DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing `LD_PRELOAD` #688

trz42 · 2024-08-27T20:36:06Z

Just to test if the tweaked hooks solve the build issue for SentencePiece on aarch64 CPUs. See #585

1 out of 2 required modules missing:

* libmad/0.15.1b-GCCcore-12.3.0 (libmad-0.15.1b-GCCcore-12.3.0.eb)

and

12 out of 137 required modules missing:

* parameterized/0.9.0-GCCcore-12.3.0 (parameterized-0.9.0-GCCcore-12.3.0.eb)
* tqdm/4.66.1-GCCcore-12.3.0 (tqdm-4.66.1-GCCcore-12.3.0.eb)
* Scalene/1.5.26-GCCcore-12.3.0 (Scalene-1.5.26-GCCcore-12.3.0.eb)
* gperftools/2.12-GCCcore-12.3.0 (gperftools-2.12-GCCcore-12.3.0.eb)
* SentencePiece/0.2.0-GCC-12.3.0 (SentencePiece-0.2.0-GCC-12.3.0.eb)
* imageio/2.33.1-gfbf-2023a (imageio-2.33.1-gfbf-2023a.eb)
* tensorboard/2.15.1-gfbf-2023a (tensorboard-2.15.1-gfbf-2023a.eb)
* libmad/0.15.1b-GCCcore-12.3.0 (libmad-0.15.1b-GCCcore-12.3.0.eb)
* SoX/14.4.2-GCCcore-12.3.0 (SoX-14.4.2-GCCcore-12.3.0.eb)
* NLTK/3.8.1-foss-2023a (NLTK-3.8.1-foss-2023a.eb)
* scikit-image/0.22.0-foss-2023a (scikit-image-0.22.0-foss-2023a.eb)
* PyTorch-bundle/2.1.2-foss-2023a (PyTorch-bundle-2.1.2-foss-2023a.eb)

…n static TLS block error

…tcmalloc is also LD_PRELOADed in this step

eessi-bot · 2024-08-27T20:36:10Z

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-hpc.org-2023.06-compat, eessi-hpc.org-2023.06-software, eessi.io-2023.06-software, eessi.io-2023.06-compat

eessi-build-deploy-bot-deucalion · 2024-08-27T20:36:10Z

Instance boegel-bot-deucalion is configured to build for:

architectures: aarch64/a64fx
repositories: eessi.io-2023.06-software

eessi-bot · 2024-08-27T20:36:11Z

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

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

trz42 · 2024-08-27T20:37:17Z

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-27T20:37:19Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17105, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-build-deploy-bot-deucalion · 2024-08-27T20:37:19Z

Updates by the bot instance boegel-bot-deucalion (click for details)

account trz42 has NO permission to send commands to the bot

eessi-bot · 2024-08-27T20:37:20Z

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

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- no jobs were submitted

eessi-bot · 2024-08-27T20:37:23Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.08/pr_688/17105

date	job status	comment
Aug 27 20:37:22 UTC 2024	submitted	job id `17105` awaits release by job manager
Aug 27 20:38:12 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 27 20:39:16 UTC 2024	running	job `17105` is running
Aug 27 21:47:17 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-17105.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-generic-1724792235.tar.gz` size: 142 MiB (149144297 bytes) entries: 4815 modules under 2023.06/software/linux/aarch64/generic/modules/all `gperftools/2.12-GCCcore-12.3.0.lua` `imageio/2.33.1-gfbf-2023a.lua` `libmad/0.15.1b-GCCcore-12.3.0.lua` `NLTK/3.8.1-foss-2023a.lua` `parameterized/0.9.0-GCCcore-12.3.0.lua` `Scalene/1.5.26-GCCcore-12.3.0.lua` `scikit-image/0.22.0-foss-2023a.lua` `SentencePiece/0.2.0-GCC-12.3.0.lua` `SoX/14.4.2-GCCcore-12.3.0.lua` `tensorboard/2.15.1-gfbf-2023a.lua` `tqdm/4.66.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `gperftools/2.12-GCCcore-12.3.0` `imageio/2.33.1-gfbf-2023a` `libmad/0.15.1b-GCCcore-12.3.0` `NLTK/3.8.1-foss-2023a` `parameterized/0.9.0-GCCcore-12.3.0` `Scalene/1.5.26-GCCcore-12.3.0` `scikit-image/0.22.0-foss-2023a` `SentencePiece/0.2.0-GCC-12.3.0` `SoX/14.4.2-GCCcore-12.3.0` `tensorboard/2.15.1-gfbf-2023a` `tqdm/4.66.1-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/generic `2023.06/init/easybuild/eb_hooks.py`
Aug 27 21:47:17 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 18/18 test case(s) from 18 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-17105.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

trz42 · 2024-08-28T21:07:35Z

Try to use bash from compat layer...

