File descriptors leaked on lvs invocation

[Paul Tomblin]

While upgrading to Kubuntu 14.04 yesterday, I got the following error messages over and over again:

Generating grub configuration file ...^M
File descriptor 3 (pipe:[4852522]) leaked on vgs invocation. Parent PID 6438: grub-probe^M
File descriptor 59 (/var/log/dist-upgrade/apt.log) leaked on vgs invocation. Parent PID 6438: grub-probe^M

The file descriptors appeared random, and the "Parent PID" was either /bin/sh, grub-install, grub-probe or /usr/sbin/grub-probe:
grep leaked ./dist-upgrade/apt-term.log |sed 's/.*Parent PID [0-9]*: //' | sort | uniq -c
     53 /bin/sh
     72 grub-install
    106 grub-probe
   1484 /usr/sbin/grub-probe

[Paul Tomblin (ptomblin)]

My full /var/log/dist-upgrade/apt-term.log:

[SatPhil (satphil)]

I also have these messages when upgrading from Ubuntu 13.10 to 14.04.

$ grep leaked ./dist-upgrade/apt-term.log |sed 's/.*Parent PID [0-9]*: //' | sort | uniq -c
     37 /bin/sh
     84 /usr/sbin/grub-probe

Don't know if this is relevant but I am also affected by bug 1289977 (https://bugs.launchpad.net/ubuntu/+source/grub2/+bug/1289977)

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[dw1 (dw1)]

Am experiencing the same or similar.

[Dwaine Gonyier (dgonyier)]

I see this error after upgrading to 14.10

[gronaix (2-ubuntuine-d)]

I'm also retrieving this message durig apt-get dist-upgrade multiple times.
while installing new kernel image, i recognized first apperance.
System is Ubuntu 14.10 amd64

[Alvin (alvind)]

Here, these errors appear on upgrading kernel in 14.10 (on encrypted LVM)

[Ronald Bruintjes (rbruintjes)]

Doing a dist-upgrade for the new kernel, the same errors occur. It looks like they're generated after starting the grub configuration file update:

Generating grub configuration file ...
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15019: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15019: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15030: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15030: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15041: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15041: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15052: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15052: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15105: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15105: /usr/sbin/grub-probe
Found linux image: /boot/vmlinuz-3.16.0-30-generic
Found initrd image: /boot/initrd.img-3.16.0-30-generic
Found linux image: /boot/vmlinuz-3.16.0-29-generic
Found initrd image: /boot/initrd.img-3.16.0-29-generic
Found linux image: /boot/vmlinuz-3.13.0-44-generic
Found initrd image: /boot/initrd.img-3.13.0-44-generic
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15557: /usr/sbin/grub-probe
File descriptor 40 (/dev/pts/5) leaked on vgs invocation. Parent PID 15557: /usr/sbin/grub-probe
Found memtest86+ image: /memtest86+.elf
Found memtest86+ image: /memtest86+.bin
File descriptor 40 (/dev/pts/5) leaked on lvs invocation. Parent PID 15721: /bin/sh
done

Cheers,

Ron.

[TranceaddicT (scottmccarthy66)]

Has there been progress on this? I was repairing my LVM and installing postfix when this occurred. Below is the CLI from the time I started the install with apt-get to final postfix updatings.

Also, just prior to this I had reduced my swap lvm size to 8MB. I've included that process as well, at the bottom; below ***, just in case.

