{zen4} prevent GObject-Introspection from setting EB-filtered environment variables #647

bedroge · 2024-07-19T13:32:22Z

Requires #646, and this will do the rebuilds for zen4. For zen4 we didn't have any at-spi2-core versions yet, and no GObject-Introspection for GCC 12.2.0 either.

eessi-bot · 2024-07-19T13:32:25Z

Instance eessi-bot-mc-aws is configured to build for:

architectures: x86_64/generic, x86_64/intel/haswell, x86_64/intel/skylake_avx512, x86_64/amd/zen2, x86_64/amd/zen3, aarch64/generic, aarch64/neoverse_n1, aarch64/neoverse_v1
repositories: eessi.io-2023.06-compat, eessi-hpc.org-2023.06-software, eessi-hpc.org-2023.06-compat, eessi.io-2023.06-software

eessi-bot · 2024-07-19T13:32:26Z

Instance eessi-bot-mc-azure is configured to build for:

architectures: x86_64/amd/zen4
repositories: eessi-hpc.org-2023.06-compat, eessi-hpc.org-2023.06-software, eessi.io-2023.06-software, eessi.io-2023.06-compat

bedroge · 2024-07-19T16:23:38Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4

eessi-bot · 2024-07-19T16:23:41Z

Updates by the bot instance eessi-bot-mc-aws (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- no jobs were submitted

eessi-bot · 2024-07-19T16:23:41Z

Updates by the bot instance eessi-bot-mc-azure (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- submitted job 153, for details & status see {zen4} prevent GObject-Introspection from setting EB-filtered environment variables #647 (comment)

eessi-bot · 2024-07-19T16:23:45Z

New job on instance eessi-bot-mc-azure for architecture x86_64-amd-zen4 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_647/153

date	job status	comment
Jul 19 16:23:44 UTC 2024	submitted	job id `153` awaits release by job manager
Jul 19 16:23:56 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 19 16:27:59 UTC 2024	running	job `153` is running
Jul 19 16:29:00 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-153.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen4-1721406495.tar.gz` size: 0 MiB (10402 bytes) entries: 1 modules under 2023.06/software/linux/x86_64/amd/zen4/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/amd/zen4/software no software packages in tarball other under 2023.06/software/linux/x86_64/amd/zen4 `2023.06/init/easybuild/eb_hooks.py`
Jul 19 16:29:00 UTC 2024	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite was not run, test step itself failed to execute. Details ✅ job output file `slurm-153.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-07-19T18:34:33Z

Looks like fakeroot doesn't work on this cluster?

FATAL:   exec /.singularity.d/libs/fakeroot failed: fork/exec /.singularity.d/libs/fakeroot: no such file or directory

ocaisa · 2024-07-21T19:35:56Z

Could be, I think I can fix this temporarily, starting the node and installing it by hand. A permanent fix would need rebuilding of the compute node image

ocaisa · 2024-07-22T09:59:38Z

It seems like we are hitting apptainer/apptainer#2189 on our AlmaLinux 9 cluster. A workaround is to do

sudo apptainer config fakeroot --add bot

on the node. This adds the bot account to /etc/subuid.

To make the hack permanent we would need to modify the image for the worker nodes.

ocaisa · 2024-07-22T10:00:32Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4

eessi-bot · 2024-07-22T10:00:35Z

Updates by the bot instance eessi-bot-mc-aws (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from ocaisa
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- no jobs were submitted

eessi-bot · 2024-07-22T10:00:35Z

Updates by the bot instance eessi-bot-mc-azure (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from ocaisa
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- submitted job 159, for details & status see {zen4} prevent GObject-Introspection from setting EB-filtered environment variables #647 (comment)

eessi-bot · 2024-07-22T10:00:39Z

New job on instance eessi-bot-mc-azure for architecture x86_64-amd-zen4 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.07/pr_647/159

date	job status	comment
Jul 22 10:00:38 UTC 2024	submitted	job id `159` awaits release by job manager
Jul 22 10:00:58 UTC 2024	released	job awaits launch by Slurm scheduler
Jul 22 10:02:00 UTC 2024	running	job `159` is running
Jul 22 10:05:04 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-159.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen4-1721642625.tar.gz` size: 5 MiB (5527686 bytes) entries: 449 modules under 2023.06/software/linux/x86_64/amd/zen4/modules/all `GObject-Introspection/1.76.1-GCCcore-12.3.0.lua` `GObject-Introspection/1.78.1-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen4/software `GObject-Introspection/1.76.1-GCCcore-12.3.0` `GObject-Introspection/1.78.1-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen4 `2023.06/init/easybuild/eb_hooks.py`
Jul 22 10:05:04 UTC 2024	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite was not run, test step itself failed to execute. Details ✅ job output file `slurm-159.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Jul 22 10:31:42 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen4-1721642625.tar.gz` to S3 bucket succeeded

ocaisa · 2024-07-22T10:29:11Z

@bedroge That worked!

bedroge · 2024-07-22T10:55:15Z

Manual ingestion procedure:

cvmfs_server transaction software.eessi.io

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen4/software/GObject-Introspection

cd /cvmfs/software.eessi.io/versions

tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-amd-zen4-1721642625.tar.gz

cd

cvmfs_server diff --worktree software.eessi.io > PR647-diff.txt
cvmfs_server publish -m "rebuilds of GObject-Introspection for zen4, PR 647" software.eessi.io

bedroge · 2024-07-22T10:58:35Z

Completed the manual ingestion, and also merged the staging PR (which will reingest/overwrite it).

rebuild GObject-Introspection for zen4

20eafc7

bedroge added bug Something isn't working 2023.06-software.eessi.io 2023.06 version of software.eessi.io labels Jul 19, 2024

ocaisa added the bot:deploy Ask bot to deploy missing software installations to EESSI label Jul 22, 2024

ocaisa approved these changes Jul 22, 2024

View reviewed changes

ocaisa merged commit 8b2a716 into EESSI:2023.06-software.eessi.io Jul 22, 2024

bedroge deleted the gobject_introspection_fix_zen4 branch July 22, 2024 11:42

ocaisa mentioned this pull request Jul 22, 2024

Issues lurking with gobject-introspection #196

Closed

{zen4} prevent GObject-Introspection from setting EB-filtered environment variables #647

{zen4} prevent GObject-Introspection from setting EB-filtered environment variables #647

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