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-28T21:07:38Z

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eessi-bot · 2024-08-28T21:07:39Z

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

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- no jobs were submitted

eessi-bot · 2024-08-28T21:07:42Z

`688.diff:29: trailing whitespace.

error: cannot apply binary patch to 'scripts/2023.06/aarch64/bash' without full index line
error: scripts/2023.06/aarch64/bash: patch does not apply
error: cannot apply binary patch to 'scripts/2023.06/x86_64/bash' without full index line
error: scripts/2023.06/x86_64/bash: patch does not apply
`Unable to download or merge changes between the source branch and the destination branch.Tip: This can usually be resolved by syncing your branch and resolving any merge conflicts.

trz42 · 2024-08-28T22:08:42Z

Second attempt to use bash from compat layer (now obtaining it from CVMFS)...

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-28T22:08:44Z

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

received bot command build arch:aarch64/generic repo:eessi.io-2023.06-software from trz42
- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17162, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-bot · 2024-08-28T22:46:18Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17164, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-bot · 2024-08-28T22:46:18Z

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handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- no jobs were submitted

eessi-bot · 2024-08-28T22:46:22Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.08/pr_688/17164

date	job status	comment
Aug 28 22:46:21 UTC 2024	submitted	job id `17164` awaits release by job manager
Aug 28 22:46:39 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 28 22:47:40 UTC 2024	running	job `17164` is running
Aug 28 22:49:42 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-17164.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts No artefacts were created or found.
Aug 28 22:49:42 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job17164.test` does not exist in job directory or reading it failed.

trz42 · 2024-08-28T22:49:46Z

One more...

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-28T22:49:48Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17165, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-bot · 2024-08-28T22:49:48Z

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handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- no jobs were submitted

eessi-bot · 2024-08-28T22:49:52Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.08/pr_688/17165

date	job status	comment
Aug 28 22:49:51 UTC 2024	submitted	job id `17165` awaits release by job manager
Aug 28 22:50:45 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 28 22:51:47 UTC 2024	running	job `17165` is running
Aug 28 22:55:51 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-17165.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts No artefacts were created or found.
Aug 28 22:55:51 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job17165.test` does not exist in job directory or reading it failed.

trz42 · 2024-08-28T22:56:34Z

+1

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-28T22:56:37Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17166, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-bot · 2024-08-28T22:56:37Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- no jobs were submitted

eessi-bot · 2024-08-28T22:56:40Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.08/pr_688/17166

date	job status	comment
Aug 28 22:56:39 UTC 2024	submitted	job id `17166` awaits release by job manager
Aug 28 22:56:53 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 28 22:57:55 UTC 2024	running	job `17166` is running
Aug 29 00:07:19 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-17166.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-generic-1724887036.tar.gz` size: 142 MiB (149143012 bytes) entries: 4815 modules under 2023.06/software/linux/aarch64/generic/modules/all `gperftools/2.12-GCCcore-12.3.0.lua` `imageio/2.33.1-gfbf-2023a.lua` `libmad/0.15.1b-GCCcore-12.3.0.lua` `NLTK/3.8.1-foss-2023a.lua` `parameterized/0.9.0-GCCcore-12.3.0.lua` `Scalene/1.5.26-GCCcore-12.3.0.lua` `scikit-image/0.22.0-foss-2023a.lua` `SentencePiece/0.2.0-GCC-12.3.0.lua` `SoX/14.4.2-GCCcore-12.3.0.lua` `tensorboard/2.15.1-gfbf-2023a.lua` `tqdm/4.66.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `gperftools/2.12-GCCcore-12.3.0` `imageio/2.33.1-gfbf-2023a` `libmad/0.15.1b-GCCcore-12.3.0` `NLTK/3.8.1-foss-2023a` `parameterized/0.9.0-GCCcore-12.3.0` `Scalene/1.5.26-GCCcore-12.3.0` `scikit-image/0.22.0-foss-2023a` `SentencePiece/0.2.0-GCC-12.3.0` `SoX/14.4.2-GCCcore-12.3.0` `tensorboard/2.15.1-gfbf-2023a` `tqdm/4.66.1-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/generic `2023.06/init/easybuild/eb_hooks.py`
Aug 29 00:07:19 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 18/18 test case(s) from 18 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-17166.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-08-29T09:29:28Z

      /bin/sh: /lib/aarch64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/generic/software/gperftools/2.12-GCCcore-12.3.0/lib64/libtcmalloc_mi
nimal.so)

@trz42 looks like you need to do the same for /bin/sh?

trz42 · 2024-08-29T15:19:23Z

Also replace /bin/sh with sh (which usually symlinks to bash)...

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-29T15:19:26Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17215, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-bot · 2024-08-29T15:19:27Z

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handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- no jobs were submitted

eessi-bot · 2024-08-29T15:19:30Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.08/pr_688/17215

date	job status	comment
Aug 29 15:19:29 UTC 2024	submitted	job id `17215` awaits release by job manager
Aug 29 15:19:34 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 29 15:25:37 UTC 2024	running	job `17215` is running
Aug 29 17:32:22 UTC 2024	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job17215.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Aug 29 17:32:22 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job17215.test` does not exist in job directory or reading it failed.

trz42 · 2024-08-29T18:43:30Z

Revert change on /bin/sh and build libmad first...

