https://launchpad.net/ubuntu/+source/apbs/3.4.1-5.1ubuntu2/+build/27987125 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-007 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64le Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~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... 2 Apr 05:09:24 ntpdate[1947]: adjust time server 10.211.37.1 offset -0.003603 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27987125 --image-type chroot /home/buildd/filecache-default/d42c54d6e204d222772cc047f01d282d9c30a0e5 Creating target for build PACKAGEBUILD-27987125 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27987125 Starting target for build PACKAGEBUILD-27987125 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27987125 '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-27987125 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27987125 Updating target for build PACKAGEBUILD-27987125 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1370 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [15.2 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6115 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main ppc64el Packages [683 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe ppc64el Packages [4545 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [704 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [247 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3558 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1752 kB] Fetched 37.2 MB in 8s (4819 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: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu gcc-14-base gcc-powerpc64le-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 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-powerpc64le-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 158 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 83.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl-dev ppc64el 1.3.0-3build3 [80.3 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6-dev ppc64el 2.39-0ubuntu8 [2104 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu8 [21.3 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1.1build1 [225 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libnss-nisplus ppc64el 1.3-5build1 [27.5 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc3t64 ppc64el 1.3.4+ds-1.1build1 [102 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-6ubuntu2 [185 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5-3 ppc64el 1.20.1-6ubuntu2 [432 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libk5crypto3 ppc64el 1.20.1-6ubuntu2 [108 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5support0 ppc64el 1.20.1-6ubuntu2 [38.6 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libacl1 ppc64el 2.3.2-1 [21.4 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapparmor1 ppc64el 4.0.0-beta3-0ubuntu3 [55.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcap-ng0 ppc64el 0.8.4-2build2 [16.3 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit1 ppc64el 1:3.1.2-2.1build1 [52.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblkid1 ppc64el 2.39.3-9ubuntu4 [155 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libcap2 ppc64el 1:2.66-5ubuntu1 [35.6 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt1 ppc64el 1:4.4.36-4 [125 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgpg-error0 ppc64el 1.47-3build1 [87.6 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcrypt20 ppc64el 1.10.3-2 [745 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblzma5 ppc64el 5.6.1+really5.4.5-1build1 [160 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libzstd1 ppc64el 1.5.5+dfsg2-2 [390 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkmod2 ppc64el 31+20240202-2ubuntu5 [64.4 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-8-0 ppc64el 10.42-4ubuntu1 [263 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libselinux1 ppc64el 3.5-2ubuntu2 [101 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmount1 ppc64el 2.39.3-9ubuntu4 [169 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-iconv-perl ppc64el 1.7-8build3 [13.7 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build3 [9536 B] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-6build1 [869 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1build1 [42.0 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1build1 [6982 B] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2build1 [4962 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2build1 [231 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2build1 [1916 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblocale-gettext-perl ppc64el 1.07-6ubuntu5 [16.1 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6 ppc64el 2.39-0ubuntu8 [3275 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-bin ppc64el 2.39-0ubuntu8 [751 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu3 [1025 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd-shared ppc64el 255.4-1ubuntu6 [2350 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcryptsetup12 ppc64el 2:2.7.0-1ubuntu3 [376 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu3 [2125 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-dev all 255.4-1ubuntu6 [104 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-sysv ppc64el 255.4-1ubuntu6 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd ppc64el 255.4-1ubuntu6 [3771 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd0 ppc64el 255.4-1ubuntu6 [526 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules-bin ppc64el 1.5.3-5ubuntu4 [57.9 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules ppc64el 1.5.3-5ubuntu4 [320 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2build1 [226 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2build1 [208 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libp11-kit0 ppc64el 0.25.3-4ubuntu1 [315 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libunistring5 ppc64el 1.1-2 [556 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu3 [1055 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapt-pkg6.0t64 ppc64el 2.7.14build2 [1064 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bzip2 ppc64el 1.0.8-5.1 [37.6 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbz2-1.0 ppc64el 1.0.8-5.1 [48.7 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-14-base ppc64el 14-20240330-1ubuntu2 [47.5 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-s1 ppc64el 14-20240330-1ubuntu2 [39.3 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++6 ppc64el 14-20240330-1ubuntu2 [893 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libudev1 ppc64el 255.4-1ubuntu6 [200 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el libxxhash0 ppc64el 0.8.2-2 [30.4 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g ppc64el 1:1.3.dfsg-3.1ubuntu2 [72.8 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el libffi8 ppc64el 3.4.6-1 [27.7 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main ppc64el libidn2-0 ppc64el 2.3.7-2 [69.8 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdebconfclient0 ppc64el 0.271ubuntu3 [11.3 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main ppc64el base-passwd ppc64el 3.6.3 [52.5 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsqlite3-0 ppc64el 3.45.1-1ubuntu2 [804 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg ppc64el 2.4.4-2ubuntu16 [706 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libreadline8t64 ppc64el 8.2-4build1 [182 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el readline-common all 8.2-4build1 [56.5 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el libncursesw6 ppc64el 6.4+20240113-1ubuntu1 [186 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el libtinfo6 ppc64el 6.4+20240113-1ubuntu1 [129 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-agent ppc64el 2.4.4-2ubuntu16 [275 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgconf ppc64el 2.4.4-2ubuntu16 [115 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el pinentry-curses ppc64el 1.2.1-3ubuntu5 [38.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnpth0t64 ppc64el 1.6-3.1build1 [8914 B] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgv ppc64el 2.4.4-2ubuntu16 [198 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libseccomp2 ppc64el 2.5.5-1ubuntu3 [62.5 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apt-utils ppc64el 2.7.14build2 [226 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apt ppc64el 2.7.14build2 [1401 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main ppc64el debconf-i18n all 1.5.86 [205 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main ppc64el debconf all 1.5.86 [124 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam0g ppc64el 1.5.3-5ubuntu4 [75.8 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main ppc64el libargon2-1 ppc64el 0~20190702+dfsg-4 [27.1 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-3ubuntu3 [182 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuuid1 ppc64el 2.39.3-9ubuntu4 [39.5 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfdisk1 ppc64el 2.39.3-9ubuntu4 [171 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mount ppc64el 2.39.3-9ubuntu4 [125 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcom-err2 ppc64el 1.47.0-2.4~exp1ubuntu3 [22.9 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main ppc64el libkeyutils1 ppc64el 1.6.3-3 [11.0 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl2 ppc64el 1.3.0-3build3 [48.9 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-20.20 [1586 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el base-files ppc64el 13ubuntu9 [74.0 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debianutils ppc64el 5.17build1 [90.5 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bash ppc64el 5.2.21-2ubuntu4 [977 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdutils ppc64el 1:2.39.3-9ubuntu4 [99.0 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el coreutils ppc64el 9.4-3ubuntu5 [1523 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main ppc64el tar ppc64el 1.35+dfsg-3 [307 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg ppc64el 1.22.6ubuntu6 [1343 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dash ppc64el 0.5.12-6ubuntu5 [108 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main ppc64el diffutils ppc64el 1:3.10-1 [200 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main ppc64el grep ppc64el 3.11-4 [189 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main ppc64el gzip ppc64el 1.12-1ubuntu2 [114 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main ppc64el hostname ppc64el 3.23+nmu2ubuntu1 [11.3 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main ppc64el login ppc64el 1:4.13+dfsg1-4ubuntu1 [205 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main ppc64el ncurses-bin ppc64el 6.4+20240113-1ubuntu1 [202 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main ppc64el sed ppc64el 4.9-2 [223 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el util-linux ppc64el 2.39.3-9ubuntu4 [1195 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main ppc64el ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main ppc64el sysvinit-utils ppc64el 3.08-6ubuntu2 [35.7 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el logsave ppc64el 1.47.0-2.4~exp1ubuntu3 [23.0 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libext2fs2t64 ppc64el 1.47.0-2.4~exp1ubuntu3 [270 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs ppc64el 1.47.0-2.4~exp1ubuntu3 [663 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el optipng ppc64el 0.7.8+ds-1build2 [118 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpng16-16t64 ppc64el 1.6.43-5build1 [242 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main ppc64el init ppc64el 1.66ubuntu1 [6190 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsmartcols1 ppc64el 2.39.3-9ubuntu4 [79.2 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el uuid-runtime ppc64el 2.39.3-9ubuntu4 [33.8 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main ppc64el libattr1 ppc64el 1:2.5.2-1 [12.4 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main ppc64el libmd0 ppc64el 1.1.0-2 [30.4 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage-common all 3.5-1build5 [10.1 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main ppc64el libsepol2 ppc64el 3.5-2 [386 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage2 ppc64el 3.5-1build5 [115 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main ppc64el passwd ppc64el 1:4.13+dfsg1-4ubuntu1 [878 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu3 [68.7 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libss2 ppc64el 1.47.0-2.4~exp1ubuntu3 [18.0 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main ppc64el mawk ppc64el 1.3.4.20240123-1 [138 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el procps ppc64el 2:4.0.4-4ubuntu3 [736 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main ppc64el sensible-utils all 0.0.22 [22.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates all 20240203 [159 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main ppc64el tzdata all 2024a-1ubuntu1 [273 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main ppc64el bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdextrautils ppc64el 2.39.3-9ubuntu4 [78.9 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgpm2 ppc64el 1.20.7-11 [15.9 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main ppc64el libip4tc2 ppc64el 1.8.10-3ubuntu1 [26.9 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjansson4 ppc64el 2.14-2build2 [40.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el psmisc ppc64el 23.7-1build1 [192 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xz-utils ppc64el 5.6.1+really5.4.5-1build1 [276 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main ppc64el libctf0 ppc64el 2.42-4ubuntu2 [112 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main ppc64el libctf-nobfd0 ppc64el 2.42-4ubuntu2 [112 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42-4ubuntu2 [2473 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main ppc64el libbinutils ppc64el 2.42-4ubuntu2 [699 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils ppc64el 2.42-4ubuntu2 [3080 B] Get:151 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils-common ppc64el 2.42-4ubuntu2 [217 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main ppc64el libsframe1 ppc64el 2.42-4ubuntu2 [16.0 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libubsan1 ppc64el 14-20240330-1ubuntu2 [1194 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el g++-13 ppc64el 13.2.0-23ubuntu3 [14.5 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++-13-dev ppc64el 13.2.0-23ubuntu3 [2510 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgomp1 ppc64el 14-20240330-1ubuntu2 [161 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libitm1 ppc64el 14-20240330-1ubuntu2 [32.3 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libatomic1 ppc64el 14-20240330-1ubuntu2 [10.7 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libasan8 ppc64el 14-20240330-1ubuntu2 [2973 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblsan0 ppc64el 14-20240330-1ubuntu2 [1325 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libquadmath0 ppc64el 14-20240330-1ubuntu2 [158 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13 ppc64el 13.2.0-23ubuntu3 [479 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-13-dev ppc64el 13.2.0-23ubuntu3 [1579 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtsan2 ppc64el 14-20240330-1ubuntu2 [2700 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcc1-0 ppc64el 14-20240330-1ubuntu2 [48.4 kB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cpp-13 ppc64el 13.2.0-23ubuntu3 [1036 B] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-base ppc64el 13.2.0-23ubuntu3 [48.7 kB] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [20.6 MB] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [12.2 MB] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [10.7 MB] Get:171 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] Get:172 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] Get:173 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] Get:175 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] Get:176 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main ppc64el lto-disabled-list all 47 [12.4 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main ppc64el libfakeroot ppc64el 1.33-1 [34.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main ppc64el fakeroot ppc64el 1.33-1 [69.2 kB] Preconfiguring packages ... 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Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-6build1) ... dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm6 (>= 1.21). libgdbm-compat4:ppc64el depends on libgdbm6 (>= 1.16). (Reading database ... 14973 files and directories currently installed.) Removing libgdbm6:ppc64el (1.23-3) ... Selecting previously unselected package libgdbm6t64:ppc64el. (Reading database ... 14968 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1build1_ppc64el.deb ... Unpacking libgdbm6t64:ppc64el (1.23-5.1build1) ... dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... 14974 files and directories currently installed.) Removing libgdbm-compat4:ppc64el (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:ppc64el. (Reading database ... 14969 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_ppc64el.deb ... Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:ppc64el. Preparing to unpack .../libperl5.38t64_5.38.2-3.2build1_ppc64el.deb ... Unpacking libperl5.38t64:ppc64el (5.38.2-3.2build1) ... Preparing to unpack .../perl-base_5.38.2-3.2build1_ppc64el.deb ... Unpacking perl-base (5.38.2-3.2build1) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-3.2build1) ... (Reading database ... 