Remove extensions that were added multiple times by Flamefire · Pull Request #23806 · easybuilders/easybuild-easyconfigs

Flamefire · 2025-09-05T12:24:29Z

Companion to the CI checks: #23802 and previous PR #23801 which is only for PYPI-bundle

Quiskit requires

Add patch for scikit-build to support newer CMake versions #23895

R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb requires RCurl, recently added to R-bundle-CRAN

Crivella · 2025-09-05T14:07:45Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath /tmp/$USER/pr-23806"

boegelbot · 2025-09-05T14:10:09Z

@Crivella: 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=23806 EB_ARGS="--installpath /tmp/$USER/pr-23806" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23806 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7870

Test results coming soon (I hope)...

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boegelbot · 2025-09-06T14:13:17Z

Test report by @boegelbot
FAILED
Build succeeded for 27 out of 33 (22 easyconfigs in total)
jsczen3c4.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/7c8c06f8c8283d7cf50122b65fa7d8e6 for a full test report.

Flamefire · 2025-09-07T09:12:14Z

Symengine fails with at static char altStackMem[SIGSTKSZ]; due to SIGSTKSZ no longer being a macro in glibc(?), see symengine/symengine#1878
So we'd need something similar to https://github.com/easybuilders/easybuild-easyconfigs/blob/c489f47c62900ffb78ff0d04dcc3a78dd1bd2512/easybuild/easyconfigs/l/Libint/Libint-2.7.2_update-catch-hpp-fix-MINSIGSTKSZ.patch or replace it by e.g. static char altStackMem = malloc(std::max<size_t>(SIGSTKSZ, 32*1024)) which is more or less the essence

--> #23817

Crivella · 2025-09-09T08:48:56Z

Symengine fails with at static char altStackMem[SIGSTKSZ]; due to SIGSTKSZ no longer being a macro in glibc(?), see symengine/symengine#1878

I think the error is as described, but the linked issue showcases a different one.

I've added a possibly different solution on the other pr #23817

Flamefire · 2025-09-15T11:56:06Z

I've added a possibly different solution on the other pr #23817

As this is merged can you retry this PR?

Crivella · 2025-09-15T15:50:16Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath /tmp/$USER/pr-23806"

boegelbot · 2025-09-15T16:00:14Z

@Crivella: 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=23806 EB_ARGS="--installpath /tmp/$USER/pr-23806" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23806 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7961

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).

boegelbot · 2025-09-17T01:36:37Z

Test report by @boegelbot
FAILED
Build succeeded for 32 out of 33 (22 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/581677587bfd1028182933ecda74e2b6 for a full test report.

Flamefire · 2025-09-17T07:29:14Z

Qiskit-0.31.0-foss-2021a.eb fails with:

CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
 Compatibility with CMake < 3.5 has been removed from CMake.

That seems unrelated to this PR and I'm wondering how that went undetected so far
I don't see where 3.5 is coming from. It isn't in the source on GitHub

Thyre · 2025-09-17T08:56:47Z

Qiskit-0.31.0-foss-2021a.eb fails with:
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
 Compatibility with CMake < 3.5 has been removed from CMake.
That seems unrelated to this PR and I'm wondering how that went undetected so far I don't see where 3.5 is coming from. It isn't in the source on GitHub

It seems to pull in CMake 4.0 from somewhere, and then probably fails for some other component (which it maybe pulls in as well?)

Crivella · 2025-09-17T11:51:42Z

Not sure how worth it is to dig into this since 2021a is deprecated.
I am wondering if we should just make an update of Qskit to a newer toolchain just to keep the logic of the EC in and move it to the archived repo

Thyre · 2025-09-17T12:00:12Z

Not sure how worth it is to dig into this since 2021a is deprecated. I am wondering if we should just make an update of Qskit to a newer toolchain just to keep the logic of the EC in and move it to the archived repo

I mean if we can find a fix for this, great. But I wouldn't block this PR because of this.

Flamefire · 2025-09-17T15:46:50Z

It is actually a larger issue that might affect more packages, in particular most of those using skikit-build: It doesn't use our CMake but downloads a pip package with that using the latest version. The "3.5" is something internal from skikit-build and since CMake 4.0 this causes an error.

The fix is in #23895 which should at least avoid the error when it decides to use CMake 4

Flamefire · 2025-09-23T00:36:13Z

Test report by @Flamefire
FAILED
Build succeeded for 20 out of 22 (22 easyconfigs in total)
n1715 - Linux RHEL 8.9 (Ootpa), x86_64, Intel(R) Xeon(R) Platinum 8470 (sapphirerapids), Python 3.9.18
See https://gist.github.com/Flamefire/bb284f446981fa394a4aeb3fd31e0391 for a full test report.

Temporary filesystem issue. Rebuild:

== Build succeeded for 2 out of 2
== Summary:
   * [SUCCESS] Perl/5.34.1-GCCcore-11.3.0
   * [SUCCESS] Perl/5.36.0-GCCcore-12.1.0

Flamefire · 2025-09-23T13:00:22Z

Test report by @Flamefire
FAILED
Build succeeded for 40 out of 44 (22 easyconfigs in total)
i8005 - Linux Rocky Linux 9.6, x86_64, AMD EPYC 7352 24-Core Processor (zen2), 8 x NVIDIA NVIDIA A100-SXM4-40GB, 580.65.06, Python 3.9.21
See https://gist.github.com/Flamefire/9d12bcc39f36ff862f6841d3c526c6c8 for a full test report.