root@Jupiter:~# apt-get install lvm2 dmsetup mdadm reiserfsprogs xfsprogs
Reading package lists... Done
Building dependency tree
Reading state information... Done
dmsetup is already the newest version.
lvm2 is already the newest version.
reiserfsprogs is already the newest version.
xfsprogs is already the newest version.
The following package was automatically installed and is no longer required:
  python-roman
Use 'apt-get autoremove' to remove it.
The following extra packages will be installed:
  postfix
Suggested packages:
  procmail postfix-mysql postfix-pgsql postfix-ldap postfix-pcre sasl2-bin dovecot-common postfix-cdb postfix-doc
Recommended packages:
  default-mta mail-transport-agent
The following NEW packages will be installed:
  mdadm postfix
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 1,500 kB of archives.
After this operation, 4,936 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://us.archive.ubuntu.com/ubuntu/ utopic/main mdadm amd64 3.3-2ubuntu1 [394 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ utopic-updates/main postfix amd64 2.11.1-1ubuntu1 [1,107 kB]
Fetched 1,500 kB in 5min 17s (4,726 B/s)
Preconfiguring packages ...
Selecting previously unselected package mdadm.
(Reading database ... 369614 files and directories currently installed.)
Preparing to unpack .../mdadm_3.3-2ubuntu1_amd64.deb ...
Unpacking mdadm (3.3-2ubuntu1) ...
Selecting previously unselected package postfix.
Preparing to unpack .../postfix_2.11.1-1ubuntu1_amd64.deb ...
Unpacking postfix (2.11.1-1ubuntu1) ...
Processing triggers for man-db (2.7.0.2-2) ...
Processing triggers for doc-base (0.10.6) ...
Processing 4 added doc-base files...
Registering documents with scrollkeeper...
Processing triggers for ureadahead (0.100.0-16) ...
ureadahead will be reprofiled on next reboot
Processing triggers for ufw (0.34~rc-0ubuntu4) ...
Setting up mdadm (3.3-2ubuntu1) ...
Generating mdadm.conf... done.
update-initramfs: deferring update (trigger activated)
Generating grub configuration file ...
File descriptor 3 (pipe:[1702559]) leaked on vgs invocation. Parent PID 11460: /usr/sbin/grub-probe
File descriptor 185 (/dev/pts/8) leaked on vgs invocation. Parent PID 11460: /usr/sbin/grub-probe
File descriptor 3 (pipe:[1702559]) leaked on vgs invocation. Parent PID 11460: /usr/sbin/grub-probe
File descriptor 185 (/dev/pts/8) leaked on vgs invocation. Parent PID 11460: /usr/sbin/grub-probe
File descriptor 3 (pipe:[1702559]) leaked on vgs invocation. Parent PID 11470: /usr/sbin/grub-probe
File descriptor 185 (/dev/pts/8) leaked on vgs invocation. Parent PID 11470: /usr/sbin/grub-probe
File descriptor 3 (pipe:[1702559]) leaked on vgs invocation. Parent PID 11470: /usr/sbin/grub-probe
F...

[hurricaneharry (harold-de-bruijn)]

Occored for me when removing a kernel with autoremove.. (ubuntu 14.10)

Removing linux-image-3.16.0-23-generic (3.16.0-23.31) ...
Examining /etc/kernel/prerm.d.
run-parts: executing /etc/kernel/prerm.d/dkms 3.16.0-23-generic /boot/vmlinuz-3.16.0-23-generic
Examining /etc/kernel/postrm.d .
run-parts: executing /etc/kernel/postrm.d/initramfs-tools 3.16.0-23-generic /boot/vmlinuz-3.16.0-23-generic
update-initramfs: Deleting /boot/initrd.img-3.16.0-23-generic
run-parts: executing /etc/kernel/postrm.d/zz-update-grub 3.16.0-23-generic /boot/vmlinuz-3.16.0-23-generic
Grub-instellingenbestand aan het maken...
File descriptor 62 (/dev/pts/11) leaked on vgs invocation. Parent PID 7372: /usr/sbin/grub-probe

[Colin Watson (cjwatson)]

This is largely pointless whining from the lvm tools and is entirely cosmetic. At some point we should dig out the environment variable that suppresses this and have GRUB pass it.

[Scott Moser (smoser)]

Debian bug https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=466138
documents LVM_SUPPRESS_FD_WARNINGS as does man (lvm(8)).