15501 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu5_ppc64el.deb ... Unpacking liblocale-gettext-perl (1.07-6ubuntu5) over (1.07-6) ... Preparing to unpack .../libc6_2.39-0ubuntu8_ppc64el.deb ... Unpacking libc6:ppc64el (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc6:ppc64el (2.39-0ubuntu8) ... 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Selecting previously unselected package libssl3t64:ppc64el. (Reading database ... 15491 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_ppc64el.deb ... Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu3) ... Setting up libssl3t64:ppc64el (3.0.13-0ubuntu3) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../systemd-dev_255.4-1ubuntu6_all.deb ... Unpacking systemd-dev (255.4-1ubuntu6) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd-sysv_255.4-1ubuntu6_ppc64el.deb ... Unpacking systemd-sysv (255.4-1ubuntu6) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd_255.4-1ubuntu6_ppc64el.deb ... Unpacking systemd (255.4-1ubuntu6) 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-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 .../libsystemd0_255.4-1ubuntu6_ppc64el.deb ... Unpacking libsystemd0:ppc64el (255.4-1ubuntu6) over (253.5-1ubuntu6) ... Setting up libsystemd0:ppc64el (255.4-1ubuntu6) ... (Reading database ... 15643 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu4_ppc64el.deb ... Unpacking libpam-modules-bin (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... Setting up libpam-modules-bin (1.5.3-5ubuntu4) ... (Reading database ... 15642 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-5ubuntu4_ppc64el.deb ... Unpacking libpam-modules:ppc64el (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/powerpc64le-linux-gnu/security': Directory not empty Setting up libpam-modules:ppc64el (1.5.3-5ubuntu4) ... Installing new version of config file /etc/security/namespace.init ... dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested: libgnutls30:ppc64el depends on libhogweed6 (>= 3.6). 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Setting up libgnutls30t64:ppc64el (3.8.3-1.1ubuntu3) ... dpkg: libapt-pkg6.0:ppc64el: dependency problems, but removing anyway as you requested: apt-utils depends on libapt-pkg6.0 (>= 2.7.3). apt depends on libapt-pkg6.0 (>= 2.7.3). (Reading database ... 15648 files and directories currently installed.) Removing libapt-pkg6.0:ppc64el (2.7.3) ... Selecting previously unselected package libapt-pkg6.0t64:ppc64el. (Reading database ... 15599 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.14build2_ppc64el.deb ... Unpacking libapt-pkg6.0t64:ppc64el (2.7.14build2) ... Setting up libapt-pkg6.0t64:ppc64el (2.7.14build2) ... (Reading database ... 15649 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.8-5.1_ppc64el.deb ... Unpacking bzip2 (1.0.8-5.1) over (1.0.8-5build1) ... dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_ppc64el.deb ... Unpacking libbz2-1.0:ppc64el (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:ppc64el (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:ppc64el. (Reading database ... 15649 files and directories currently installed.) 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(Reading database ... 15654 files and directories currently installed.) Removing libreadline8:ppc64el (8.2-1.3) ... Selecting previously unselected package libreadline8t64:ppc64el. (Reading database ... 15642 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4build1_ppc64el.deb ... Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8 to /lib/powerpc64le-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8.2 to /lib/powerpc64le-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8 to /lib/powerpc64le-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8.2 to /lib/powerpc64le-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:ppc64el (8.2-4build1) ... 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Unpacking sysvinit-utils (3.08-6ubuntu2) over (3.07-1ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-6ubuntu2) ... (Reading database ... 15655 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.4~exp1ubuntu3_ppc64el.deb ... Unpacking logsave (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... dpkg: libext2fs2:ppc64el: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). (Reading database ... 15655 files and directories currently installed.) Removing libext2fs2:ppc64el (1.47.0-2ubuntu1) ... Selecting previously unselected package libext2fs2t64:ppc64el. (Reading database ... 15648 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu3_ppc64el.deb ... Adding 'diversion of /lib/powerpc64le-linux-gnu/libe2p.so.2 to /lib/powerpc64le-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libe2p.so.2.3 to /lib/powerpc64le-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libext2fs.so.2 to /lib/powerpc64le-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libext2fs.so.2.4 to /lib/powerpc64le-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:ppc64el (1.47.0-2.4~exp1ubuntu3) ... Setting up libcom-err2:ppc64el (1.47.0-2.4~exp1ubuntu3) ... Setting up libext2fs2t64:ppc64el (1.47.0-2.4~exp1ubuntu3) ... (Reading database ... 15664 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu3_ppc64el.deb ... Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty Preparing to unpack .../optipng_0.7.8+ds-1build2_ppc64el.deb ... Unpacking optipng (0.7.8+ds-1build2) over (0.7.7-2build1) ... (Reading database ... 15662 files and directories currently installed.) Removing libpng16-16:ppc64el (1.6.40-1) ... Selecting previously unselected package libpng16-16t64:ppc64el. (Reading database ... 15652 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-5build1_ppc64el.deb ... Unpacking libpng16-16t64:ppc64el (1.6.43-5build1) ... Setting up libapparmor1:ppc64el (4.0.0-beta3-0ubuntu3) ... Setting up libargon2-1:ppc64el (0~20190702+dfsg-4) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.185-3ubuntu3) ... Setting up libcryptsetup12:ppc64el (2:2.7.0-1ubuntu3) ... Setting up libfdisk1:ppc64el (2.39.3-9ubuntu4) ... Setting up libkmod2:ppc64el (31+20240202-2ubuntu5) ... Setting up libsystemd-shared:ppc64el (255.4-1ubuntu6) ... Setting up systemd-dev (255.4-1ubuntu6) ... Setting up mount (2.39.3-9ubuntu4) ... Setting up systemd (255.4-1ubuntu6) ... 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 (255.4-1ubuntu6) ... (Reading database ... 15663 files and directories currently installed.) Preparing to unpack .../init_1.66ubuntu1_ppc64el.deb ... Unpacking init (1.66ubuntu1) over (1.65.2ubuntu1) ... Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu4_ppc64el.deb ... Unpacking libsmartcols1:ppc64el (2.39.3-9ubuntu4) over (2.39.1-4ubuntu2) ... Setting up libsmartcols1:ppc64el (2.39.3-9ubuntu4) ... (Reading database ... 15664 files and directories currently installed.) Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu4_ppc64el.deb ... Unpacking uuid-runtime (2.39.3-9ubuntu4) over (2.39.1-4ubuntu2) ... dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../libattr1_1%3a2.5.2-1_ppc64el.deb ... Unpacking libattr1:ppc64el (1:2.5.2-1) over (1:2.5.1-4) ... Setting up libattr1:ppc64el (1:2.5.2-1) ... (Reading database ... 15662 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_ppc64el.deb ... Unpacking libmd0:ppc64el (1.1.0-2) over (1.1.0-1) ... Setting up libmd0:ppc64el (1.1.0-2) ... (Reading database ... 15662 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu4_all.deb ... Unpacking libpam-runtime (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... Setting up libpam-runtime (1.5.3-5ubuntu4) ... (Reading database ... 15661 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1build5_all.deb ... Unpacking libsemanage-common (3.5-1build5) over (3.5-1) ... Setting up libsemanage-common (3.5-1build5) ... (Reading database ... 15661 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_ppc64el.deb ... Unpacking libsepol2:ppc64el (3.5-2) over (3.5-1) ... Setting up libsepol2:ppc64el (3.5-2) ... (Reading database ... 15661 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1build5_ppc64el.deb ... Unpacking libsemanage2:ppc64el (3.5-1build5) over (3.5-1) ... Setting up libsemanage2:ppc64el (3.5-1build5) ... (Reading database ... 15661 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4ubuntu1_ppc64el.deb ... Unpacking passwd (1:4.13+dfsg1-4ubuntu1) over (1:4.13+dfsg1-1ubuntu1) ... Setting up passwd (1:4.13+dfsg1-4ubuntu1) ... (Reading database ... 15661 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4ubuntu3_ppc64el.deb ... Unpacking libproc2-0:ppc64el (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu3_ppc64el.deb ... Unpacking libss2:ppc64el (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... Preparing to unpack .../02-mawk_1.3.4.20240123-1_ppc64el.deb ... Unpacking mawk (1.3.4.20240123-1) over (1.3.4.20230730-1) ... Preparing to unpack .../03-procps_2%3a4.0.4-4ubuntu3_ppc64el.deb ... Unpacking procps (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../04-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) over (0.0.20) ... Preparing to unpack .../05-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) over (20230311ubuntu1) ... Preparing to unpack .../06-krb5-locales_1.20.1-6ubuntu2_all.deb ... Unpacking krb5-locales (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../07-tzdata_2024a-1ubuntu1_all.deb ... Unpacking tzdata (2024a-1ubuntu1) over (2023c-9ubuntu1) ... Preparing to unpack .../08-bash-completion_1%3a2.11-8_all.deb ... Unpacking bash-completion (1:2.11-8) over (1:2.11-7) ... Preparing to unpack .../09-bsdextrautils_2.39.3-9ubuntu4_ppc64el.deb ... Unpacking bsdextrautils (2.39.3-9ubuntu4) over (2.39.1-4ubuntu2) ... Preparing to unpack .../10-libgpm2_1.20.7-11_ppc64el.deb ... Unpacking libgpm2:ppc64el (1.20.7-11) over (1.20.7-10build1) ... Preparing to unpack .../11-libip4tc2_1.8.10-3ubuntu1_ppc64el.deb ... Unpacking libip4tc2:ppc64el (1.8.10-3ubuntu1) over (1.8.9-2ubuntu2) ... Preparing to unpack .../12-libjansson4_2.14-2build2_ppc64el.deb ... Unpacking libjansson4:ppc64el (2.14-2build2) over (2.14-2) ... Preparing to unpack .../13-psmisc_23.7-1build1_ppc64el.deb ... Unpacking psmisc (23.7-1build1) over (23.6-1) ... Preparing to unpack .../14-xz-utils_5.6.1+really5.4.5-1build1_ppc64el.deb ... Unpacking xz-utils (5.6.1+really5.4.5-1build1) over (5.4.1-0.2) ... Preparing to unpack .../15-libctf0_2.42-4ubuntu2_ppc64el.deb ... Unpacking libctf0:ppc64el (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../16-libctf-nobfd0_2.42-4ubuntu2_ppc64el.deb ... Unpacking libctf-nobfd0:ppc64el (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../17-binutils-powerpc64le-linux-gnu_2.42-4ubuntu2_ppc64el.deb ... Unpacking binutils-powerpc64le-linux-gnu (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../18-libbinutils_2.42-4ubuntu2_ppc64el.deb ... 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Preparing to unpack .../32-libgcc-13-dev_13.2.0-23ubuntu3_ppc64el.deb ... Unpacking libgcc-13-dev:ppc64el (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../33-libtsan2_14-20240330-1ubuntu2_ppc64el.deb ... Unpacking libtsan2:ppc64el (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../34-libcc1-0_14-20240330-1ubuntu2_ppc64el.deb ... Unpacking libcc1-0:ppc64el (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../35-cpp-13_13.2.0-23ubuntu3_ppc64el.deb ... Unpacking cpp-13 (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../36-gcc-13-base_13.2.0-23ubuntu3_ppc64el.deb ... Unpacking gcc-13-base:ppc64el (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. Preparing to unpack .../37-gcc-13-powerpc64le-linux-gnu_13.2.0-23ubuntu3_ppc64el.deb ... Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... 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Preparing to unpack .../50-fakeroot_1.33-1_ppc64el.deb ... Unpacking fakeroot (1.33-1) over (1.32.1-1) ... Setting up libip4tc2:ppc64el (1.8.10-3ubuntu1) ... Setting up libtext-iconv-perl:ppc64el (1.7-8build3) ... Setting up libtext-charwidth-perl:ppc64el (0.04-11build3) ... Setting up libkeyutils1:ppc64el (1.6.3-3) ... Setting up lto-disabled-list (47) ... Setting up libgpm2:ppc64el (1.20.7-11) ... Setting up libgdbm6t64:ppc64el (1.23-5.1build1) ... Setting up bsdextrautils (2.39.3-9ubuntu4) ... Setting up init (1.66ubuntu1) ... Setting up libgdbm-compat4t64:ppc64el (1.23-5.1build1) ... Setting up psmisc (23.7-1build1) ... Setting up libtirpc-common (1.3.4+ds-1.1build1) ... Setting up libsqlite3-0:ppc64el (3.45.1-1ubuntu2) ... Setting up binutils-common:ppc64el (2.42-4ubuntu2) ... Setting up linux-libc-dev:ppc64el (6.8.0-20.20) ... Setting up libctf-nobfd0:ppc64el (2.42-4ubuntu2) ... Setting up krb5-locales (1.20.1-6ubuntu2) ... Setting up libgomp1:ppc64el (14-20240330-1ubuntu2) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:ppc64el (2.42-4ubuntu2) ... Setting up libfakeroot:ppc64el (1.33-1) ... Setting up libjansson4:ppc64el (2.14-2build2) ... Setting up libkrb5support0:ppc64el (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 2 05:10:20 UTC 2024. Universal Time is now: Tue Apr 2 05:10:20 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:ppc64el (13.2.0-23ubuntu3) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.1+really5.4.5-1build1) ... Setting up perl-modules-5.38 (5.38.2-3.2build1) ... Setting up libquadmath0:ppc64el (14-20240330-1ubuntu2) ... Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:ppc64el (1.6.43-5build1) ... Setting up libatomic1:ppc64el (14-20240330-1ubuntu2) ... Setting up libss2:ppc64el (1.47.0-2.4~exp1ubuntu3) ... Setting up libncursesw6:ppc64el (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:ppc64el (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu3) ... Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-6build1) ... Setting up libubsan1:ppc64el (14-20240330-1ubuntu2) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu4) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... Setting up libasan8:ppc64el (14-20240330-1ubuntu2) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:ppc64el (1.20.1-6ubuntu2) ... Setting up libperl5.38t64:ppc64el (5.38.2-3.2build1) ... Setting up libtsan2:ppc64el (14-20240330-1ubuntu2) ... Setting up libbinutils:ppc64el (2.42-4ubuntu2) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:ppc64el (14-20240330-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up liblsan0:ppc64el (14-20240330-1ubuntu2) ... Setting up libitm1:ppc64el (14-20240330-1ubuntu2) ... Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libctf0:ppc64el (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14build2) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu3) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:ppc64el (8.2-4build1) ... Setting up libgcc-13-dev:ppc64el (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:ppc64el (2.39-0ubuntu8) ... Setting up binutils-powerpc64le-linux-gnu (2.42-4ubuntu2) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:ppc64el (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up libtirpc3t64:ppc64el (1.3.4+ds-1.1build1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:ppc64el (1.3.4+ds-1.1build1) ... Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up libnsl2:ppc64el (1.3.0-3build3) ... Setting up libnss-nisplus:ppc64el (1.3-5build1) ... Setting up g++-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:ppc64el (1.3.0-3build3) ... Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15707 files and directories currently installed.) Purging configuration files for libssl3:ppc64el (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27987125 ppc64el noble-proposed -c chroot:build-PACKAGEBUILD-27987125 --arch=ppc64el --dist=noble-proposed --nolog apbs_3.4.1-5.1ubuntu2.dsc Initiating build PACKAGEBUILD-27987125 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-ppc64el-007.buildd +==============================================================================+ | apbs 3.4.1-5.1ubuntu2 (ppc64el) Tue, 02 Apr 2024 05:10:29 +0000 | +==============================================================================+ Package: apbs Version: 3.4.1-5.1ubuntu2 Source Version: 3.4.1-5.1ubuntu2 Distribution: noble-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27987125/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-v9CwPK/resolver-YDj1jb' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- apbs_3.4.1-5.1ubuntu2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/apbs-v9CwPK/apbs-3.