GNU bug report logs - #41484
guix gc fails catastrophically if the disk has no space left

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Package: guix; Severity: important; Reported by: Stefan <stefan-guix@HIDDEN>; merged with #45266; dated Sat, 23 May 2020 14:50:02 UTC; Maintainer for guix is bug-guix@HIDDEN.
Merged 41484 45266. Request was from Ludovic Courtès <ludo@HIDDEN> to control <at> debbugs.gnu.org. Full text available.
Severity set to 'important' from 'normal' Request was from Ludovic Courtès <ludo@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

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Date: Sat, 23 May 2020 21:57:33 +0200
From: raingloom <raingloom@HIDDEN>
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Subject: Re: bug#41484: guix gc fails catastrophically if the disk has no
 space left
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On Sat, 23 May 2020 16:49:02 +0200
Stefan <stefan-guix@HIDDEN> wrote:

> Hi!
>=20
> While trying to build guix, my disk ran out of space.
>=20
> building
> /gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv...
> 100%
> [########################################################################=
#]note:
> build failure may have been caused by lack of free disk space builder
> for
> `/gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv'
> failed with exit code 1 build of
> /gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv
> failed View build log at
> '/var/log/guix/drvs/w5/l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801=
e.drv.bz2'.
> guix system: error: build of
> `/gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv'
> failed
>=20
> stefan@guix ~$ df -h /
> Dateisystem                                       Gr=C3=B6=C3=9Fe Benutzt=
 Verf.
> Verw% Eingeh=C3=A4ngt auf
> :/volume5/RaspberryPi/Betriebssysteme/guix-system  1,4T    1,4T     0
>  100% /
>=20
> OK, well, there=E2=80=99s certainly a lot of garbage to collect. Due to b=
ad
> experiences in the past with the same situation, I first try to
> collect only a little garbage.
>=20
> stefan@guix ~$ guix gc -F 100M
> guix gc: 100 MiB werden freigegeben
> finding garbage collector roots...
> note: can't create trash directory: creating directory
> `/gnu/store/trash': No space left on device deleting garbage...
> [0%] deleting
> '/gnu/store/g30aknl5yxk9jbpx2w7r5d0ak6xa5dl2-grub.cfg.lock' [0%]
> deleting
> '/gnu/store/gidc7jrgbnvfm38qx4sc012kn9llgsvz-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04-collection.lock'
> [0%] deleting
> '/gnu/store/9cpj3ir8fnsg5fiqs3x8alai713xzfz0-grub-keymap.de.lock'
> [0%] deleting
> '/gnu/store/z08s3kwlnpqq6aa1v6ydni5qp2k7gkkb-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04'
> [0%] deleting
> '/gnu/store/wv7iwd66q6n5775qa4hgaq9j9f2vyvl4-guix-1.1.0-4.bdc801e.lock'
> [0%] deleting
> '/gnu/store/pab2ylsvas12824qw6j8q2h1qm3gh4x6-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04-union.lock'
> [0%] deleting
> '/gnu/store/3ldyga22s6ym9g2pc9ycjwdwqb4i41v2-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04.lock'
> [0%] deleting
> '/gnu/store/nfxgqhjyzwngiadn0l180hsbfnw3h4zy-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04-collection.lock'
> [0%] deleting
> '/gnu/store/pab2ylsvas12824qw6j8q2h1qm3gh4x6-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04-union'
> [0%] deleting
> '/gnu/store/dahbiixsbi1xhjiim9phl1vginm83bbm-grub.cfg.lock' [0%]
> deleting
> '/gnu/store/61mwka1h77kkhylcs9jj4ij167qgfj39-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04.lock'
> [0%] deleting
> '/gnu/store/q829h36vnwhbdlnzkgdrx2b51kp2mvdv-grub.cfg.lock' [0%]
> deleting '/gnu/store/ragpi42x39sf5qwcmcmdn751fp4jfhmv-grub.cfg.lock'
> [0%] deleting
> '/gnu/store/ncdsjfl245k6r7zym6w4sr9fyxrwhb38-grub.cfg.lock' [0%]
> deleting
> '/gnu/store/z08s3kwlnpqq6aa1v6ydni5qp2k7gkkb-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04.lock'
> [0%] deleting
> '/gnu/store/gidc7jrgbnvfm38qx4sc012kn9llgsvz-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04-collection'
> [0%] deleting
> '/gnu/store/61mwka1h77kkhylcs9jj4ij167qgfj39-package-collection-grub-efi-=
raspberrypi-firmware-u-boot-rpi-3-2.04'
> [0%] deleting
> '/gnu/store/hmy4ni005digrilzjf93wr9gaj5cq536-computed-files.lock'
> [0%] deleting
> '/gnu/store/hmy4ni005digrilzjf93wr9gaj5cq536-computed-files' error
> (ignored): aborting transaction: cannot rollback - no transaction is
> active guix gc: error: committing transaction: disk I/O error
> stefan@guix ~$=20
>=20
> And that=E2=80=99s it. Repeating the guix gc command now results in this
> immediate error:
>=20
> stefan@guix ~$ guix gc -F 100M
> warning: SQLite database is busy (SQLITE_PROTOCOL)
> guix gc: error: setting synchronous mode: locking protocol
> stefan@guix ~$ guix gc -F 100M
> warning: SQLite database is busy (SQLITE_PROTOCOL)
> guix gc: error: setting synchronous mode: locking protocol
>=20
> A reboot is needed to solve this SQLite error. But retrying all this
> leads to the same situation again and again. It is kind of a deadlock.
>=20
> Well, as my guix system boots from an NFS share, in the past I solved
> this by removing other stuff =E2=80=93 not related to guix =E2=80=93 from=
 the same
> disk. But right now there isn't unrelated stuff left to be deleted.=20
>=20
> I intend to remove the listed /gnu/store/=E2=80=A6 files by hand from the=
 NFS
> server side (which is much easier than removing the read-only
> bind-mount.) Is this save at least?
>=20
> This is all on a Raspberry Pi 3b aarch64 machine, if it matters.
>=20
>=20
> Bye
>=20
> Stefan
>=20
>=20
>=20
>=20

