/root 1153 2023-01-10 18:37 ./usr/share/apbs/cmake/FindUMFPACK.cmake drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs-dev/ -rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/README lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs-dev/changelog.Debian.gz -> ../libapbs3/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libapbs-dev/copyright -rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/releases.rst.gz libapbs3_3.4.1-5build5_amd64.deb -------------------------------- new Debian package, version 2.0. size 266426 bytes: control archive=1006 bytes. 760 bytes, 19 lines control 527 bytes, 7 lines md5sums 179 bytes, 5 lines shlibs 75 bytes, 2 lines triggers Package: libapbs3 Source: apbs Version: 3.4.1-5build5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 769 Depends: libc6 (>= 2.29), libfetk1.9 (>= 3.4.1), libgomp1 (>= 4.9), libmaloc1 (>= 0.2-1) Section: libs Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the libapbs_* shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 69800 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_fem.so.3 -rw-r--r-- root/root 206992 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 -rw-r--r-- root/root 174224 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_mg.so.3 -rw-r--r-- root/root 202896 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3 -rw-r--r-- root/root 104592 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs3/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs3/changelog.Debian.gz -> ../libfetk1.9/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libapbs3/copyright drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 108 2023-01-10 18:37 ./usr/share/lintian/overrides/libapbs3 libfetk-dev_3.4.1-5build5_amd64.deb ----------------------------------- new Debian package, version 2.0. size 144488 bytes: control archive=1988 bytes. 1344 bytes, 32 lines control 2509 bytes, 40 lines md5sums Package: libfetk-dev Source: apbs Version: 3.4.1-5build5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 1505 Depends: libfetk1.9 (= 3.4.1-5build5), libmaloc-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: FETK libraries for APBS (development headers) The Finite Element ToolKit (FETK) is a collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C++, and include a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC) . This package provides a fork of FETK intended for use by APBS (Adaptive Poisson Boltzmann Solver). . The FETK component MALOC (Minimal Abstraction Layer for Object-oriented C/C++ programs) is provided separately by libmaloc-dev. . This package contains the development headers to build against libapbs_* shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/gamer/ -rw-r--r-- root/root 11439 2023-01-10 18:37 ./usr/include/fetk/gamer/biom.h -rw-r--r-- root/root 1459 2023-01-10 18:37 ./usr/include/fetk/gamer/gamer.h -rw-r--r-- root/root 2282 2023-01-10 18:37 ./usr/include/fetk/gamer/gamer_base.h -rw-r--r-- root/root 106910 2023-01-10 18:37 ./usr/include/fetk/gamer/tetgen.h -rw-r--r-- root/root 22024 2023-01-10 18:37 ./usr/include/fetk/gamer/triangle.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/mc/ -rw-r--r-- root/root 27753 2023-01-10 18:37 ./usr/include/fetk/mc/am.h -rw-r--r-- root/root 49795 2023-01-10 18:37 ./usr/include/fetk/mc/aprx.h -rw-r--r-- root/root 1297 2023-01-10 18:37 ./usr/include/fetk/mc/bam.h -rw-r--r-- root/root 29085 2023-01-10 18:37 ./usr/include/fetk/mc/bmat.h -rw-r--r-- root/root 5029 2023-01-10 18:37 ./usr/include/fetk/mc/bnode.h -rw-r--r-- root/root 32284 2023-01-10 18:37 ./usr/include/fetk/mc/bvec.h -rw-r--r-- root/root 13191 2023-01-10 18:37 ./usr/include/fetk/mc/dyn.h -rw-r--r-- root/root 130602 2023-01-10 18:37 ./usr/include/fetk/mc/gem.h -rw-r--r-- root/root 47965 2023-01-10 18:37 ./usr/include/fetk/mc/mat.h -rw-r--r-- root/root 1457 2023-01-10 18:37 ./usr/include/fetk/mc/mc.h -rw-r--r-- root/root 5705 2023-01-10 18:37 ./usr/include/fetk/mc/mc_base.h -rw-r--r-- root/root 4665 2023-01-10 18:37 ./usr/include/fetk/mc/mcsh.h -rw-r--r-- root/root 14987 2023-01-10 18:37 ./usr/include/fetk/mc/mtool.h -rw-r--r-- root/root 1189 2023-01-10 18:37 ./usr/include/fetk/mc/nam.h -rw-r--r-- root/root 4772 2023-01-10 18:37 ./usr/include/fetk/mc/node.h -rw-r--r-- root/root 17885 2023-01-10 18:37 ./usr/include/fetk/mc/pde.h -rw-r--r-- root/root 17026 2023-01-10 18:37 ./usr/include/fetk/mc/re.h -rw-r--r-- root/root 4823 2023-01-10 18:37 ./usr/include/fetk/mc/slu.h -rw-r--r-- root/root 12682 2023-01-10 18:37 ./usr/include/fetk/mc/vec.h -rw-r--r-- root/root 14016 2023-01-10 18:37 ./usr/include/fetk/mc/vec3.h -rw-r--r-- root/root 26120 2023-01-10 18:37 ./usr/include/fetk/mc/vel.h -rw-r--r-- root/root 68269 2023-01-10 18:37 ./usr/include/fetk/mc/ves.h -rw-r--r-- root/root 50938 2023-01-10 18:37 ./usr/include/fetk/mc/whb.h -rw-r--r-- root/root 7767 2023-01-10 18:37 ./usr/include/fetk/mc/zslu.