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-v9CwPK' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), 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 Filtered Build-Depends: dpkg-dev (>= 1.22.5), 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 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 [507 B] Get:5 copy:/<>/apt_archive ./ Packages [590 B] Fetched 2054 B in 0s (68.3 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 libnsl-dev libnsl2 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 gettext gettext-base gfortran-13 gfortran-13-powerpc64le-linux-gnu groff-base ibverbs-providers intltool-debian libamd-comgr2 libamd3 libamdhip64-5 libarchive-zip-perl libarchive13t64 libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli1 libbsd0 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcurl4t64 libcxsparse4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 libklu2 liblapack-dev liblapack3 libldap2 libldl3 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 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 libopenmpi3t64 libparu0 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librbio4 librdmacm1t64 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 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 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-docutils python3-idna python3-imagesize python3-installer python3-jinja2 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-toml python3-tz python3-urllib3 python3-wheel python3.12 python3.12-dev python3.12-minimal sgml-base sphinx-common swig 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-doc libcoarrays-dev groff lrzip liblapack-doc libjs-jquery-ui-docs 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 python-build-doc 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 libjs-mathjax python3-lib2to3 python3-sphinx-rtd-theme 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 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 gettext gettext-base gfortran-13 gfortran-13-powerpc64le-linux-gnu groff-base ibverbs-providers intltool-debian libamd-comgr2 libamd3 libamdhip64-5 libarchive-zip-perl libarchive13t64 libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli1 libbsd0 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcurl4t64 libcxsparse4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 libklu2 liblapack-dev liblapack3 libldap2 libldl3 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 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 libopenmpi3t64 libparu0 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librbio4 librdmacm1t64 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 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 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-docutils python3-idna python3-imagesize python3-installer python3-jinja2 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-toml python3-tz python3-urllib3 python3-wheel python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common swig xml-core zlib1g-dev 0 upgraded, 190 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB of archives. After this operation, 676 MB of additional disk space will be used. 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ppc64el libarchive13t64 ppc64el 3.7.2-2 [518 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbrotli1 ppc64el 1.1.0-2build2 [410 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg1-5ubuntu2 [23.4 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg1-5ubuntu2 [68.0 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libldap2 ppc64el 2.6.7+dfsg-1~exp1ubuntu7 [233 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build7 [64.4 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssh-4 ppc64el 0.10.6-2build2 [234 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl4t64 ppc64el 8.5.0-2ubuntu9 [428 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el libjsoncpp25 ppc64el 1.9.5-6 [86.8 kB] Get:57 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[5362 B] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdw1t64 ppc64el 0.190-1.1build3 [301 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debugedit ppc64el 1:5.0-5build1 [51.4 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el debhelper all 13.14.1ubuntu5 [869 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-setuptools all 68.1.2-2ubuntu1 [396 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el dh-python all 6.20240401 [110 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main ppc64el docutils-common all 0.20.1+dfsg-3 [132 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgfortran5 ppc64el 14-20240330-1ubuntu2 [575 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgfortran-13-dev ppc64el 13.2.0-23ubuntu3 [604 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gfortran-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [11.2 MB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gfortran-13 ppc64el 13.2.0-23ubuntu3 [10.9 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el libnl-3-200 ppc64el 3.7.0-0.3 [72.8 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el libnl-route-3-200 ppc64el 3.7.0-0.3 [206 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libibverbs1 ppc64el 50.0-2build2 [74.4 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ibverbs-providers ppc64el 50.0-2build2 [420 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libllvm17t64 ppc64el 1:17.0.6-9build3 [27.3 MB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3build2 [15.3 MB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsuitesparseconfig7 ppc64el 1:7.6.1+dfsg-1build1 [12.9 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libamd3 ppc64el 1:7.6.1+dfsg-1build1 [36.6 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhsakmt1 ppc64el 5.7.0-1build1 [76.4 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-2build1 [330 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libamdhip64-5 ppc64el 5.2.3-13 [5008 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libarpack2t64 ppc64el 3.9.1-1.1build2 [107 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas-dev ppc64el 3.12.0-3 [301 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack-dev ppc64el 3.12.0-3 [6100 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libarpack2-dev ppc64el 3.9.1-1.1build2 [132 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libbtf2 ppc64el 1:7.6.1+dfsg-1build1 [15.7 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libcamd3 ppc64el 1:7.6.1+dfsg-1build1 [30.7 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libccolamd3 ppc64el 1:7.6.1+dfsg-1build1 [31.3 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcolamd3 ppc64el 1:7.6.1+dfsg-1build1 [21.6 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libcholmod5 ppc64el 1:7.6.1+dfsg-1build1 [901 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libcxsparse4 ppc64el 1:7.6.1+dfsg-1build1 [101 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-2.1-7t64 ppc64el 2.1.12-stable-9ubuntu2 [174 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-core-2.1-7t64 ppc64el 2.1.12-stable-9ubuntu2 [110 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-extra-2.1-7t64 ppc64el 2.1.12-stable-9ubuntu2 [77.0 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-pthreads-2.1-7t64 ppc64el 2.1.12-stable-9ubuntu2 [8102 B] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-openssl-2.1-7t64 ppc64el 2.1.12-stable-9ubuntu2 [17.1 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-dev ppc64el 2.1.12-stable-9ubuntu2 [335 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libexpat1-dev ppc64el 2.6.1-2build1 [152 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el librdmacm1t64 ppc64el 50.0-2build2 [80.9 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libfabric1 ppc64el 1.17.0-3build2 [694 kB] Get:115 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:117 http://ftpmaster.internal/ubuntu noble/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-6 [149 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libklu2 ppc64el 1:7.6.1+dfsg-1build1 [99.7 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libldl3 ppc64el 1:7.6.1+dfsg-1build1 [15.4 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main ppc64el libltdl7 ppc64el 2.4.7-7 [48.0 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main ppc64el libltdl-dev ppc64el 2.4.7-7 [178 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libmaloc1 ppc64el 1.5-1build2 [103 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libmaloc-dev ppc64el 1.5-1build2 [120 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main ppc64el libnl-3-dev ppc64el 3.7.0-0.3 [130 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main ppc64el libnl-route-3-dev ppc64el 3.7.0-0.3 [258 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libmunge2 ppc64el 0.5.15-4build1 [17.7 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu4 [12.6 kB] Get:132 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] Get:133 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1build1 [765 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libucx0 ppc64el 1.16.0+ds-4build1 [1203 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-7ubuntu2 [2721 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libumfpack6 ppc64el 1:7.6.1+dfsg-1build1 [323 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libparu0 ppc64el 1:7.6.1+dfsg-1build1 [62.1 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main ppc64el libpkgconf3 ppc64el 1.8.1-2 [36.9 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main ppc64el libnuma-dev ppc64el 2.0.18-1 [45.6 kB] Get:141 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-dev ppc64el 2.10.0-1 [316 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3.1ubuntu2 [902 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix-dev ppc64el 5.0.1-4.1build1 [4143 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12t64 ppc64el 3.12.2-4build4 [2551 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-dev ppc64el 3.12.2-4build4 [6116 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3-dev ppc64el 3.12.2-0ubuntu2 [10.1 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el librbio4 ppc64el 1:7.6.1+dfsg-1build1 [35.6 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libspex2 ppc64el 1:7.6.1+dfsg-1build1 [40.9 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libspqr4 ppc64el 1:7.6.1+dfsg-1build1 [184 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libsuitesparse-mongoose3 ppc64el 1:7.6.1+dfsg-1build1 [43.3 kB] Get:151 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libsuitesparse-dev ppc64el 1:7.6.1+dfsg-1build1 [2036 kB] Get:152 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsuperlu6 ppc64el 6.0.1+dfsg1-1 [234 kB] Get:153 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsuperlu-dev ppc64el 6.0.1+dfsg1-1 [20.7 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-common all 4.1.6-7ubuntu2 [170 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-bin ppc64el 4.1.6-7ubuntu2 [118 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf-bin ppc64el 1.8.1-2 [22.0 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf ppc64el 1.8.1-2 [16.7 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main ppc64el pkg-config ppc64el 1.8.1-2 [7170 B] Get:159 http://ftpmaster.internal/ubuntu noble/universe ppc64el pybind11-dev all 2.11.1-2 [159 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] Get:161 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pyproject-hooks all 1.0.0-2 [9434 B] Get:162 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-toml all 0.10.2-1 [16.5 kB] Get:163 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-wheel all 0.42.0-2 [53.1 kB] Get:164 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-build all 1.0.3-2 [27.3 kB] Get:165 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-installer all 0.7.0+dfsg1-2 [18.1 kB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el pybuild-plugin-pyproject all 6.20240401 [1726 B] Get:167 http://ftpmaster.internal/ubuntu noble/main ppc64el python-babel-localedata all 2.10.3-3build1 [6357 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tz all 2024.1-2 [31.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-babel all 2.10.3-3build1 [87.5 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-certifi all 2023.11.17-1 [165 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12-dev ppc64el 3.12.2-4build4 [498 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-dev ppc64el 3.12.2-0ubuntu2 [26.7 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-roman all 3.3-3 [9632 B] Get:175 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-docutils all 0.20.1+dfsg-3 [393 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-idna all 3.6-2 [46.0 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-imagesize all 1.4.1-1 [6844 B] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-markupsafe ppc64el 2.1.5-1build2 [13.3 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-jinja2 all 3.1.2-1ubuntu1 [107 kB] Get:180 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pybind11 all 2.11.1-2 [167 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-urllib3 all 2.0.7-1 [113 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:183 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-snowballstemmer all 2.2.0-4 [59.7 kB] Get:184 http://ftpmaster.internal/ubuntu noble/main ppc64el sphinx-common all 7.2.6-6 [739 kB] Get:185 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-alabaster all 0.7.12-1 [17.8 kB] Get:186 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-sphinx all 7.2.6-6 [557 kB] Get:187 http://ftpmaster.internal/ubuntu noble/universe ppc64el swig ppc64el 4.2.0-2ubuntu1 [1261 kB] Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libibverbs-dev ppc64el 50.0-2build2 [743 kB] Get:189 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi-dev ppc64el 4.1.6-7ubuntu2 [866 kB] Get:190 http://ftpmaster.internal/ubuntu noble/universe ppc64el mpi-default-dev ppc64el 1.15 [3120 B] Preconfiguring packages ... Fetched 157 MB in 8s (20.9 MB/s) Selecting previously unselected package libpython3.12-minimal:ppc64el. (Reading database ... 15707 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-4build4_ppc64el.deb ... Unpacking libpython3.12-minimal:ppc64el (3.12.2-4build4) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.6.1-2build1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-4build4_ppc64el.deb ... Unpacking python3.12-minimal (3.12.2-4build4) ... Setting up libpython3.12-minimal:ppc64el (3.12.2-4build4) ... Setting up libexpat1:ppc64el (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.2-4build4) ... Selecting previously unselected package python3-minimal. (Reading database ... 16025 files and directories currently installed.) 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Setting up python3-minimal (3.12.2-0ubuntu2) ... Selecting previously unselected package python3. (Reading database ... 16465 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.2-0ubuntu2_ppc64el.deb ... Unpacking python3 (3.12.2-0ubuntu2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../002-libbsd0_0.12.1-1build1_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.12.1-1build1) ... Selecting previously unselected package libelf1t64:ppc64el. Preparing to unpack .../003-libelf1t64_0.190-1.1build3_ppc64el.deb ... Unpacking libelf1t64:ppc64el (0.190-1.1build3) ... Selecting previously unselected package libicu74:ppc64el. Preparing to unpack .../004-libicu74_74.2-1ubuntu1_ppc64el.deb ... Unpacking libicu74:ppc64el (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. 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Selecting previously unselected package libblas3:ppc64el. Preparing to unpack .../083-libblas3_3.12.0-3_ppc64el.deb ... Unpacking libblas3:ppc64el (3.12.0-3) ... Selecting previously unselected package liblapack3:ppc64el. Preparing to unpack .../084-liblapack3_3.12.0-3_ppc64el.deb ... Unpacking liblapack3:ppc64el (3.12.0-3) ... Selecting previously unselected package libarpack2t64:ppc64el. Preparing to unpack .../085-libarpack2t64_3.9.1-1.1build2_ppc64el.deb ... Unpacking libarpack2t64:ppc64el (3.9.1-1.1build2) ... Selecting previously unselected package libblas-dev:ppc64el. Preparing to unpack .../086-libblas-dev_3.12.0-3_ppc64el.deb ... Unpacking libblas-dev:ppc64el (3.12.0-3) ... Selecting previously unselected package liblapack-dev:ppc64el. Preparing to unpack .../087-liblapack-dev_3.12.0-3_ppc64el.deb ... Unpacking liblapack-dev:ppc64el (3.12.0-3) ... Selecting previously unselected package libarpack2-dev:ppc64el. 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Selecting previously unselected package libpciaccess0:ppc64el. Preparing to unpack .../119-libpciaccess0_0.17-3_ppc64el.deb ... Unpacking libpciaccess0:ppc64el (0.17-3) ... Selecting previously unselected package libxnvctrl0:ppc64el. Preparing to unpack .../120-libxnvctrl0_510.47.03-0ubuntu4_ppc64el.deb ... Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... Selecting previously unselected package ocl-icd-libopencl1:ppc64el. Preparing to unpack .../121-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... Selecting previously unselected package libhwloc-plugins:ppc64el. Preparing to unpack .../122-libhwloc-plugins_2.10.0-1_ppc64el.deb ... Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... Selecting previously unselected package libpmix2t64:ppc64el. Preparing to unpack .../123-libpmix2t64_5.0.1-4.1build1_ppc64el.deb ... Unpacking libpmix2t64:ppc64el (5.0.1-4.1build1) ... Selecting previously unselected package libucx0:ppc64el. Preparing to unpack .../124-libucx0_1.16.0+ds-4build1_ppc64el.deb ... Unpacking libucx0:ppc64el (1.16.0+ds-4build1) ... Selecting previously unselected package libopenmpi3t64:ppc64el. Preparing to unpack .../125-libopenmpi3t64_4.1.6-7ubuntu2_ppc64el.deb ... Unpacking libopenmpi3t64:ppc64el (4.1.6-7ubuntu2) ... Selecting previously unselected package libumfpack6:ppc64el. Preparing to unpack .../126-libumfpack6_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... Unpacking libumfpack6:ppc64el (1:7.6.1+dfsg-1build1) ... Selecting previously unselected package libparu0:ppc64el. Preparing to unpack .../127-libparu0_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... Unpacking libparu0:ppc64el (1:7.6.1+dfsg-1build1) ... Selecting previously unselected package libpkgconf3:ppc64el. Preparing to unpack .../128-libpkgconf3_1.8.1-2_ppc64el.deb ... Unpacking libpkgconf3:ppc64el (1.8.1-2) ... Selecting previously unselected package libnuma-dev:ppc64el. Preparing to unpack .../129-libnuma-dev_2.0.18-1_ppc64el.deb ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../180-sbuild-build-depends-main-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libmaloc1 (1.5-1build2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:ppc64el (1.5.7-2) ... Setting up libpciaccess0:ppc64el (0.17-3) ... Setting up libxau6:ppc64el (1:1.0.9-1build5) ... Setting up swig (4.2.0-2ubuntu1) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libcbor0.10:ppc64el (0.10.2-1.2ubuntu2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libbrotli1:ppc64el (1.1.0-2build2) ... Setting up libuv1t64:ppc64el (1.48.0-1.1build1) ... Setting up libmagic1t64:ppc64el (1:5.45-3build1) ... Setting up libcxsparse4:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libpsl5t64:ppc64el (0.21.2-1.1build1) ... Setting up libnghttp2-14:ppc64el (1.59.0-1build2) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:ppc64el (2.1.12-stable-9ubuntu2) ... Setting up libldl3:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up file (1:5.45-3build1) ... Setting up libelf1t64:ppc64el (0.190-1.1build3) ... Setting up python-babel-localedata (2.10.3-3build1) ... Setting up libdw1t64:ppc64el (0.190-1.1build3) ... Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg1-5ubuntu2) ... Setting up libbtf2:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:ppc64el (3.12.0-3) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Setting up libpkgconf3:ppc64el (1.8.1-2) ... Setting up libmunge2:ppc64el (0.5.15-4build1) ... Setting up libexpat1-dev:ppc64el (2.6.1-2build1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libhwloc15:ppc64el (2.10.0-1) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libjsoncpp25:ppc64el (1.9.5-6) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libltdl7:ppc64el (2.4.7-7) ... Setting up libsasl2-2:ppc64el (2.1.28+dfsg1-5ubuntu2) ... Setting up libssh-4:ppc64el (0.10.6-2build2) ... Setting up libgfortran5:ppc64el (14-20240330-1ubuntu2) ... Setting up autoconf (2.71-3) ... Setting up libicu74:ppc64el (74.2-1ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3.1ubuntu2) ... Setting up libnuma1:ppc64el (2.0.18-1) ... Setting up dwz (0.15-1build6) ... Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... Setting up librhash0:ppc64el (1.4.3-3) ... Setting up libuchardet0:ppc64el (0.0.8-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:ppc64el (3.7.0-0.3) ... Setting up openmpi-common (4.1.6-7ubuntu2) ... Setting up debugedit (1:5.0-5build1) ... Setting up libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.28.3-1build6) ... Setting up libevent-core-2.1-7t64:ppc64el (2.1.12-stable-9ubuntu2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:ppc64el (1.14.0-1build2) ... Setting up libgfortran-13-dev:ppc64el (13.2.0-23ubuntu3) ... Setting up libbsd0:ppc64el (0.12.1-1build1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu3) ... Setting up libmaloc-dev (1.5-1build2) ... Setting up libldap2:ppc64el (2.6.7+dfsg-1~exp1ubuntu7) ... Setting up libblas-dev:ppc64el (3.12.0-3) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... 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 libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Setting up liblapack3:ppc64el (3.12.0-3) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up libxcb1:ppc64el (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libarpack2t64:ppc64el (3.9.1-1.1build2) ... Setting up gfortran-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up libamd3:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libpython3.12-stdlib:ppc64el (3.12.2-4build4) ... Setting up libcurl4t64:ppc64el (8.5.0-2ubuntu9) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libsuitesparse-mongoose3:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libevent-pthreads-2.1-7t64:ppc64el (2.1.12-stable-9ubuntu2) ... Setting up python3.12 (3.12.2-4build4) ... Setting up libedit2:ppc64el (3.1-20230828-1) ... Setting up libevent-openssl-2.1-7t64:ppc64el (2.1.12-stable-9ubuntu2) ... Setting up libsuperlu6:ppc64el (6.0.1+dfsg1-1) ... Setting up libcamd3:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up pkgconf:ppc64el (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:ppc64el (2.0.18-1) ... Setting up libnl-route-3-200:ppc64el (3.7.0-0.3) ... Setting up libpython3.12t64:ppc64el (3.12.2-4build4) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:ppc64el (2.4.7-7) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:ppc64el (1:17.0.6-9build3) ... Setting up gfortran-13 (13.2.0-23ubuntu3) ... Setting up librbio4:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up liblapack-dev:ppc64el (3.12.0-3) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode Setting up pkg-config:ppc64el (1.8.1-2) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libevent-extra-2.1-7t64:ppc64el (2.1.12-stable-9ubuntu2) ... Setting up libccolamd3:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:ppc64el (2.4.120-2) ... Setting up libnl-3-dev:ppc64el (3.7.0-0.3) ... Setting up groff-base (1.23.0-3build2) ... Setting up xml-core (0.19) ... Setting up libx11-6:ppc64el (2:1.8.7-1) ... Setting up libhwloc-dev:ppc64el (2.10.0-1) ... Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3build2) ... Setting up libsuperlu-dev:ppc64el (6.0.1+dfsg1-1) ... Setting up libarchive13t64:ppc64el (3.7.2-2) ... Setting up libpython3-stdlib:ppc64el (3.12.2-0ubuntu2) ... Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... Setting up libibverbs1:ppc64el (50.0-2build2) ... Setting up libcholmod5:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libarpack2-dev:ppc64el (3.9.1-1.1build2) ... Setting up libspex2:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up ibverbs-providers:ppc64el (50.0-2build2) ... Setting up libspqr4:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up openssh-client (1:9.6p1-3ubuntu12) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:ppc64el (2:1.3.4-1build1) ... Setting up python3 (3.12.2-0ubuntu2) ... Setting up libpython3.12-dev:ppc64el (3.12.2-4build4) ... Setting up man-db (2.12.0-4build1) ... 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 (2.1.5-1build2) ... Setting up python3-wheel (0.42.0-2) ... Setting up python3-tz (2024.1-2) ... Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu4) ... Setting up libnl-route-3-dev:ppc64el (3.7.0-0.3) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1ubuntu1) ... 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:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libevent-dev (2.1.12-stable-9ubuntu2) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.2-4build4) ... 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:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up cmake (3.28.3-1build6) ... Setting up librdmacm1t64:ppc64el (50.0-2build2) ... Setting up python3-build (1.0.3-2) ... Setting up libhsakmt1:ppc64el (5.7.0-1build1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libfabric1:ppc64el (1.17.0-3build2) ... Setting up libpython3-dev:ppc64el (3.12.2-0ubuntu2) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... 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 debhelper (13.14.1ubuntu5) ... Setting up libparu0:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up libibverbs-dev:ppc64el (50.0-2build2) ... Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.12.2-0ubuntu2) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up libpmix2t64:ppc64el (5.0.1-4.1build1) ... Setting up libhsa-runtime64-1 (5.7.1-2build1) ... Setting up libpmix-dev:ppc64el (5.0.1-4.1build1) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20240401) ... Setting up libsuitesparse-dev:ppc64el (1:7.6.1+dfsg-1build1) ... Setting up pybuild-plugin-pyproject (6.20240401) ... Setting up libamdhip64-5 (5.2.3-13) ... Setting up libucx0:ppc64el (1.16.0+ds-4build1) ... Setting up libopenmpi3t64:ppc64el (4.1.6-7ubuntu2) ... Setting up openmpi-bin (4.1.6-7ubuntu2) ... 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:ppc64el (4.1.6-7ubuntu2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openmpi/include to provide /usr/include/powerpc64le-linux-gnu/mpi (mpi-powerpc64le-linux-gnu) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for systemd (255.4-1ubuntu6) ... 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 (7.2.6-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64el (ppc64le) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-powerpc64le-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu4 bsdutils_1:2.39.3-9ubuntu4 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 cmake_3.28.3-1build6 cmake-data_3.28.3-1build6 coreutils_9.4-3ubuntu5 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu3 cpp-13-powerpc64le-linux-gnu_13.2.0-23ubuntu3 cpp-powerpc64le-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-python_6.20240401 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu3 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu3 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pinentry-curses_1.2.1-3ubuntu5 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_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 pybind11-dev_2.11.1-2 pybuild-plugin-pyproject_6.20240401 python-babel-localedata_2.10.3-3build1 python3_3.12.2-0ubuntu2 python3-alabaster_0.7.12-1 python3-babel_2.10.3-3build1 python3-build_1.0.3-2 python3-certifi_2023.11.17-1 python3-chardet_5.2.0+dfsg-1 python3-dev_3.12.2-0ubuntu2 python3-docutils_0.20.1+dfsg-3 python3-idna_3.6-2 python3-imagesize_1.4.1-1 python3-installer_0.7.0+dfsg1-2 python3-jinja2_3.1.2-1ubuntu1 python3-markupsafe_2.1.5-1build2 python3-minimal_3.12.2-0ubuntu2 python3-packaging_23.2-1 python3-pkg-resources_68.1.2-2ubuntu1 python3-pybind11_2.11.1-2 python3-pygments_2.17.2+dfsg-1 python3-pyproject-hooks_1.0.0-2 python3-requests_2.31.0+dfsg-1ubuntu1 python3-roman_3.3-3 python3-setuptools_68.1.2-2ubuntu1 python3-snowballstemmer_2.2.0-4 python3-sphinx_7.2.6-6 python3-toml_0.10.2-1 python3-tz_2024.1-2 python3-urllib3_2.0.7-1 python3-wheel_0.42.0-2 python3.12_3.12.2-4build4 python3.12-dev_3.12.2-4build4 python3.12-minimal_3.12.2-4build4 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sgml-base_1.31 sphinx-common_7.2.6-6 swig_4.2.0-2ubuntu1 systemd_255.4-1ubuntu6 systemd-dev_255.4-1ubuntu6 systemd-sysv_255.4-1ubuntu6 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu4 uuid-runtime_2.39.3-9ubuntu4 xml-core_0.19 xz-utils_5.6.1+really5.4.5-1build1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: apbs Binary: apbs, python3-apbslib, libapbs-dev, libapbs3t64, apbs-data, apbs-doc, libfetk-dev, libfetk1.9t64 Architecture: any all Version: 3.4.1-5.1ubuntu2 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: dpkg-dev (>= 1.22.5), 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 libapbs3t64 deb libs optional arch=any libfetk-dev deb libdevel optional arch=any libfetk1.9t64 deb libs optional arch=any python3-apbslib deb python optional arch=any Checksums-Sha1: 584fd36dc1424cb22fd8846f1cf2c7ead60ce0c6 85806314 apbs_3.4.1.orig.tar.gz c7015e0b69d57e9d2a7064382ddda314a0235e2a 20426692 apbs_3.4.1-5.1ubuntu2.debian.tar.xz Checksums-Sha256: 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2 85806314 apbs_3.4.1.orig.tar.gz d3b0ec29894c276ef5c848d3ceff119303035c99f5c00476bd31ea77fc1ad91c 20426692 apbs_3.4.1-5.1ubuntu2.debian.tar.xz Files: 5d2af7c3592f8c410a5df39887361520 85806314 apbs_3.4.1.orig.tar.gz 5299f4a54dd8368c2c05f697945c773d 20426692 apbs_3.4.1-5.1ubuntu2.debian.tar.xz Original-Maintainer: Debichem Team -----BEGIN PGP SIGNATURE----- iQJOBAEBCgA4FiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmYJn+UaHHN0ZXZlLmxh bmdhc2VrQHVidW50dS5jb20ACgkQVo0w8yGyEz33ghAAg34l8w8jt2y2e6D0k2LG mTSQUrKSPSjtVj0pOomyxHASQxMK3yQi4RTHh80H91Qghp+1Se75GqhapuoQtIqS 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dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-5.1ubuntu2.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-27987125 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27987125 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27987125 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 3.4.1-5.1ubuntu2 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el 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-arch dh build-arch --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -a -O--buildsystem=cmake cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf -a -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-powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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-powerpc64le-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-powerpc64le-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/powerpc64le-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/powerpc64le-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/powerpc64le-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/powerpc64le-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/powerpc64le-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/powerpc64le-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/powerpc64le-linux-gnu/librt.a -- Adding librt: /usr/lib/powerpc64le-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-powerpc64le-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: 2024-03-31T17:39:33 -- ** 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/powerpc64le-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/powerpc64le-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/powerpc64le-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/powerpc64le-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/powerpc64le-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/powerpc64le-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/powerpc64le-linux-gnu/librt.a -- Adding librt: /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 "4.2.0") -- Found Python3: /usr/bin/python3 (found suitable version "3.12.2", 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/powerpc64le-linux-gnu/libpython3.12.so -- ***** Python3 library dir is: /usr/lib/powerpc64le-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 "3.12.2", minimum required is "3.6") -- Found PythonLibs: /usr/lib/powerpc64le-linux-gnu/libpython3.12.so -- Found pybind11: /usr/include (found version "2.11.1") -- LIBS mc;util;dl;m;stdc++;/usr/lib/powerpc64le-linux-gnu/libumfpack.so;/usr/lib/powerpc64le-linux-gnu/libspqr.so;/usr/lib/powerpc64le-linux-gnu/libcholmod.so;/usr/lib/powerpc64le-linux-gnu/libccolamd.so;/usr/lib/powerpc64le-linux-gnu/libcamd.so;/usr/lib/powerpc64le-linux-gnu/libcolamd.so;/usr/lib/powerpc64le-linux-gnu/libamd.so;/usr/lib/powerpc64le-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/powerpc64le-linux-gnu/libblas.so;/usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so;/usr/lib/powerpc64le-linux-gnu/librt.a;/usr/lib/powerpc64le-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 "3.12.2") 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 (18.9s) -- Generating done (0.4s) 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-powerpc64le-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -a -O--buildsystem=cmake cd obj-powerpc64le-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-powerpc64le-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-powerpc64le-linux-gnu/CMakeFiles /<>/obj-powerpc64le-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-powerpc64le-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[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src/cgcode /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src/cgcode /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake "--color=" make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src/vf2c /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src/vf2c /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake "--color=" make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/gamer/src /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake "--color=" make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/tools/python /<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake "--color=" 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]: Leaving directory '/<>/obj-powerpc64le-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 make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' Dependee "/<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Dependee "/<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' Scanning dependencies of target apbslib_swig_compilation [ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o [ 0%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 1%] Swig compile apbslib.i for python cd /<>/obj-powerpc64le-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /<>/obj-powerpc64le-linux-gnu/tools/python /<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/_apbslib.dir cd /<>/obj-powerpc64le-linux-gnu/tools/python && /usr/bin/cmake -E touch /<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp cd /<>/obj-powerpc64le-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /<>/obj-powerpc64le-linux-gnu/tools/python -interface _apbslib -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/python3.12 -I/<>/tools/python -o /<>/obj-powerpc64le-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /<>/tools/python/apbslib.i [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/cgcode/CMakeFiles/cgcode.dir/scr.c.o [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 4%] Built target apbslib_swig_compilation [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/signal_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/spcgnr.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 7%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 7%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/spcgca.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/sig_die.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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_ci.