Test 550 with GROMACS rebuild in #576 by trz42 · Pull Request #577 · EESSI/software-layer

trz42 · 2024-05-15T13:26:10Z

We are interested in verifying if the ReFrame tests run are using the updated GROMACS build. We probably have to inspect the log files on the build cluster for this.

`PSM2` was introduced as a dependency of `libfabric` in easybuilders/easybuild-easyconfigs#20501. We already have PSM2 in the compat layer, so we can filter this dependency out, but longer term we probably actually want it since it should be built with accelerator support.

…ware-layer into test_550_with_GROMACS_rebuild_in_576

eessi-bot · 2024-05-15T13:26:14Z

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

arch x86_64/generic for repo eessi-hpc.org-2023.06-compat
arch x86_64/generic for repo eessi-hpc.org-2023.06-software
arch x86_64/generic for repo eessi.io-2023.06-compat
arch x86_64/generic for repo eessi.io-2023.06-software
arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-compat
arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-software
arch x86_64/intel/haswell for repo eessi.io-2023.06-compat
arch x86_64/intel/haswell for repo eessi.io-2023.06-software
arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-compat
arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-software
arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-compat
arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-software
arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-compat
arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-software
arch x86_64/amd/zen2 for repo eessi.io-2023.06-compat
arch x86_64/amd/zen2 for repo eessi.io-2023.06-software
arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-compat
arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-software
arch x86_64/amd/zen3 for repo eessi.io-2023.06-compat
arch x86_64/amd/zen3 for repo eessi.io-2023.06-software
arch aarch64/generic for repo eessi-hpc.org-2023.06-compat
arch aarch64/generic for repo eessi-hpc.org-2023.06-software
arch aarch64/generic for repo eessi.io-2023.06-compat
arch aarch64/generic for repo eessi.io-2023.06-software
arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-compat
arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-software
arch aarch64/neoverse_n1 for repo eessi.io-2023.06-compat
arch aarch64/neoverse_n1 for repo eessi.io-2023.06-software
arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-compat
arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-software
arch aarch64/neoverse_v1 for repo eessi.io-2023.06-compat
arch aarch64/neoverse_v1 for repo eessi.io-2023.06-software

eessi-bot · 2024-05-15T13:26:15Z

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

arch x86_64/amd/zen4 for repo eessi-hpc.org-2023.06-compat
arch x86_64/amd/zen4 for repo eessi-hpc.org-2023.06-software
arch x86_64/amd/zen4 for repo eessi.io-2023.06-compat
arch x86_64/amd/zen4 for repo eessi.io-2023.06-software

trz42 · 2024-05-15T13:27:26Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3

eessi-bot · 2024-05-15T13:27:29Z

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/zen3 from trz42
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 10793, for details & status see Test 550 with GROMACS rebuild in #576 #577 (comment)

eessi-bot · 2024-05-15T13:27:29Z

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/zen3 from trz42
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted

eessi-bot · 2024-05-15T13:27:33Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen3 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.05/pr_577/10793

date	job status	comment
May 15 13:27:32 UTC 2024	submitted	job id `10793` awaits release by job manager
May 15 13:27:49 UTC 2024	released	job awaits launch by Slurm scheduler
May 15 13:28:51 UTC 2024	running	job `10793` is running
May 15 13:33:56 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-10793.out` ❌ found 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-zen3-1715779762.tar.gz` size: 0 MiB (402291 bytes) entries: 210 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `scikit-build-core/0.9.3-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `scikit-build-core/0.9.3-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen3 no other files in tarball
May 15 13:33:56 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-10793.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

trz42 · 2024-05-15T13:49:03Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3

eessi-bot · 2024-05-15T13:49:05Z

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/zen3 from trz42
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 10794, for details & status see Test 550 with GROMACS rebuild in #576 #577 (comment)

eessi-bot · 2024-05-15T13:49:06Z

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/zen3 from trz42
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted

eessi-bot · 2024-05-15T13:49:10Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen3 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.05/pr_577/10794

date	job status	comment
May 15 13:49:09 UTC 2024	submitted	job id `10794` awaits release by job manager
May 15 13:50:00 UTC 2024	released	job awaits launch by Slurm scheduler
May 15 13:51:02 UTC 2024	running	job `10794` is running
May 15 14:34:46 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-10794.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-zen3-1715783356.tar.gz` size: 47 MiB (49816382 bytes) entries: 980 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `GROMACS/2024.1-foss-2023b.lua` `scikit-build-core/0.9.3-GCCcore-13.2.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `GROMACS/2024.1-foss-2023b` `scikit-build-core/0.9.3-GCCcore-13.2.0` other under 2023.06/software/linux/x86_64/amd/zen3 no other files in tarball
May 15 14:34:46 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-10794.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

Issues seen when trying to use `from-commit` in EESSI#577

ocaisa · 2024-05-15T15:11:42Z

@trz42 Can you do your check of the log to see if this worked as expected. I would really like to get #576 merged ASAP

trz42 · 2024-05-15T15:47:57Z

@trz42 Can you do your check of the log to see if this worked as expected. I would really like to get #576 merged ASAP

Checked the logs. Didn't find anything that lists the "build" time of the GROMACS executable. I'd say, just go ahead with deploying #576

trz42 · 2024-07-29T10:11:01Z

Obsolete.

truib and others added 7 commits April 21, 2024 21:16

enable mounting previous overlay-upper read-only

08f8854

Update configure_easybuild

ec2e8bd

Add a rebuild of GROMACS

3cdb7b2

Also add new dependency on scikit-build-core

fb329a4

Use from-commit for merged PRs

792ea3e

Merge branch 'mount_overlay-upper_read-only' of github-trz:trz42/soft…

28739c4

…ware-layer into test_550_with_GROMACS_rebuild_in_576

trz42 added tests Related to software testing 2023.06-software.eessi.io 2023.06 version of software.eessi.io labels May 15, 2024

use from-pr instead of from-commit

29dd14d

ocaisa added a commit to ocaisa/software-layer that referenced this pull request May 15, 2024

Update 20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml

375bf37

Issues seen when trying to use `from-commit` in EESSI#577

trz42 closed this Jul 29, 2024

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