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/punc/ -rw-r--r-- root/root 1569 2023-01-10 18:37 ./usr/include/fetk/punc/punc.h -rw-r--r-- root/root 1272 2023-01-10 18:37 ./usr/include/fetk/punc/punc_base.h -rw-r--r-- root/root 1455 2023-01-10 18:37 ./usr/include/fetk/punc/punc_base_p.h -rw-r--r-- root/root 3987 2024-01-19 18:56 ./usr/include/fetk/punc/punccf.h -rw-r--r-- root/root 46865 2023-01-10 18:37 ./usr/include/fetk/punc/varpack.h -rw-r--r-- root/root 39886 2023-01-10 18:37 ./usr/include/fetk/punc/vblas.h -rw-r--r-- root/root 17098 2023-01-10 18:37 ./usr/include/fetk/punc/vcgcode.h -rw-r--r-- root/root 13077 2023-01-10 18:37 ./usr/include/fetk/punc/vf2c.h -rw-r--r-- root/root 552778 2023-01-10 18:37 ./usr/include/fetk/punc/vlapack.h -rw-r--r-- root/root 82089 2023-01-10 18:37 ./usr/include/fetk/punc/vpmg.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libcgcode.so -> libcgcode.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libgamer.so -> libgamer.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libmc.so -> libmc.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libpunc.so -> libpunc.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libvf2c.so -> libvf2c.so.1.9 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libfetk-dev/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/libfetk-dev/changelog.Debian.gz -> ../libfetk1.9/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libfetk-dev/copyright libfetk1.9_3.4.1-5build5_amd64.deb ---------------------------------- new Debian package, version 2.0. size 598072 bytes: control archive=1391 bytes. 1432 bytes, 32 lines control 602 bytes, 8 lines md5sums 171 bytes, 5 lines shlibs 75 bytes, 2 lines triggers Package: libfetk1.9 Source: apbs Version: 3.4.1-5build5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 1465 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libmaloc1 (>= 0.2-1), libstdc++6 (>= 5), libsuperlu6 (>= 6.0.1+dfsg1), libumfpack6 (>= 1:7.0.1) Section: libs Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: FETK libraries for APBS (shared libraries) The Finite Element ToolKit (FETK) is a collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C++, and include a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC) . This package provides a fork of FETK intended for use by APBS (Adaptive Poisson Boltzmann Solver). . The FETK component MALOC (Minimal Abstraction Layer for Object-oriented C/C++ programs) is provided separately via libmaloc-dev. . This package contains the libgamer, libmc, libpunc (and libcgcode, libvf2c) shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libcgcode.so.1.9 -> libcgcode.so.1.9.3 -rw-r--r-- root/root 110392 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libgamer.so.1.9 -> libgamer.so.1.9.3 -rw-r--r-- root/root 765768 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libgamer.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libmc.so.1.9 -> libmc.so.1.9.3 -rw-r--r-- root/root 473176 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libmc.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libpunc.so.1.9 -> libpunc.so.1.9.3 -rw-r--r-- root/root 14120 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libpunc.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libvf2c.so.1.9 -> libvf2c.so.1.9.3 -rw-r--r-- root/root 105328 2024-01-19 18:56 ./usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libfetk1.9/ -rw-r--r-- root/root 3605 2024-01-19 18:56 ./usr/share/doc/libfetk1.9/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libfetk1.9/copyright drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 80 2023-01-10 18:37 ./usr/share/lintian/overrides/libfetk1.9 python3-apbslib_3.4.1-5build5_amd64.deb --------------------------------------- new Debian package, version 2.0. size 211282 bytes: control archive=2041 bytes. 920 bytes, 19 lines control 2860 bytes, 36 lines md5sums 277 bytes, 12 lines * postinst #!/bin/sh 390 bytes, 12 lines * prerm #!