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 24%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 29%] Linking C shared library libcgcode.so cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /usr/src/apbs-3.4.1-5.1ubuntu2/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-3.4.1-5.1ubuntu2/debian/external_deps/fetk/punc/src/cgcode/sratqr.c:12:22: note: ‘sratqr_’ was previously declared here /usr/src/apbs-3.4.1-5.1ubuntu2/debian/external_deps/fetk/punc/src/cgcode/sratqr.c:12:22: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [ 35%] Built target cgcode [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 *"); | ^~~~~~~~~ /<>/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"); | ^~~~~ [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 45%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o [ 46%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /<>/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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/ReadLattice.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 51%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 52%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /<>/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"); | ^~~~~~~~ [ 53%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 54%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 55%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 56%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 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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-powerpc64le-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-powerpc64le-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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-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-powerpc64le-linux-gnu' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /<>/obj-powerpc64le-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-powerpc64le-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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/mc/src /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-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-powerpc64le-linux-gnu' [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/bam/bmat.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/bmat.c: In function ‘Bmat_ctor’: /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 2147483646] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 3] In file included from /usr/include/stdio.h:980, 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_ctor’ at /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17: /usr/include/powerpc64le-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 22 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_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:980, 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/powerpc64le-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/powerpc64le-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/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/powerpc64le-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/powerpc64le-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/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 function ‘sprintf’, inlined from ‘Bmat_galerkin’ at /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/powerpc64le-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_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/powerpc64le-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/powerpc64le-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/mat.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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 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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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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 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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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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_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:980, 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/powerpc64le-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/powerpc64le-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/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/powerpc64le-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/powerpc64le-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:980, 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/powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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:980, 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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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:980, 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/powerpc64le-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/powerpc64le-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/powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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, | ^~~~~~~~~~~ /<>/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:980, 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/powerpc64le-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/powerpc64le-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 ()); | ~~~~~~~~~~~~~~~~~ [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src 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-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/nsolv.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src 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-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 [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/powerpc64le-linux-gnu/libblas.so -lmaloc /usr/lib/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-3.4.1-5.1ubuntu2/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/powerpc64le-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-3.4.1-5.1ubuntu2/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/powerpc64le-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-powerpc64le-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-powerpc64le-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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/generic /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/src/generic /<>/obj-powerpc64le-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/pmgc /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/src/pmgc /<>/obj-powerpc64le-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o cd /<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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 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cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-linux-gnu/_deps/fetk-build/mc/src 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-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 [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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 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/<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src 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/<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src 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&& /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 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-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-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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-powerpc64le-linux-gnu' [ 79%] Built target gamer [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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%] Linking C shared library libapbs_generic.so cd /<>/obj-powerpc64le-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libblas.so [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-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-powerpc64le-linux-gnu' [ 84%] Built target apbs_generic [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /<>/obj-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/fem /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/src/fem /<>/obj-powerpc64le-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /<>/obj-powerpc64le-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-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:980, 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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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-powerpc64le-linux-gnu/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-powerpc64le-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-powerpc64le-linux-gnu' [ 86%] Built target apbs_fem cd /<>/obj-powerpc64le-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-powerpc64le-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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/mg /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/src/mg /<>/obj-powerpc64le-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /<>/obj-powerpc64le-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /<>/obj-powerpc64le-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 cd /<>/obj-powerpc64le-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /<>/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-powerpc64le-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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:184:12: note: in a call to function ‘fclose’ declared ‘nonnull’ 184 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 87%] Linking C shared library libapbs_mg.so cd /<>/obj-powerpc64le-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-powerpc64le-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-powerpc64le-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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/src /<>/obj-powerpc64le-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /<>/obj-powerpc64le-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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:980, 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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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-powerpc64le-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-powerpc64le-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-powerpc64le-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/src /<>/obj-powerpc64le-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/tools/mesh /<>/obj-powerpc64le-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake "--color=" 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-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/tools/mesh /<>/obj-powerpc64le-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/tools/mesh /<>/obj-powerpc64le-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu/src && /usr/bin/cc -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build [ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd 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-I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse 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-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 [ 89%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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 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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-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 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../bin/dxmath cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 /usr/bin/cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libarpack.so 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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 [ 94%] Linking C executable ../bin/analysis cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1 make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 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-fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so 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'/<>/obj-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 96%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/tools/mesh /<>/obj-powerpc64le-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 97%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /<>/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-powerpc64le-linux-gnu' [ 97%] Built target dx2uhbd make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/tools/mesh /<>/obj-powerpc64le-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 97%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-linux-gnu/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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 /<>/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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking C executable ../bin/del2dx cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp /<>/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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking C executable ../bin/tensor2dx cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 [ 98%] Linking C executable ../bin/uhbd_asc2bin cd /<>/obj-powerpc64le-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-linux-gnu/libsuperlu.so 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'/<>/obj-powerpc64le-linux-gnu' [ 99%] Built target born [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /<>/obj-powerpc64le-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [100%] Built target _apbslib [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /<>/obj-powerpc64le-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/powerpc64le-linux-gnu/openmpi/include -I/usr/lib/powerpc64le-linux-gnu/openmpi/include/openmpi -I/<>/src -I/<>/obj-powerpc64le-linux-gnu/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-powerpc64le-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-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-linux-gnu.so cd /<>/obj-powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5.1ubuntu2 -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-powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so /usr/lib/powerpc64le-linux-gnu/libblas.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libarpack.so /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libumfpack.so /usr/lib/powerpc64le-linux-gnu/libspqr.so /usr/lib/powerpc64le-linux-gnu/libcholmod.so /usr/lib/powerpc64le-linux-gnu/libccolamd.so /usr/lib/powerpc64le-linux-gnu/libcamd.so /usr/lib/powerpc64le-linux-gnu/libcolamd.so /usr/lib/powerpc64le-linux-gnu/libamd.so -lm -ldl /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/libsuitesparseconfig.so /usr/lib/powerpc64le-linux-gnu/librt.a /usr/lib/powerpc64le-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-powerpc64le-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3,sphinxdoc --buildsystem=cmake dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install -a -O--buildsystem=cmake cd obj-powerpc64le-linux-gnu && make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-powerpc64le-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-powerpc64le-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 -- 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-- Installing: /<>/debian/tmp/usr/include/punc/vf2c.h -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libvf2c.so -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libgamer.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libgamer.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-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 -- 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/<>/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/powerpc64le-linux-gnu/libapbs_generic.so.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libapbs_pmgc.so.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libapbs_mg.so.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libapbs_fem.so.3 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libapbs_fem.so -- Installing: /<>/debian/tmp/usr/lib/apbs.cpython-312-powerpc64le-linux-gnu.so -- Installing: /<>/debian/tmp/usr/share/apbs/examples -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- 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/Apbs_solv-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/run_selected_examples.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.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_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -- 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/prot3.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/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/run_examples.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/README.md -- 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/geoflow -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa -- 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-noASP66.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/2LZT-noASH66.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-ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.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/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/lys.param -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.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.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.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_stern.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.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_2.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.config -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr -- 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.