Try deleting /var/log. That's what I did on my tiny Pentium II desktop
with 4 gigs of HDD space.
Information forwarded to bug-guix@HIDDEN:
bug#41484; Package guix. Full text available.

Message received at 41484 <at> debbugs.gnu.org:


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Subject: guix gc fails catastrophically if the disk has no space left
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Hi!

After this trouble with guix gc I did a sudo reboot, and it got worse. =
At startup I now see these errors:

GC Warning: pthread_getattr_up or pthread_attr_getstack failed for main =
thread
GC Warning: Couldn't read /proc/stat
Welcome, this is GNU's early boot Guile.
Use --repl for an initrd REPL.

loading kernel modules=E2=80=A6
loading '/gnu/store/=E2=80=A6-system/boot'...
making '/gnu/store/=E2=80=A6-system' the current system...
setting up setuid programs in '/run/setuid-programs'...
warning: failed to make '/gnu/store/=E2=80=A6-shadow-4.8.1/bin/newuidmap' =
setuid-root: No space left on device
warning: failed to make '/gnu/store/=E2=80=A6' setuid-root: No space =
left on device
=E2=80=A6
populating /etc from /gnu/store/=E2=80=A6-etc...
ERROR: In procedure fsync:
In procedure fsync: No space left on device

Entering a new prompt.  Type `,bt' for a backtrace or `,q' to continue.
GNU Guile 2.2.6
Copyright =E2=80=A6
=E2=80=A6

Enter `help' for help.
scheme@(guile-user)> ,bt
In gnu/build/linux-boot.scm:
   561:14 10 (_)
In unknown file:
           9 (primitive-load "/gnu/store/=E2=80=A6")
In ice-9/eval.scm:
   619:8 (_ #f)
In unknown file:
           7 (primitive-load "/gnu/store/=E2=80=A6")
In ice-9/boot-9.scm:
   260:13  6 (for-each #<procedure primitive-load (_)> _)
In unknown file:
           5 (primitive-load "/gnu/store/_")
In gnu/build/activation.scm:
    136:2  4 (activate-users+groups _ _)
In guix/build/syscalls.scm:
   1089:4  3 (call-with-file-lock _ _)
In gnu/build/activation.scm:
    139:6  2 (_)
In gnu/build/accounts.scm:
   253:14  1 (_ (#<<group-entry> name: "root" password: #f gid: =E2=80=A6>=
 =E2=80=A6) =E2=80=A6)
In unknown file:
           0 (fsync #<input-output: /etc/group.bJpcke 18>)
scheme@(guile-user)>


Now this is the very end. Even selecting an older system generation is =
obviously not an option any more.=20

I=E2=80=99m happy that all this is on my NFS share to which I have =
access via my server.


Bye

Stefan=
Information forwarded to bug-guix@HIDDEN:
bug#41484; Package guix. Full text available.

Message received at submit <at> debbugs.gnu.org:


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Subject: guix gc fails catastrophically if the disk has no space left
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Hi!

