use the included gmxapi for GROMACS 2024.1 by bedroge · Pull Request #20522 · easybuilders/easybuild-easyconfigs

bedroge · 2024-05-14T09:44:45Z

Seems like #20102 forgot to bump the gmxapi version and source tarball, it was still using an older version from the 2023.3 tarball. Looking at https://gitlab.com/gromacs/gromacs/-/blob/v2024.1/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags#L68, the 2024.1 release includes gmxapi 0.5.0.

bedroge · 2024-05-14T09:45:41Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16

boegelbot · 2024-05-14T09:50:09Z

@bedroge: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20522 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20522 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4115

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

bedroge · 2024-05-14T10:12:13Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2024-05-14T10:15:09Z

@bedroge: Request for testing this PR well received on login1

PR test command 'EB_PR=20522 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20522 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13457

Test results coming soon (I hope)...

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boegelbot · 2024-05-14T10:16:41Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/2f11c046451bfb404af020ab16dded57 for a full test report.

ocaisa · 2024-05-14T10:27:55Z

@bedroge Looks like it needs another build dependency:

ModuleNotFoundError: No module named 'scikit_build_core'

boegelbot · 2024-05-14T10:51:36Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/3825dab1d52daa45ef231f7b03fce59c for a full test report.

bedroge · 2024-05-14T15:06:32Z

@bedroge Looks like it needs another build dependency:
ModuleNotFoundError: No module named 'scikit_build_core'

Opened a PR for a new scikit-build-core, which seems to work (based on a manual/interactive test): #20526

…asyconfigs into gromacs_2024.1_bump_gmxapi

bedroge · 2024-05-14T16:49:03Z

@bedroge Looks like it needs another build dependency:
ModuleNotFoundError: No module named 'scikit_build_core'
Opened a PR for a new scikit-build-core, which seems to work (based on a manual/interactive test): #20526

That PR just got merged, and I've done another test build without scikit-build (as I couldn't find anywhere that this is required) but with scikit-build-core, and that worked fine.

bedroge · 2024-05-14T16:49:21Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16

boegelbot · 2024-05-14T16:50:08Z

@bedroge: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20522 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20522 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4119

Test results coming soon (I hope)...

Details

- notification for comment with ID 2110691946 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-05-14T17:16:51Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/df320479170d74543d06d84975cb8eeb for a full test report.

bedroge · 2024-05-14T17:20:28Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2024-05-14T17:25:09Z

@bedroge: Request for testing this PR well received on login1

PR test command 'EB_PR=20522 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20522 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13462

Test results coming soon (I hope)...

Details

- notification for comment with ID 2110751313 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-05-14T18:02:19Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/e48d2e6e9e8e791e7112c455e6ab4f42 for a full test report.

SebastianAchilles

lgtm

SebastianAchilles · 2024-05-14T18:07:56Z

Going in, thanks @bedroge!

ocaisa · 2024-05-14T18:08:06Z

What about adding the SVE patch in https://gitlab.com/gromacs/gromacs/-/merge_requests/4299 ?

SebastianAchilles · 2024-05-14T18:12:12Z

What about adding the SVE patch in https://gitlab.com/gromacs/gromacs/-/merge_requests/4299 ?

I would suggest to open a follow-up PR for that.

bedroge · 2024-05-14T18:12:49Z

What about adding the SVE patch in https://gitlab.com/gromacs/gromacs/-/merge_requests/4299 ?

I haven't tested their patch yet, and since it's unrelated to the change in this PR, we can do it in a follow-up PR. But maybe we should also be a bit careful and wait for it to get merged upstream (or only apply it to Neoverse V1 or something)?

boegel · 2024-05-15T14:39:21Z

What about adding the SVE patch in https://gitlab.com/gromacs/gromacs/-/merge_requests/4299 ?

I haven't tested their patch yet, and since it's unrelated to the change in this PR, we can do it in a follow-up PR. But maybe we should also be a bit careful and wait for it to get merged upstream (or only apply it to Neoverse V1 or something)?

I think they're waiting for feedback from us to confirm that the fix works on our side too, I'm looking into that (but it's difficult to find time for that during ISC'24)...

boegel · 2024-05-16T05:37:14Z

easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb

        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
-        'source_tmpl': 'gromacs-2023.3.tar.gz',
+        'source_tmpl': 'gromacs-2024.1.tar.gz',


@bedroge @ocaisa We should use %(version)s here to avoid running into this again in the future?

And a comment on how to determine the gmxapi version that is shipped with GROMACS

bump gmxapi version to 0.5.0 and use correct gromacs source tarball

3882e66

bedroge added the bug fix label May 14, 2024

bedroge added 2 commits May 14, 2024 18:47

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

43fca17

…asyconfigs into gromacs_2024.1_bump_gmxapi

replace scikit-build by scikit-build-core

e5861a0

SebastianAchilles added this to the release after 4.9.1 milestone May 14, 2024

SebastianAchilles approved these changes May 14, 2024

View reviewed changes

SebastianAchilles merged commit a0a467a into easybuilders:develop May 14, 2024

bedroge deleted the gromacs_2024.1_bump_gmxapi branch May 14, 2024 18:13

ocaisa mentioned this pull request May 15, 2024

Fix CI: Rebuild GROMACS, and fix check for missing installations after updates upstream to libfabric EESSI/software-layer#576

Merged

boegel reviewed May 16, 2024

View reviewed changes

bedroge mentioned this pull request May 19, 2024

Notes on kickstarting the RISC-V software layer EESSI/software-layer#552

Open

boegel mentioned this pull request Oct 3, 2024

{bio}[foss/2023b] GROMACS v2024.3 #21430

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