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/dmso-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -- 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.inp -- 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.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind -- 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/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -- 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.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/README.md -- 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/fas2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/mache.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize -- 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/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.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.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -- 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.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr -- 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/1d30.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/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/apbs_dx.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/test.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/model_outNB.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py -- 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/postprocess.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD -- 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/UHBD/solv.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/pmf.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD -- 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/UHBD/491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr -- 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/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh -- 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/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in -- 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/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tests -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_results.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_logger.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/test_cases.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_tester.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/smooth.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.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/mgmesh.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/value.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/analysis.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/similarity.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- 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/pot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/born.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/psize.py -- 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/manip/coulomb.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk -- 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/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/amber2uhbd.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/module.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 -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/main.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt -- 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/vgrid -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.i -- 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/getReleases.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/release-data.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin -- 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/dx2mol -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/analysis -- 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/benchmark -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/similarity make[1]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/<>' (cd tests; PATH=/<>/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/<>/debian/tmp/usr/lib/powerpc64le-linux-gnu:${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: 0.002009 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in 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: 3.059484 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in 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: 3.365668 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Processor 2 results: 2.401768459091e+02 8.142935605695e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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 = 8.142935605695E+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! 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'] Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344953e+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: 18.600223 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 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: 14.25883 seconds -------------------------------------------------------------------------------- Total elapsed time: 39.286214 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 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 Mar 31 2024 at 17:39:33 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) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+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! Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 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 3257.1427835730997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867462003 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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'] 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 (1.048683058621e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 106.352733 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in 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 (1.095841077688e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 76.099956 seconds -------------------------------------------------------------------------------- Total elapsed time: 182.452689 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in 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: 16.275984 seconds -------------------------------------------------------------------------------- Total elapsed time: 16.275984 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 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 Mar 31 2024 at 17:39:33 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) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+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! 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, 104.8683058621] 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 104.8683058621 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 Mar 31 2024 at 17:39:33 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) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+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! 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, 109.5841077688] 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 109.5841077688 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 Mar 31 2024 at 17:39:33 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! 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'] 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 (1.500810086373e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 16.682385 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in 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 (1.624454192074e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 14.370012 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in 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 (1.442499933664e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 15.990271 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 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 Mar 31 2024 at 17:39:33 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) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+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! 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, 15.00810086373] 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 15.00810086373 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 Mar 31 2024 at 17:39:33 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) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+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! 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, 16.24454192074] 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 16.24454192074 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 Mar 31 2024 at 17:39:33 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) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+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! 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, 14.42499933664] 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 14.42499933664 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] 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 (1.545150742843e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 13.199727 seconds -------------------------------------------------------------------------------- Total elapsed time: 60.242395 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in 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 (-5.246475812684e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 15.39531 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in 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 (-5.405979017059e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 11.46561 seconds -------------------------------------------------------------------------------- Total elapsed time: 26.86092 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 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 Mar 31 2024 at 17:39:33 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) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+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! 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, 15.45150742843] 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 15.45150742843 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 Mar 31 2024 at 17:39:33 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) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+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! 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, -52.46475812684] 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 -52.46475812684 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 Mar 31 2024 at 17:39:33 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) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+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! 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, -54.05979017059] 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 -54.05979017059 Running tests for ionize section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] 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: 7.201788 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in 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: 5.804869 seconds -------------------------------------------------------------------------------- Total elapsed time: 13.006657 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in 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: 10.078339 seconds -------------------------------------------------------------------------------- Total elapsed time: 10.078339 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in 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 (8.083515648803e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 15.869959 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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 9.128e-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 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-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 -2.768e-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: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+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 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+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 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-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 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-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! Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65306965532 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 Mar 31 2024 at 17:39:33 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) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+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! 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, 8.083515648803] 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 8.083515648803 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] 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 (2.096300255720e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 11.964181 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in 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 (1.192607686582e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 12.683976 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in 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: 10.466458 seconds -------------------------------------------------------------------------------- Total elapsed time: 50.984574 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in 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: 1.008553 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in 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 (8.906694086751e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 0.84638 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in 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: 0.875131 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 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 Mar 31 2024 at 17:39:33 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) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+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! 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, 20.9630025572] 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 20.9630025572 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 Mar 31 2024 at 17:39:33 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) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+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! 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, 119.2607686582] 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 119.2607686582 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+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! 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, 8.906694086751] 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 8.906694086751 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 Mar 31 2024 at 17:39:33 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! 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'] 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: 0.996448 seconds -------------------------------------------------------------------------------- Total elapsed time: 3.726512 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in 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 (-3.624863488075e+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: 1.786856 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in 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 (-3.757593772492e+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: 1.62123 seconds -------------------------------------------------------------------------------- Total elapsed time: 3.408086 seconds Test results have been logged -------------------------------------------------------------------------------- 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 Mar 31 2024 at 17:39:33 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! 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 Mar 31 2024 at 17:39:33 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) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+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! 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, -36.24863488075, -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 -36.24863488075 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 Mar 31 2024 at 17:39:33 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) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+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! 