bot: build arch:aarch64/generic repo:eessi.io-2023.06-software

eessi-bot · 2024-08-29T18:43:32Z

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- expanded format: build architecture:aarch64/generic repository:eessi.io-2023.06-software
handling command build architecture:aarch64/generic repository:eessi.io-2023.06-software resulted in:
- submitted job 17216, for details & status see DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688 (comment)

eessi-bot · 2024-08-29T18:43:32Z

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eessi-bot · 2024-08-29T18:43:36Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.08/pr_688/17216

date	job status	comment
Aug 29 18:43:35 UTC 2024	submitted	job id `17216` awaits release by job manager
Aug 29 18:44:31 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 29 18:50:33 UTC 2024	running	job `17216` is running
Aug 29 20:00:01 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-17216.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-generic-1724958582.tar.gz` size: 142 MiB (149142604 bytes) entries: 4815 modules under 2023.06/software/linux/aarch64/generic/modules/all `gperftools/2.12-GCCcore-12.3.0.lua` `imageio/2.33.1-gfbf-2023a.lua` `libmad/0.15.1b-GCCcore-12.3.0.lua` `NLTK/3.8.1-foss-2023a.lua` `parameterized/0.9.0-GCCcore-12.3.0.lua` `Scalene/1.5.26-GCCcore-12.3.0.lua` `scikit-image/0.22.0-foss-2023a.lua` `SentencePiece/0.2.0-GCC-12.3.0.lua` `SoX/14.4.2-GCCcore-12.3.0.lua` `tensorboard/2.15.1-gfbf-2023a.lua` `tqdm/4.66.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `gperftools/2.12-GCCcore-12.3.0` `imageio/2.33.1-gfbf-2023a` `libmad/0.15.1b-GCCcore-12.3.0` `NLTK/3.8.1-foss-2023a` `parameterized/0.9.0-GCCcore-12.3.0` `Scalene/1.5.26-GCCcore-12.3.0` `scikit-image/0.22.0-foss-2023a` `SentencePiece/0.2.0-GCC-12.3.0` `SoX/14.4.2-GCCcore-12.3.0` `tensorboard/2.15.1-gfbf-2023a` `tqdm/4.66.1-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/generic `2023.06/init/easybuild/eb_hooks.py`
Aug 29 20:00:01 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 18/18 test case(s) from 18 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-17216.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

trz42 · 2024-08-30T12:58:55Z

The last job failed while building the wheel for torchtext when running ninja which is using /bin/sh. It might be that ninja has this path hard-coded vs using sh from the compat layer. See below

$ strings /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/generic/software/Ninja/1.11.1-GCCcore-12.3.0/bin/ninja | grep /bin
#!/usr/bin/env python
/bin/sh

We could try to figure out how to use /bin/sh (and maybe /usr/bin/env) from the compat layer. We have to look into how ninja was built and try to change that, then rebuild it ... we could probably test if a change helps solving the problem by installing a changed ninja into some other location employing EESSI-extend/2023.06-easybuild.

laraPPr · 2025-06-27T14:19:59Z

@trz42 Can you retarget this pr?

trz42 · 2025-08-13T07:27:40Z

Closing this. If we want to take the package up again, we need to start over fresh.

Caspar van Leeuwen and others added 11 commits May 23, 2024 11:20

Add PyTorch-Bundle for 2023a for CPU

cc9a640

Switch to from-pr

ca08b19

Merge branch '2023.06-software.eessi.io' into pytorch-bundle-cpu

7de9b31

Build with eb 4.9.2 instead to get the updated EasyBlock from PR 3322

1183a5d

Merge branch '2023.06-software.eessi.io' into pytorch-bundle-cpu

5b015bd

Merge branch '2023.06-software.eessi.io' into pytorch-bundle-cpu

2eb7044

Workaround for the libtcmalloc_minimal.so.4: cannot allocate memory i…

db513ca

…n static TLS block error

Only apply workaround for AARCH64, since it's only a problem there

3d72e34

Make sure hook gets applied before the sanity check step, so that lib…

a777e47

…tcmalloc is also LD_PRELOADed in this step

Take out debugging print statement

71679c7

tweak hooks for LD_PRELOAD to fix TLS issue on aarch64

a635ff2

trz42 added aarch64 related to Arm 64-bit targets (aarch64) 2023.06-software.eessi.io 2023.06 version of software.eessi.io labels Aug 27, 2024

use bash from compat layer when running commands in container

b741ca7

truib added 2 commits August 28, 2024 23:24

remove binaries from PR

dcb8b94

obtain compat layer bash from CVMFS

324d2f9

use different run mode

f33f5dd

try plain cp again

536bac0

also replace /bin/sh (symlinks to bash)

fbce0bd

revert change on /bin/sh, build libmad first

9e2fb59

laraPPr added clean-up This label indicates that the pr was because the original pr required a significant update. and removed clean-up This label indicates that the pr was because the original pr required a significant update. labels Jul 1, 2025

trz42 closed this Aug 13, 2025

DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688

DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing LD_PRELOAD #688

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DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing `LD_PRELOAD` #688

DEBUG only {2023.06}[2023a] PyTorch-Bundle v2.1.2 -- tweaked hooks employing `LD_PRELOAD` #688

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