[Phillip Susi (psusi)]

Any idea why lvm engages in such seemingly pointless winging and why we can't just get them to take out the message?

[Alexander List (alexlist)]

Still visible on 16.04 LTS today.

[atimonin (atimonin)]

Also hit this doing apt-get upgrade

[navgust (oid)]

Upgrading from 15.10 to 16.04.1: my last messages on the terminal is:
<code>
update-initramfs: deferring update (trigger activated)
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-4.4.0-36-generic
Found linux image: /boot/vmlinuz-4.2.0-42-generic
Found initrd image: /boot/initrd.img-4.2.0-42-generic
Found linux image: /boot/vmlinuz-4.2.0-41-generic
Found initrd image: /boot/initrd.img-4.2.0-41-generic
Found linux image: /boot/vmlinuz-4.2.0-38-generic
Found initrd image: /boot/initrd.img-4.2.0-38-generic
Found linux image: /boot/vmlinuz-4.2.0-36-generic
Found initrd image: /boot/initrd.img-4.2.0-36-generic
Found linux image: /boot/vmlinuz-4.2.0-17-generic
Found initrd image: /boot/initrd.img-4.2.0-17-generic
UUID = vom Btrfs-Dateisystem gefunden
Startmenü für ein Btrfs-Dateisystem eingefügt
Found memtest86+ image: /memtest86+.elf
Found memtest86+ image: /memtest86+.bin
File descriptor 3 (pipe:[9852102]) leaked on lvs invocation. Parent PID 18816: /bin/sh
</code>
After that the upgrade hangs, I am still investigating&trying to finish it.

[Mikkel Kirkgaard Nielsen (mikini)]

Still got this today on dist-upgrading a 16.04 Server. Not very neat and caused some concern for bootability until reading here and the Debian bug made me realize that it is caused by the way triggers invocate lvm tools:

Setting up mdadm (3.3-2ubuntu7.4) ...
update-initramfs: deferring update (trigger activated)
Generating grub configuration file ...
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2303: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2303: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2316: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2316: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2329: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2329: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2342: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2342: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2402: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 2402: /usr/sbin/grub-probe
Found linux image: /boot/vmlinuz-4.4.0-98-generic
Found linux image: /boot/vmlinuz-4.4.0-97-generic
Found initrd image: /boot/initrd.img-4.4.0-97-generic
Found linux image: /boot/vmlinuz-4.4.0-96-generic
Found initrd image: /boot/initrd.img-4.4.0-96-generic
Found linux image: /boot/vmlinuz-4.4.0-93-generic
Found initrd image: /boot/initrd.img-4.4.0-93-generic
Found linux image: /boot/vmlinuz-4.4.0-87-generic
Found initrd image: /boot/initrd.img-4.4.0-87-generic
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 3125: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on vgs invocation. Parent PID 3125: /usr/sbin/grub-probe
File descriptor 3 (pipe:[379519083]) leaked on lvs invocation. Parent PID 3241: /bin/sh
done
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults

[Scott Stensland (scottstensland)]

I own several remote VPS servers and I see this error on many of them ... here is one example which happend on May 22 2019

Ubuntu 18.04.2 LTS
Linux-4.15.0-50-generic-x86_64-with-Ubuntu-18.04-bionic

DEBIAN_FRONTEND=noninteractive sudo apt-get update && DEBIAN_FRONTEND=noninteractive sudo apt-get --fix-broken install -y
Hit:1 http://nova.clouds.archive.ubuntu.com/ubuntu bionic InRelease
Get:2 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
Hit:3 https://download.docker.com/linux/ubuntu bionic InRelease
Get:4 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
Get:5 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
Get:6 http://security.ubuntu.com/ubuntu bionic-security/main Sources [90.6 kB]
Get:7 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [349 kB]
Fetched 692 kB in 1s (647 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.