/bin/sh Package: python3-apbslib Source: apbs Version: 3.4.1-5build5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 1047 Depends: libapbs3 (= 3.4.1-5build5), python3 (<< 3.13), python3 (>= 3.12~), python3:any, libc6 (>= 2.32), libgcc-s1 (>= 3.3.1), libmaloc1 (>= 0.2-1), libpython3.12 (>= 3.12.1), libstdc++6 (>= 11) Section: python Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package provides both the apbs and apbslib modules for Python3 enabling Python applications to access apbs. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 334360 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbs.cpython-312-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbslib/ -rw-r--r-- root/root 23 2021-01-10 13:57 ./usr/lib/python3/dist-packages/apbslib/__init__.py -rw-r--r-- root/root 130608 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-312-x86_64-linux-gnu.so -rw-r--r-- root/root 14524 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbslib/apbslib.py drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/python-pybind/ -rw-r--r-- root/root 551 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/CMakeLists.txt -rw-r--r-- root/root 812 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_constants.hpp -rw-r--r-- root/root 4224 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.cpp -rw-r--r-- root/root 1906 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.hpp -rw-r--r-- root/root 3131 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.cpp -rw-r--r-- root/root 1018 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.hpp -rw-r--r-- root/root 1601 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.cpp -rw-r--r-- root/root 702 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.hpp -rw-r--r-- root/root 988 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/module.cpp drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/python/ -rw-r--r-- root/root 1896 2024-01-19 18:56 ./usr/share/apbs/tools/python/CMakeLists.txt -rw-r--r-- root/root 20999 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile -rw-r--r-- root/root 898 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile.am -rw-r--r-- root/root 20457 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile.in -rw-r--r-- root/root 1834 2022-04-29 18:53 ./usr/share/apbs/tools/python/README -rw-r--r-- root/root 6111 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbs.in -rw-r--r-- root/root 260435 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.c -rw-r--r-- root/root 14676 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.i -rw-r--r-- root/root 11686 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib_wrap.doc -rw-r--r-- root/root 66 2022-04-29 18:53 ./usr/share/apbs/tools/python/ion.pqr -rw-r--r-- root/root 15725 2022-04-29 18:53 ./usr/share/apbs/tools/python/main.py -rw-r--r-- root/root 19499 2024-01-19 18:56 ./usr/share/apbs/tools/python/noinput.py drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/python/vgrid/ -rw-r--r-- root/root 15551 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile -rw-r--r-- root/root 845 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.am -rw-r--r-- root/root 15036 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.in -rw-r--r-- root/root 1638 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/README -rw-r--r-- root/root 3134 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/average.py -rw-r--r-- root/root 14146 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/mergedx.py -rw-r--r-- root/root 2514 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/read.py -rw-r--r-- root/root 3038 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgrid.i -rw-r--r-- root/root 4711 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgrid.py -rw-r--r-- root/root 97354 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgridlib.c drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/python3-apbslib/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/python3-apbslib/changelog.Debian.gz -> ../libapbs3/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/python3-apbslib/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 409368 Build-Time: 277 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 25 Job: apbs_3.4.1-5build5.dsc Machine Architecture: amd64 Package: apbs Package-Time: 306 Source-Version: 3.4.1-5build5 Space: 409368 Status: successful Version: 3.4.1-5build5 -------------------------------------------------------------------------------- Finished at 2024-01-19T19:05:03Z Build needed 00:05:06, 409368k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27660350 Scanning for processes to kill in build PACKAGEBUILD-27660350