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, -37.57593772492, -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 -37.57593772492 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/<>' dh_install -a -O--buildsystem=cmake dh_installdocs -a -O--buildsystem=cmake dh_sphinxdoc -a -O--buildsystem=cmake dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -a -O--buildsystem=cmake dh_installman -a -O--buildsystem=cmake dh_python3 -a -O--buildsystem=cmake I: dh_python3 fs:418: renaming _apbslib.so to _apbslib.cpython-312-powerpc64le-linux-gnu.so dh_installsystemduser -a -O--buildsystem=cmake dh_lintian -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 445048 new size 448767 dwz: debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 978948 new size 980801 dwz: debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 105702 new size 106362 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-312-powerpc64le-linux-gnu.so: DWARF compression not beneficial - old size 4463534 new size 4463768 dh_strip -a -O--buildsystem=cmake debugedit: debian/apbs/usr/lib/apbs/tools/bin/multivalue: Unknown DWARF DW_FORM_0x1f20 06e5e8b7254d47037cbd5732e231b94d4a30bb83 debugedit: debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin: Unknown DWARF DW_FORM_0x1f20 f907698fff0122dbe02c07ddde628242aa52eae0 9743c080678cb389d3c4c6798e6e6227db1753c6 debugedit: debian/libapbs3t64/usr/lib/powerpc64le-linux-gnu/libapbs_fem.so.3: Unknown DWARF DW_FORM_0x1f21 6c5d64339cf1fd2d8b25306abe920a1167cd3345 debugedit: debian/apbs/usr/lib/apbs/tools/bin/dx2mol: Unknown DWARF DW_FORM_0x1f20 0e5c88cef7ed1b37f2c919290c03439aac63ce9a debugedit: debian/libapbs3t64/usr/lib/powerpc64le-linux-gnu/libapbs_mg.so.3: Unknown DWARF DW_FORM_0x1f21 4ab406812cf49b2430f38cb53cfb9ad9929f1941 debugedit: debian/apbs/usr/lib/apbs/tools/bin/value: Unknown DWARF DW_FORM_0x1f20 6c1b9c007bf4153eab59fd7f734a158989edf0aa debugedit: debian/libapbs3t64/usr/lib/powerpc64le-linux-gnu/libapbs_pmgc.so.3: Unknown DWARF DW_FORM_0x1f20 41fc1e5f83d8dabf38ef878e45b5284c58c1e17b debugedit: debian/apbs/usr/lib/apbs/tools/bin/analysis: Unknown DWARF DW_FORM_0x1f20 263cb1180881c97f9fc9edc266c16703d71fe099 debugedit: debian/libapbs3t64/usr/lib/powerpc64le-linux-gnu/libapbs_routines.so.3: Unknown DWARF DW_FORM_0x1f20 a1d954267f75a0e12c64a0c8716fe22f8d29d0e7 debugedit: debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libpunc.so.1.9.3: Unknown DWARF DW_FORM_0x1f21 cb4340536877d06154164531e2acf82810159046 debugedit: debian/apbs/usr/lib/apbs/tools/bin/coulomb: Unknown DWARF DW_FORM_0x1f20 54754d360ea11e3b8cd717ef083c3ab5f07d1f24 823e48a57889df87c902ba135222834bc45c8a37 debugedit: debian/libapbs3t64/usr/lib/powerpc64le-linux-gnu/libapbs_generic.so.3: Unknown DWARF DW_FORM_0x1f20 256ba48729e8a9a1af15ae36f06e93d5cb9acb5f debugedit: debian/apbs/usr/lib/apbs/tools/bin/tensor2dx: Unknown DWARF DW_FORM_0x1f20 719da04347001932b9d5fe079b6de019a25ae687 debugedit: debian/apbs/usr/lib/apbs/tools/bin/benchmark: Unknown DWARF DW_FORM_0x1f20 b9ffa0a4ea297879bd2b837d3296acaca1173d55 c5d635fe603b9c36a93687482583b30ac4bb4121 debugedit: debian/apbs/usr/lib/apbs/tools/bin/mergedx: Unknown DWARF DW_FORM_0x1f20 9e33c8b86272044cf5580325acb00edbe3abd6d8 debugedit: debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3: Unknown DWARF DW_FORM_0x1f20 dfa3067a59984af927a67a7c2f30533a92499ab3 debugedit: debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd: Unknown DWARF DW_FORM_0x1f20 23f63cd55e96f1d2ba4c79fb9f70308a294b96af debugedit: debian/apbs/usr/lib/apbs/tools/bin/born: Unknown DWARF DW_FORM_0x1f20 cacb194378f06064fc2ee9752c182e9d31bab400 debugedit: debian/apbs/usr/lib/apbs/tools/bin/mergedx2: Unknown DWARF DW_FORM_0x1f20 899e11c883224429722d94057f159b15fd5f7f07 debugedit: debian/apbs/usr/lib/apbs/tools/bin/smooth: Unknown DWARF DW_FORM_0x1f20 3b97db5f5ea5b960225c9ac7277badf043aaddec debugedit: debian/apbs/usr/lib/apbs/tools/bin/dxmath: Unknown DWARF DW_FORM_0x1f21 508cf5d5a845456007d84242b607deacfea3fcfb debugedit: debian/apbs/usr/lib/apbs/tools/bin/mgmesh: Unknown DWARF DW_FORM_0x1f20 2b76d9e1dd94d70896ada84b3421b01661cd0cee debugedit: debian/apbs/usr/lib/apbs/tools/bin/del2dx: Unknown DWARF DW_FORM_0x1f20 0d1276b139f154d9583a9ccfbbcaa24c95efa1ef debugedit: debian/apbs/usr/lib/apbs/tools/bin/similarity: Unknown DWARF DW_FORM_0x1f21 c3de6996f5d64fa70b08a6ac7b63f8f23cf47de5 debugedit: debian/apbs/usr/bin/apbs: Unknown DWARF DW_FORM_0x1f20 6d1e29d5bdf26497e563b10b16f3a316e934cc46 80bd018c3ac261c5a3738b63241d1e7c6953c09c debugedit: debian/python3-apbslib/usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-312-powerpc64le-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 d386c442d7ce572e356b4427f2f4068432d16c76 dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol ddot_ used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dcopy_ used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol s_wsfe used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dnrm2_ used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_ri used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol daxpy_ used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrtf used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_dd used by debian/libfetk1.9t64/usr/lib/powerpc64le-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 sqrt used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol asin used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol acos used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erfc used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan2 used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cos used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sincos used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9t64/usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tan used by debian/libfetk1.9t64/usr/lib/powerpc64le-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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd were not linked against libmpi.so.40 (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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd 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/similarity debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd were not linked against libccolamd.so.3 (they use none of the library's symbols) dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libfetk-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 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 dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libapbs3t64-dbgsym (in debian/.debhelper/libapbs3t64/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-apbslib-dbgsym (in debian/.debhelper/python3-apbslib/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing apbs (in debian/apbs); do_strip: , oemstrip: pkgstriptranslations: processing libfetk1.9t64-dbgsym (in debian/.debhelper/libfetk1.9t64/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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_3.4.1-5.1ubuntu2_ppc64el.deb'. pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/libapbs3t64/dbgsym-root/DEBIAN/control, package libapbs3t64-dbgsym, directory debian/.debhelper/libapbs3t64/dbgsym-root dpkg-deb: building package 'libapbs3t64-dbgsym' in 'debian/.debhelper/scratch-space/build-libapbs3t64/libapbs3t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.deb'. Renaming python3-apbslib-dbgsym_3.4.1-5.1ubuntu2_ppc64el.deb to python3-apbslib-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb Renaming libapbs3t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.deb to libapbs3t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb pkgstripfiles: processing control file: debian/.debhelper/libfetk1.9t64/dbgsym-root/DEBIAN/control, package libfetk1.9t64-dbgsym, directory debian/.debhelper/libfetk1.9t64/dbgsym-root dpkg-deb: building package 'libfetk1.9t64-dbgsym' in 'debian/.debhelper/scratch-space/build-libfetk1.9t64/libfetk1.9t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.deb'. Renaming libfetk1.9t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.deb to libfetk1.9t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libapbs-dev (in debian/libapbs-dev); do_strip: , oemstrip: pkgstriptranslations: processing libfetk-dev (in debian/libfetk-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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) ... pkgstripfiles: processing control file: debian/libfetk-dev/DEBIAN/control, package libfetk-dev, directory debian/libfetk-dev INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/apbs/DEBIAN/control, package apbs, directory debian/apbs .. removing usr/share/doc/apbs/ChangeLog.md Searching for duplicated docs in dependency libapbs3t64... symlinking changelog.Debian.gz in apbs to file in libapbs3t64 INFO: pkgstripfiles: waiting for lock (libapbs-dev) ... Searching for duplicated docs in dependency libfetk1.9t64... pkgstripfiles: Running PNG optimization (using 4 cpus) for package apbs ... pkgstripfiles: No PNG files. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-5.1ubuntu2_ppc64el.deb'. INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing apbs-dbgsym (in debian/.debhelper/apbs/dbgsym-root); do_strip: , oemstrip: INFO: pkgstripfiles: waiting for lock (libapbs-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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_3.4.1-5.1ubuntu2_ppc64el.deb'. INFO: pkgstripfiles: waiting for lock (libapbs-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... Renaming apbs-dbgsym_3.4.1-5.1ubuntu2_ppc64el.deb to apbs-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-apbslib (in debian/python3-apbslib); do_strip: , oemstrip: INFO: pkgstripfiles: waiting for lock (libapbs-dev) ... INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... 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 libapbs3t64... symlinking changelog.Debian.gz in python3-apbslib to file in libapbs3t64 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-apbslib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-5.1ubuntu2_ppc64el.deb'. Searching for duplicated docs in dependency libapbs3t64... symlinking changelog.Debian.gz in libapbs-dev to file in libapbs3t64 INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-5.1ubuntu2_ppc64el.deb'. INFO: pkgstriptranslations version 154 INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgstriptranslations: processing libapbs3t64 (in debian/libapbs3t64); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libapbs3t64/DEBIAN/control, package libapbs3t64, directory debian/libapbs3t64 Searching for duplicated docs in dependency libfetk1.9t64... symlinking changelog.Debian.gz in libapbs3t64 to file in libfetk1.9t64 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs3t64 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs3t64' in '../libapbs3t64_3.4.1-5.1ubuntu2_ppc64el.deb'. Searching for duplicated docs in dependency libfetk1.9t64... symlinking changelog.Debian.gz in libfetk-dev to file in libfetk1.9t64 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libfetk-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-5.1ubuntu2_ppc64el.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libfetk1.9t64 (in debian/libfetk1.9t64); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libfetk1.9t64/DEBIAN/control, package libfetk1.9t64, directory debian/libfetk1.9t64 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libfetk1.9t64 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libfetk1.9t64' in '../libfetk1.9t64_3.4.1-5.1ubuntu2_ppc64el.deb'. dpkg-genbuildinfo --build=any -O../apbs_3.4.1-5.1ubuntu2_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../apbs_3.4.1-5.1ubuntu2_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-04-02T05:21:56Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ apbs_3.4.1-5.1ubuntu2_ppc64el.changes: -------------------------------------- Format: 1.8 Date: Sun, 31 Mar 2024 17:39:33 +0000 Source: apbs Binary: apbs libapbs-dev libapbs3t64 libfetk-dev libfetk1.9t64 python3-apbslib Built-For-Profiles: noudeb Architecture: ppc64el Version: 3.4.1-5.1ubuntu2 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: apbs - Adaptive Poisson Boltzmann Solver libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs3t64 - Adaptive Poisson Boltzmann Solver libfetk-dev - FETK libraries for APBS (development headers) libfetk1.9t64 - FETK libraries for APBS (shared libraries) python3-apbslib - Adaptive Poisson Boltzmann Solver Changes: apbs (3.4.1-5.1ubuntu2) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: 3e587d5d382887e1b883e3a0e98aecc3cfa2f98f 113382 apbs-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb 730ff4f9efb943a52694af8b0104ce674b36fcdc 14803 apbs_3.4.1-5.1ubuntu2_ppc64el.buildinfo 05a146c190da27ed0bd32d8fa3d111345a9dda77 80294 apbs_3.4.1-5.1ubuntu2_ppc64el.deb db08642eb60958991ee965ffc19e24923cc6138e 99418 libapbs-dev_3.4.1-5.1ubuntu2_ppc64el.deb 57caaead0df038e695f04fe56af1e32025cf613b 589166 libapbs3t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb 0fa77924ac535bb6fb3e6deebe525a10284b09d5 307508 libapbs3t64_3.4.1-5.1ubuntu2_ppc64el.deb a1912005b2227d2c4271e1f49ea8a6db313e98f5 144500 libfetk-dev_3.4.1-5.1ubuntu2_ppc64el.deb 72c7d59183872b5b527a0a76afda32c3091df662 1725550 libfetk1.9t64-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb 3a99e7f99e96c31ed998b7c1dde8410ffbce6a9a 660522 libfetk1.9t64_3.4.1-5.1ubuntu2_ppc64el.deb 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6ba847180c06857e10fa9c105d6885118b3a9104a11e266ce1de5072825f38c5 660522 libfetk1.9t64_3.4.1-5.1ubuntu2_ppc64el.deb 855d20bc8f28f15f81038a98f00a9579e841c8d58f2d35cd95a06cc88ca53d42 1937070 python3-apbslib-dbgsym_3.4.1-5.1ubuntu2_ppc64el.ddeb efed1af130862a0c3c5b88fbf5b4f0402d41b45fb80c03bc8e074a45f113bdb8 213222 python3-apbslib_3.4.1-5.1ubuntu2_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Tue, 02 Apr 2024 05:21:56 +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 (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-powerpc64le-linux-gnu (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu4), bsdutils (= 1:2.39.3-9ubuntu4), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), cmake (= 3.28.3-1build6), cmake-data (= 3.28.3-1build6), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), cpp-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build1), dh-autoreconf (= 20), dh-python (= 6.20240401), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), docutils-common (= 0.20.1+dfsg-3), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), g++-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), gfortran-13 (= 13.2.0-23ubuntu3), gfortran-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), grep (= 3.11-4), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu2), hostname (= 3.23+nmu2ubuntu1), ibverbs-providers (= 50.0-2build2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3build2), libamd3 (= 1:7.6.1+dfsg-1build1), libamdhip64-5 (= 5.2.3-13), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.2-2), libarpack2-dev (= 3.9.1-1.1build2), libarpack2t64 (= 3.9.1-1.1build2), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbinutils (= 2.42-4ubuntu2), libblas-dev (= 3.12.0-3), libblas3 (= 3.12.0-3), libblkid1 (= 2.39.3-9ubuntu4), libbrotli1 (= 1.1.0-2build2), libbsd0 (= 0.12.1-1build1), libbtf2 (= 1:7.6.1+dfsg-1build1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8), libc-dev-bin (= 2.39-0ubuntu8), libc6 (= 2.39-0ubuntu8), libc6-dev (= 2.39-0ubuntu8), libcamd3 (= 1:7.6.1+dfsg-1build1), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu1), libcbor0.10 (= 0.10.2-1.2ubuntu2), libcc1-0 (= 14-20240330-1ubuntu2), libccolamd3 (= 1:7.6.1+dfsg-1build1), libcholmod5 (= 1:7.6.1+dfsg-1build1), libcolamd3 (= 1:7.6.1+dfsg-1build1), libcom-err2 (= 1.47.0-2.4~exp1ubuntu3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcurl4t64 (= 8.5.0-2ubuntu9), libcxsparse4 (= 1:7.6.1+dfsg-1build1), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdpkg-perl (= 1.22.6ubuntu6), libdrm-amdgpu1 (= 2.4.120-2), libdrm-common (= 2.4.120-2), libdrm2 (= 2.4.120-2), libdw1t64 (= 0.190-1.1build3), libedit2 (= 3.1-20230828-1), libelf1t64 (= 0.190-1.1build3), libevent-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-core-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-dev (= 2.1.12-stable-9ubuntu2), libevent-extra-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-openssl-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libexpat1 (= 2.6.1-2build1), libexpat1-dev (= 2.6.1-2build1), libfabric1 (= 1.17.0-3build2), libffi8 (= 3.4.6-1), libfido2-1 (= 1.14.0-1build2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240330-1ubuntu2), libgcrypt20 (= 1.10.3-2), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgfortran-13-dev (= 13.2.0-23ubuntu3), libgfortran5 (= 14-20240330-1ubuntu2), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240330-1ubuntu2), libgpg-error0 (= 1.47-3build1), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libhogweed6t64 (= 3.9.1-2.2build1), libhsa-runtime64-1 (= 5.7.1-2build1), libhsakmt1 (= 5.7.0-1build1), libhwloc-dev (= 2.10.0-1), libhwloc-plugins (= 2.10.0-1), libhwloc15 (= 2.10.0-1), libibverbs-dev (= 50.0-2build2), libibverbs1 (= 50.0-2build2), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3), libitm1 (= 14-20240330-1ubuntu2), libjansson4 (= 2.14-2build2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-sphinxdoc (= 7.2.6-6), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3), libklu2 (= 1:7.6.1+dfsg-1build1), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblapack-dev (= 3.12.0-3), liblapack3 (= 3.12.0-3), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu7), libldl3 (= 1:7.6.1+dfsg-1build1), libllvm17t64 (= 1:17.0.6-9build3), liblsan0 (= 14-20240330-1ubuntu2), libltdl-dev (= 2.4.7-7), libltdl7 (= 2.4.7-7), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.6.1+really5.4.5-1build1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmaloc-dev (= 1.5-1build2), libmaloc1 (= 1.5-1build2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-9ubuntu4), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libmunge2 (= 0.5.15-4build1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnettle8t64 (= 3.9.1-2.2build1), libnghttp2-14 (= 1.59.0-1build2), 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), libnuma-dev (= 2.0.18-1), libnuma1 (= 2.0.18-1), libopenmpi-dev (= 4.1.6-7ubuntu2), libopenmpi3t64 (= 4.1.6-7ubuntu2), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.3-5ubuntu4), libpam-modules-bin (= 1.5.3-5ubuntu4), libpam-runtime (= 1.5.3-5ubuntu4), libpam0g (= 1.5.3-5ubuntu4), libparu0 (= 1:7.6.1+dfsg-1build1), libpciaccess0 (= 0.17-3), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38t64 (= 5.38.2-3.2build1), libpipeline1 (= 1.5.7-2), libpkgconf3 (= 1.8.1-2), libpmix-dev (= 5.0.1-4.1build1), libpmix2t64 (= 5.0.1-4.1build1), libproc2-0 (= 2:4.0.4-4ubuntu3), libpsl5t64 (= 0.21.2-1.1build1), libpython3-dev (= 3.12.2-0ubuntu2), libpython3-stdlib (= 3.12.2-0ubuntu2), libpython3.12-dev (= 3.12.2-4build4), libpython3.12-minimal (= 3.12.2-4build4), libpython3.12-stdlib (= 3.12.2-4build4), libpython3.12t64 (= 3.12.2-4build4), libquadmath0 (= 14-20240330-1ubuntu2), librbio4 (= 1:7.6.1+dfsg-1build1), librdmacm1t64 (= 50.0-2build2), libreadline8t64 (= 8.2-4build1), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7), libsasl2-2 (= 2.1.28+dfsg1-5ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu2), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsemanage-common (= 3.5-1build5), libsemanage2 (= 3.5-1build5), libsepol2 (= 3.5-2), libsframe1 (= 2.42-4ubuntu2), libsmartcols1 (= 2.39.3-9ubuntu4), libspex2 (= 1:7.6.1+dfsg-1build1), libspqr4 (= 1:7.6.1+dfsg-1build1), libsqlite3-0 (= 3.45.1-1ubuntu2), libssh-4 (= 0.10.6-2build2), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu3), libstdc++6 (= 14-20240330-1ubuntu2), libsub-override-perl (= 0.10-1), libsuitesparse-dev (= 1:7.6.1+dfsg-1build1), libsuitesparse-mongoose3 (= 1:7.6.1+dfsg-1build1), libsuitesparseconfig7 (= 1:7.6.1+dfsg-1build1), libsuperlu-dev (= 6.0.1+dfsg1-1), libsuperlu6 (= 6.0.1+dfsg1-1), libsystemd0 (= 255.4-1ubuntu6), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtirpc-common (= 1.3.4+ds-1.1build1), libtirpc-dev (= 1.3.4+ds-1.1build1), libtirpc3t64 (= 1.3.4+ds-1.1build1), libtool (= 2.4.7-7), libtsan2 (= 14-20240330-1ubuntu2), libubsan1 (= 14-20240330-1ubuntu2), libuchardet0 (= 0.0.8-1), libucx0 (= 1.16.0+ds-4build1), libudev1 (= 255.4-1ubuntu6), libumfpack6 (= 1:7.6.1+dfsg-1build1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu4), libuv1t64 (= 1.48.0-1.1build1), 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-1.3ubuntu3), libxnvctrl0 (= 510.47.03-0ubuntu4), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-20.20), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-4build1), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), mpi-default-dev (= 1.15), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1), openmpi-bin (= 4.1.6-7ubuntu2), openmpi-common (= 4.1.6-7ubuntu2), openssh-client (= 1:9.6p1-3ubuntu12), openssl (= 3.0.13-0ubuntu3), passwd (= 1:4.13+dfsg1-4ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2build1), perl-base (= 5.38.2-3.2build1), perl-modules-5.38 (= 5.38.2-3.2build1), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-4ubuntu3), pybind11-dev (= 2.11.1-2), pybuild-plugin-pyproject (= 6.20240401), python-babel-localedata (= 2.10.3-3build1), python3 (= 3.12.2-0ubuntu2), python3-alabaster (= 0.7.12-1), python3-babel (= 2.10.3-3build1), python3-build (= 1.0.3-2), python3-certifi (= 2023.11.17-1), python3-chardet (= 5.2.0+dfsg-1), python3-dev (= 3.12.2-0ubuntu2), python3-docutils (= 0.20.1+dfsg-3), python3-idna (= 3.6-2), python3-imagesize (= 1.4.1-1), python3-installer (= 0.7.0+dfsg1-2), python3-jinja2 (= 3.1.2-1ubuntu1), python3-markupsafe (= 2.1.5-1build2), python3-minimal (= 3.12.2-0ubuntu2), python3-packaging (= 23.2-1), python3-pkg-resources (= 68.1.2-2ubuntu1), python3-pybind11 (= 2.11.1-2), python3-pygments (= 2.17.2+dfsg-1), python3-pyproject-hooks (= 1.0.0-2), python3-requests (= 2.31.0+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-setuptools (= 68.1.2-2ubuntu1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 7.2.6-6), python3-toml (= 0.10.2-1), python3-tz (= 2024.1-2), python3-urllib3 (= 2.0.7-1), python3-wheel (= 0.42.0-2), python3.12 (= 3.12.2-4build4), python3.12-dev (= 3.12.2-4build4), python3.12-minimal (= 3.12.2-4build4), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sgml-base (= 1.31), sphinx-common (= 7.2.6-6), swig (= 4.2.0-2ubuntu1), sysvinit-utils (= 3.08-6ubuntu2), tar (= 1.35+dfsg-3), tzdata (= 2024a-1ubuntu1), util-linux (= 2.39.3-9ubuntu4), xml-core (= 0.19), xz-utils (= 5.6.1+really5.4.5-1build1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711906773" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ apbs_3.4.1-5.1ubuntu2_ppc64el.deb --------------------------------- new Debian package, version 2.0. size 80294 bytes: control archive=1746 bytes. 1853 bytes, 30 lines control 1479 bytes, 23 lines md5sums Package: apbs Version: 3.4.1-5.1ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 1254 Depends: apbs-data (= 3.4.1-5.1ubuntu2), libapbs3t64 (= 3.4.1-5.1ubuntu2), libjs-mathjax, libamd3 (>= 1:7.0.1), libarpack2t64 (>= 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), libfetk1.9t64 (>= 3.4.1), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi3t64 (>= 4.1.6), libspqr4 (>= 1:7.6.1+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 2024-03-31 17:39 ./ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/bin/ -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/bin/apbs drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/apbs/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/apbs/tools/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/ -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/analysis -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/benchmark -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/born -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/coulomb -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/del2dx -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/dx2mol -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/dx2uhbd -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/dxmath -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/mergedx -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/mergedx2 -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/mgmesh -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/multivalue -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/similarity -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/smooth -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/tensor2dx -rwxr-xr-x root/root 67744 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/uhbd_asc2bin -rwxr-xr-x root/root 67840 2024-03-31 17:39 ./usr/lib/apbs/tools/bin/value drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./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 2024-03-29 13:58 ./usr/share/doc/apbs/README.test lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/share/doc/apbs/changelog.Debian.gz -> ../libapbs3t64/changelog.Debian.gz -rw-r--r-- root/root 6898 2024-03-29 13:58 ./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 2024-03-31 17:39 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/man/man1/ -rw-r--r-- root/root 835 2024-03-31 17:39 ./usr/share/man/man1/apbs.1.gz libapbs-dev_3.4.1-5.1ubuntu2_ppc64el.deb ---------------------------------------- new Debian package, version 2.0. size 99418 bytes: control archive=2157 bytes. 763 bytes, 20 lines control 3873 bytes, 58 lines md5sums Package: libapbs-dev Source: apbs Version: 3.4.1-5.1ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 713 Depends: libapbs3t64 (= 3.4.1-5.1ubuntu2) 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 2024-03-31 17:39 ./ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/include/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./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 2024-03-31 17:39 ./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 2024-03-31 17:39 ./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 2024-03-31 17:39 ./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 2024-03-31 17:39 ./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 2024-03-31 17:39 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/ lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_fem.so -> libapbs_fem.so.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_generic.so -> libapbs_generic.so.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_mg.so -> libapbs_mg.so.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_pmgc.so -> libapbs_pmgc.so.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_routines.so -> libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/apbs/cmake/ -rw-r--r-- root/root 949 2024-03-29 13:58 ./usr/share/apbs/cmake/FindAMD.cmake -rw-r--r-- root/root 2501 2024-03-29 13:58 ./usr/share/apbs/cmake/FindARPACK.cmake -rw-r--r-- root/root 22563 2024-03-29 13:58 ./usr/share/apbs/cmake/FindLAPACK.cmake -rw-r--r-- root/root 23393 2024-03-29 13:58 ./usr/share/apbs/cmake/FindSuiteSparse.cmake -rw-r--r-- root/root 2578 2024-03-29 13:58 ./usr/share/apbs/cmake/FindSuperLU.cmake -rw-r--r-- root/root 1153 2024-03-29 13:58 ./usr/share/apbs/cmake/FindUMFPACK.cmake drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./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 2024-03-31 17:39 ./usr/share/doc/libapbs-dev/changelog.Debian.gz -> ../libapbs3t64/changelog.Debian.gz -rw-r--r-- root/root 6898 2024-03-29 13:58 ./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 libapbs3t64_3.4.1-5.1ubuntu2_ppc64el.deb ---------------------------------------- new Debian package, version 2.0. size 307508 bytes: control archive=1042 bytes. 869 bytes, 22 lines control 558 bytes, 7 lines md5sums 194 bytes, 5 lines shlibs 75 bytes, 2 lines triggers Package: libapbs3t64 Source: apbs Version: 3.4.1-5.1ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 936 Depends: libc6 (>= 2.29), libfetk1.9t64 (>= 3.4.1), libgomp1 (>= 4.9), libmaloc1 (>= 0.2-1) Breaks: libapbs3 (<< 3.4.1-5.1ubuntu2) Replaces: libapbs3 Provides: libapbs3 (= 3.4.1-5.1ubuntu2) 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 2024-03-31 17:39 ./ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/ -rw-r--r-- root/root 135152 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_fem.so.3 -rw-r--r-- root/root 264216 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_generic.so.3 -rw-r--r-- root/root 198680 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_mg.so.3 -rw-r--r-- root/root 198680 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_pmgc.so.3 -rw-r--r-- root/root 133144 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/libapbs3t64/ lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/share/doc/libapbs3t64/changelog.Debian.gz -> ../libfetk1.9t64/changelog.Debian.gz -rw-r--r-- root/root 6898 2024-03-29 13:58 ./usr/share/doc/libapbs3t64/copyright drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 164 2024-03-29 13:58 ./usr/share/lintian/overrides/libapbs3t64 libfetk-dev_3.4.1-5.1ubuntu2_ppc64el.deb ---------------------------------------- new Debian package, version 2.0. size 144500 bytes: control archive=1992 bytes. 1355 bytes, 32 lines control 2509 bytes, 40 lines md5sums Package: libfetk-dev Source: apbs Version: 3.4.1-5.1ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 1505 Depends: libfetk1.9t64 (= 3.4.1-5.1ubuntu2), 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 2024-03-31 17:39 ./ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/include/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/include/fetk/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/include/fetk/gamer/ -rw-r--r-- root/root 11439 2024-03-29 13:58 ./usr/include/fetk/gamer/biom.h -rw-r--r-- root/root 1459 2024-03-29 13:58 ./usr/include/fetk/gamer/gamer.h -rw-r--r-- root/root 2282 2024-03-29 13:58 ./usr/include/fetk/gamer/gamer_base.h -rw-r--r-- root/root 106910 2024-03-29 13:58 ./usr/include/fetk/gamer/tetgen.h -rw-r--r-- root/root 22024 2024-03-29 13:58 ./usr/include/fetk/gamer/triangle.h drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/include/fetk/mc/ -rw-r--r-- root/root 27753 2024-03-29 13:58 ./usr/include/fetk/mc/am.h -rw-r--r-- root/root 49795 2024-03-29 13:58 ./usr/include/fetk/mc/aprx.h -rw-r--r-- root/root 1297 2024-03-29 13:58 ./usr/include/fetk/mc/bam.h -rw-r--r-- root/root 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./usr/include/fetk/punc/vblas.h -rw-r--r-- root/root 17098 2024-03-29 13:58 ./usr/include/fetk/punc/vcgcode.h -rw-r--r-- root/root 13077 2024-03-29 13:58 ./usr/include/fetk/punc/vf2c.h -rw-r--r-- root/root 552778 2024-03-29 13:58 ./usr/include/fetk/punc/vlapack.h -rw-r--r-- root/root 82089 2024-03-29 13:58 ./usr/include/fetk/punc/vpmg.h drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/ lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libcgcode.so -> libcgcode.so.1.9 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libgamer.so -> libgamer.so.1.9 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libmc.so -> libmc.so.1.9 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libpunc.so -> libpunc.so.1.9 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libvf2c.so -> libvf2c.so.1.9 drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/libfetk-dev/ lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/share/doc/libfetk-dev/changelog.Debian.gz -> ../libfetk1.9t64/changelog.Debian.gz -rw-r--r-- root/root 6898 2024-03-29 13:58 ./usr/share/doc/libfetk-dev/copyright libfetk1.9t64_3.4.1-5.1ubuntu2_ppc64el.deb ------------------------------------------ new Debian package, version 2.0. size 660522 bytes: control archive=1434 bytes. 1544 bytes, 35 lines control 636 bytes, 8 lines md5sums 186 bytes, 5 lines shlibs 75 bytes, 2 lines triggers Package: libfetk1.9t64 Source: apbs Version: 3.4.1-5.1ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 1875 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) Breaks: libfetk1.9 (<< 3.4.1-5.1ubuntu2) Replaces: libfetk1.9 Provides: libfetk1.9 (= 3.4.1-5.1ubuntu2) 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 2024-03-31 17:39 ./ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/ lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9 -> libcgcode.so.1.9.3 -rw-r--r-- root/root 150256 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libcgcode.so.1.9.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libgamer.so.1.9 -> libgamer.so.1.9.3 -rw-r--r-- root/root 872024 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libgamer.so.1.9.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libmc.so.1.9 -> libmc.so.1.9.3 -rw-r--r-- root/root 599960 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libmc.so.1.9.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libpunc.so.1.9 -> libpunc.so.1.9.3 -rw-r--r-- root/root 67288 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libpunc.so.1.9.3 lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9 -> libvf2c.so.1.9.3 -rw-r--r-- root/root 199304 2024-03-31 17:39 ./usr/lib/powerpc64le-linux-gnu/libvf2c.so.1.9.3 drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/libfetk1.9t64/ -rw-r--r-- root/root 3653 2024-03-31 17:39 ./usr/share/doc/libfetk1.9t64/changelog.Debian.gz -rw-r--r-- root/root 6898 2024-03-29 13:58 ./usr/share/doc/libfetk1.9t64/copyright drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 140 2024-03-29 13:58 ./usr/share/lintian/overrides/libfetk1.9t64 python3-apbslib_3.4.1-5.1ubuntu2_ppc64el.deb -------------------------------------------- new Debian package, version 2.0. size 213222 bytes: control archive=2050 bytes. 934 bytes, 19 lines control 2870 bytes, 36 lines md5sums 281 bytes, 12 lines * postinst #!/bin/sh 394 bytes, 12 lines * prerm #!/bin/sh Package: python3-apbslib Source: apbs Version: 3.4.1-5.1ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 1182 Depends: libapbs3t64 (= 3.4.1-5.1ubuntu2), python3 (<< 3.13), python3 (>= 3.12~), python3:any, libc6 (>= 2.32), libgcc-s1 (>= 3.3.1), libmaloc1 (>= 0.2-1), libpython3.12t64 (>= 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 2024-03-31 17:39 ./ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 395488 2024-03-31 17:39 ./usr/lib/python3/dist-packages/apbs.cpython-312-powerpc64le-linux-gnu.so drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/lib/python3/dist-packages/apbslib/ -rw-r--r-- root/root 23 2024-03-29 13:58 ./usr/lib/python3/dist-packages/apbslib/__init__.py -rw-r--r-- root/root 207848 2024-03-31 17:39 ./usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-312-powerpc64le-linux-gnu.so -rw-r--r-- root/root 14524 2024-03-31 17:39 ./usr/lib/python3/dist-packages/apbslib/apbslib.py drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/apbs/tools/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./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 2024-03-31 17:39 ./usr/share/apbs/tools/python/ -rw-r--r-- root/root 1896 2024-03-31 17:39 ./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 2024-03-31 17:39 ./usr/share/apbs/tools/python/noinput.py drwxr-xr-x root/root 0 2024-03-31 17:39 ./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 2024-03-31 17:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 17:39 ./usr/share/doc/python3-apbslib/ lrwxrwxrwx root/root 0 2024-03-31 17:39 ./usr/share/doc/python3-apbslib/changelog.Debian.gz -> ../libapbs3t64/changelog.Debian.gz -rw-r--r-- root/root 6898 2024-03-29 13:58 ./usr/share/doc/python3-apbslib/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 361680 Build-Time: 629 Distribution: noble-proposed Host Architecture: ppc64el Install-Time: 52 Job: apbs_3.4.1-5.1ubuntu2.dsc Machine Architecture: ppc64el Package: apbs Package-Time: 687 Source-Version: 3.4.1-5.1ubuntu2 Space: 361680 Status: successful Version: 3.4.1-5.1ubuntu2 -------------------------------------------------------------------------------- Finished at 2024-04-02T05:21:56Z Build needed 00:11:27, 361680k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27987125 Scanning for processes to kill in build PACKAGEBUILD-27987125