DEBIAN_FRONTEND=noninteractive sudo apt-get -f install -y
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.

sudo env DEBIAN_FRONTEND=noninteractive UCF_FORCE_CONFFNEW=YES apt-get -o Dpkg::Options::=--force-confnew -yy dist-upgrade -yq
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  curl libcurl3-gnutls libcurl4 mdadm netplan.io nplan python3-distupgrade
  python3-software-properties python3-urllib3 software-properties-common
  ubuntu-release-upgrader-core
11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 643 kB/1,314 kB of archives.
After this operation, 17.4 kB of additional disk space will be used.
Get:1 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 netplan.io amd64 0.97-0ubuntu1~18.04.1 [60.6 kB]
Get:2 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 nplan all 0.97-0ubuntu1~18.04.1 [1,800 B]
Get:3 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 ubuntu-release-upgrader-core all 1:18.04.33 [25.1 kB]
Get:4 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3-distupgrade all 1:18.04.33 [107 kB]
Get:5 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mdadm amd64 4.1~rc1-3~ubuntu18.04.2 [416 kB]
Get:6 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 software-properties-common all 0.96.24.32.8 [9,992 B]
Get:7 http://nova.clouds.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3-software-properties all 0.96.24.32.8 [23.7 kB]
Preconfiguring packages ...
Fetched 643 kB in 1s (598 kB/s)
(Reading database ... 30%
Preparing to unpack .../00-netplan.io_0.97-0ubuntu1~18.04.1_amd64.deb ...
Unpacking netplan.io (0.97-0ubuntu1~18.04.1) over (0.96-0ubuntu0.18.04.4) ...
Preparing to unpack .../01-nplan_0.97-0ubuntu1~18.04.1_all.deb ...
Unpacking nplan (0.97-0ubuntu1~18.04.1) over (0.96-0ubuntu0.18.04.4) ...
Preparing to unpack .../02-ubunt...

[Laurent Bonnaud (laurent-bonnaud)]

I see this error in Ubuntu 19.10:

# grub-install
Installing for x86_64-efi platform.
File descriptor 4 (/dev/nvme0n1p1) leaked on vgs invocation. Parent PID 6830: grub-install
File descriptor 4 (/dev/nvme0n1p1) leaked on vgs invocation. Parent PID 6830: grub-install
Installation finished. No error reported.

Package: grub2-common
Version: 2.04-1ubuntu11

[iGadget (igadget)]

Glad I found this bugreport. The message got me worried, and I can imagine it will keep on creating the same thought with many more people until it (finally!) gets suppressed.
Just got this on 20.04 today while running apt autoremove:

Generating grub configuration file ...
Found linux image: /boot/vmlinuz-5.4.0-54-generic
Found initrd image: /boot/initrd.img-5.4.0-54-generic
Found linux image: /boot/vmlinuz-5.4.0-53-generic
Found initrd image: /boot/initrd.img-5.4.0-53-generic
File descriptor 10 (/var/lib/dpkg/triggers/linux-update-5.4.0-48-generic (deleted)) leaked on lvs invocation. Parent PID 55702: /bin/sh
done

[MarcH (marc-h38)]