While trying to build guix, my disk ran out of space.

building =
/gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv...
100% =
[#########################################################################=
]note: build failure may have been caused by lack of free disk space
builder for =
`/gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv' =
failed with exit code 1
build of =
/gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv =
failed
View build log at =
'/var/log/guix/drvs/w5/l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e=
.drv.bz2'.
guix system: error: build of =
`/gnu/store/w5l7acwbfvn0n8zj2v9by4j3jwbiimj9-guix-1.1.0-4.bdc801e.drv' =
failed

stefan@guix ~$ df -h /
Dateisystem                                       Gr=C3=B6=C3=9Fe =
Benutzt Verf. Verw% Eingeh=C3=A4ngt auf
:/volume5/RaspberryPi/Betriebssysteme/guix-system  1,4T    1,4T     0  =
100% /

OK, well, there=E2=80=99s certainly a lot of garbage to collect. Due to =
bad experiences in the past with the same situation, I first try to =
collect only a little garbage.

stefan@guix ~$ guix gc -F 100M
guix gc: 100 MiB werden freigegeben
finding garbage collector roots...
note: can't create trash directory: creating directory =
`/gnu/store/trash': No space left on device
deleting garbage...
[0%] deleting =
'/gnu/store/g30aknl5yxk9jbpx2w7r5d0ak6xa5dl2-grub.cfg.lock'
[0%] deleting =
'/gnu/store/gidc7jrgbnvfm38qx4sc012kn9llgsvz-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04-collection.lock'
[0%] deleting =
'/gnu/store/9cpj3ir8fnsg5fiqs3x8alai713xzfz0-grub-keymap.de.lock'
[0%] deleting =
'/gnu/store/z08s3kwlnpqq6aa1v6ydni5qp2k7gkkb-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04'
[0%] deleting =
'/gnu/store/wv7iwd66q6n5775qa4hgaq9j9f2vyvl4-guix-1.1.0-4.bdc801e.lock'
[0%] deleting =
'/gnu/store/pab2ylsvas12824qw6j8q2h1qm3gh4x6-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04-union.lock'
[0%] deleting =
'/gnu/store/3ldyga22s6ym9g2pc9ycjwdwqb4i41v2-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04.lock'
[0%] deleting =
'/gnu/store/nfxgqhjyzwngiadn0l180hsbfnw3h4zy-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04-collection.lock'
[0%] deleting =
'/gnu/store/pab2ylsvas12824qw6j8q2h1qm3gh4x6-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04-union'
[0%] deleting =
'/gnu/store/dahbiixsbi1xhjiim9phl1vginm83bbm-grub.cfg.lock'
[0%] deleting =
'/gnu/store/61mwka1h77kkhylcs9jj4ij167qgfj39-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04.lock'
[0%] deleting =
'/gnu/store/q829h36vnwhbdlnzkgdrx2b51kp2mvdv-grub.cfg.lock'
[0%] deleting =
'/gnu/store/ragpi42x39sf5qwcmcmdn751fp4jfhmv-grub.cfg.lock'
[0%] deleting =
'/gnu/store/ncdsjfl245k6r7zym6w4sr9fyxrwhb38-grub.cfg.lock'
[0%] deleting =
'/gnu/store/z08s3kwlnpqq6aa1v6ydni5qp2k7gkkb-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04.lock'
[0%] deleting =
'/gnu/store/gidc7jrgbnvfm38qx4sc012kn9llgsvz-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04-collection'
[0%] deleting =
'/gnu/store/61mwka1h77kkhylcs9jj4ij167qgfj39-package-collection-grub-efi-r=
aspberrypi-firmware-u-boot-rpi-3-2.04'
[0%] deleting =
'/gnu/store/hmy4ni005digrilzjf93wr9gaj5cq536-computed-files.lock'
[0%] deleting =
'/gnu/store/hmy4ni005digrilzjf93wr9gaj5cq536-computed-files'
error (ignored): aborting transaction: cannot rollback - no transaction =
is active
guix gc: error: committing transaction: disk I/O error
stefan@guix ~$=20

And that=E2=80=99s it. Repeating the guix gc command now results in this =
immediate error:

stefan@guix ~$ guix gc -F 100M
warning: SQLite database is busy (SQLITE_PROTOCOL)
guix gc: error: setting synchronous mode: locking protocol
stefan@guix ~$ guix gc -F 100M
warning: SQLite database is busy (SQLITE_PROTOCOL)
guix gc: error: setting synchronous mode: locking protocol

A reboot is needed to solve this SQLite error. But retrying all this =
leads to the same situation again and again. It is kind of a deadlock.

Well, as my guix system boots from an NFS share, in the past I solved =
this by removing other stuff =E2=80=93 not related to guix =E2=80=93 =
from the same disk. But right now there isn't unrelated stuff left to be =
deleted.=20

I intend to remove the listed /gnu/store/=E2=80=A6 files by hand from =
the NFS server side (which is much easier than removing the read-only =
bind-mount.) Is this save at least?

This is all on a Raspberry Pi 3b aarch64 machine, if it matters.


Bye

Stefan
Acknowledgement sent to Stefan <stefan-guix@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#41484; Package guix. Full text available.
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