Still happening with 20.04

# sudo apt autoremove

Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  linux-image-5.4.0-92-generic linux-image-5.4.0-96-generic linux-image-5.4.0-97-generic linux-modules-5.4.0-92-generic
  linux-modules-5.4.0-96-generic linux-modules-5.4.0-97-generic linux-modules-extra-5.4.0-92-generic
  linux-modules-extra-5.4.0-96-generic linux-modules-extra-5.4.0-97-generic linux-tools-5.4.0-92
  linux-tools-5.4.0-92-generic linux-tools-5.4.0-96 linux-tools-5.4.0-96-generic linux-tools-5.4.0-97
  linux-tools-5.4.0-97-generic
0 upgraded, 0 newly installed, 15 to remove and 0 not upgraded.
After this operation, 959 MB disk space will be freed.
Do you want to continue? [Y/n] y
(Reading database ... 232284 files and directories currently installed.)
Removing linux-modules-extra-5.4.0-92-generic (5.4.0-92.103) ...
Removing linux-image-5.4.0-92-generic (5.4.0-92.103) ...
/etc/kernel/postrm.d/initramfs-tools:
update-initramfs: Deleting /boot/initrd.img-5.4.0-92-generic
/etc/kernel/postrm.d/zz-update-grub:
Sourcing file `/etc/default/grub'
Sourcing file `/etc/default/grub.d/init-select.cfg'
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-5.4.0-100-generic
Found initrd image: /boot/initrd.img-5.4.0-100-generic
Found linux image: /boot/vmlinuz-5.4.0-99-generic
Found initrd image: /boot/initrd.img-5.4.0-99-generic
Found linux image: /boot/vmlinuz-5.4.0-97-generic
Found initrd image: /boot/initrd.img-5.4.0-97-generic
Found linux image: /boot/vmlinuz-5.4.0-96-generic
Found initrd image: /boot/initrd.img-5.4.0-96-generic
Found linux image: /boot/vmlinuz-5.4.0-88-generic
Found initrd image: /boot/initrd.img-5.4.0-88-generic
Adding boot menu entry for UEFI Firmware Settings
done
Removing linux-modules-extra-5.4.0-96-generic (5.4.0-96.109) ...
Removing linux-image-5.4.0-96-generic (5.4.0-96.109) ...
/etc/kernel/postrm.d/initramfs-tools:
update-initramfs: Deleting /boot/initrd.img-5.4.0-96-generic
/etc/kernel/postrm.d/zz-update-grub:
Sourcing file `/etc/default/grub'
Sourcing file `/etc/default/grub.d/init-select.cfg'
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-5.4.0-100-generic
Found initrd image: /boot/initrd.img-5.4.0-100-generic
Found linux image: /boot/vmlinuz-5.4.0-99-generic
Found initrd image: /boot/initrd.img-5.4.0-99-generic
Found linux image: /boot/vmlinuz-5.4.0-97-generic
Found initrd image: /boot/initrd.img-5.4.0-97-generic
Found linux image: /boot/vmlinuz-5.4.0-88-generic
Found initrd image: /boot/initrd.img-5.4.0-88-generic
File descriptor 10 (/var/lib/dpkg/triggers/linux-update-5.4.0-92-generic (deleted)) leaked on lvs invocation. Parent PID 16647: /bin/sh
Adding boot menu entry for UEFI Firmware Settings
done
Removing linux-modules-extra-5.4.0-97-generic (5.4.0-97.110) ...
Removing linux-image-5.4.0-97-generic (5.4.0-97.110) ...
/etc/kernel/postrm.d/initramfs-tools:
update-initramfs: Deleting /boot/initrd.img-5.4.0-97-generic
/etc/kernel/postrm.d/zz-update-grub:
Sourcing file `/etc/default/grub'
Sourcing file `/etc/default/grub.d/init-select.cfg'
Generating grub configuration file ...
Fo...

[Laurent Bonnaud (laurent-bonnaud)]

In Ubuntu 23.04/lunar those are gone on my system:

# update-initramfs -u -k all
update-initramfs: Generating /boot/initrd.img-6.2.0-1002-lowlatency
update-initramfs: Generating /boot/initrd.img-6.2.0-18-generic

# grub-install
Installing for x86_64-efi platform.
Installation finished. No error reported.

# update-grub
Sourcing file `/etc/default/grub'
Sourcing file `/etc/default/grub.d/init-select.cfg'
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-6.2.0-1002-lowlatency
Found initrd image: /boot/initrd.img-6.2.0-1002-lowlatency
Found linux image: /boot/vmlinuz-6.2.0-18-generic
Found initrd image: /boot/initrd.img-6.2.0-18-generic
Adding boot menu entry for UEFI Firmware Settings ...
done