Can be considered SUCCESS:
Missing RCurl in R-bundle-CRAN-2023.12-foss-2023a.eb

Flamefire · 2025-10-02T13:05:57Z

Test report by @Flamefire
SUCCESS
Build succeeded for 22 out of 22 (22 easyconfigs in total)
c144 - Linux AlmaLinux 9.4, x86_64, AMD EPYC 9334 32-Core Processor (zen4), 4 x NVIDIA NVIDIA H100, 560.35.03, Python 3.9.18
See https://gist.github.com/Flamefire/20c5daa0f607e8903eaafebb612a273a for a full test report.

Crivella · 2025-10-07T15:03:00Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath /tmp/$USER/pr-23806"

boegelbot · 2025-10-07T15:10:12Z

@Crivella: 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=23806 EB_ARGS="--installpath /tmp/$USER/pr-23806" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23806 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8193

Test results coming soon (I hope)...

Details

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Message to humans: this is just bookkeeping information for me,
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boegelbot · 2025-10-08T23:55:15Z

Test report by @boegelbot
FAILED
Build succeeded for 32 out of 33 (22 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/9439e841a9673a8d99e9d2a5813c3068 for a full test report.

Flamefire · 2025-10-09T06:42:07Z

Test report by @boegelbot FAILED Build succeeded for 32 out of 33 (22 easyconfigs in total) jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21 See https://gist.github.com/boegelbot/9439e841a9673a8d99e9d2a5813c3068 for a full test report.

@Crivella The single failure (Quiskit) is due to requiring the fix for scikit-build: #23895 So the PR should be fine.

Thyre · 2025-10-09T07:11:23Z

@boegelbot please test @ jsc-zen3
EB_ARGS="scikit-build-0.11.1-GCCcore-10.3.0.eb Qiskit-0.31.0-foss-2021a.eb --installpath=/tmp/$USER/ecpr-23806"

boegelbot · 2025-10-09T07:20:15Z

@Thyre: 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=23806 EB_ARGS="scikit-build-0.11.1-GCCcore-10.3.0.eb Qiskit-0.31.0-foss-2021a.eb --installpath=/tmp/$USER/ecpr-23806" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23806 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8235

Test results coming soon (I hope)...

Details

- notification for comment with ID 3384436006 processed

Message to humans: this is just bookkeeping information for me,
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Crivella · 2025-10-09T08:01:17Z

@Crivella The single failure (Quiskit) is due to requiring the fix for scikit-build: #23895 So the PR should be fine.

Yeah forgot to add a rebuild for it i see @Thyre already launched it

boegelbot · 2025-10-09T09:43:22Z

Test report by @boegelbot
FAILED
Build succeeded for 11 out of 12 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/828429bad140489abc4ab62841d5257e for a full test report.

Flamefire · 2025-10-09T10:12:08Z

Hm, broken numba package or parallel installation modifying it?

failing sanity check for 'sparse' extension: command "/project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.9.5-GCCcore-10.3.0/bin/python -c "import sparse"" failed; output:
...
OSError: Could not load shared object file: libllvmlite.so

The `continue` caused the test to skip checking 2 other conditions

Covered already by the general template test when parsing easyconfigs

Flamefire · 2025-10-29T08:10:14Z

@Crivella Can we merge this? I'd like to get #23802 merged ASAP to avoid this issue getting reintroduced by new PRs

Crivella · 2025-10-29T09:11:56Z

Agree the Qskit/numba failure is not really related to this and happening on a non-supported TC so i would not block this

Crivella

LGTM

Crivella · 2025-10-29T09:19:23Z

Going in, thanks @Flamefire!

Flamefire changed the title ~~Remove dup exts~~ Remove extensions added multiple times Sep 5, 2025

github-actions Bot added the change label Sep 5, 2025

Flamefire mentioned this pull request Sep 5, 2025

CI: Add test for extensions added multiple times #23802

Merged

1 task

Flamefire force-pushed the remove-dup-exts branch from 3cc81af to 7a719ab Compare September 5, 2025 12:41

Crivella added bug fix and removed change labels Sep 5, 2025

Flamefire commented Sep 7, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/c/Cellformer/Cellformer-20240917-foss-2023a-R-4.3.2.eb Outdated

github-actions Bot added the change label Sep 7, 2025

boegel added this to the release after 5.1.2 (5.2.0?) milestone Sep 10, 2025

Flamefire and others added 6 commits October 16, 2025 10:31

Fix missed checks in CI

c07bd25

The `continue` caused the test to skip checking 2 other conditions

Add test for extensions added multiple times

a6f0ab3

Remove duplicate CI check for duplicated R packages

b5b8dec

Covered already by the general template test when parsing easyconfigs

Remove extensions added multiple times

493f032

Fix qcg checksum

3d7b20c

Fix torchmetrics checksum

6f7c082

Flamefire force-pushed the remove-dup-exts branch from 2b104b5 to 6f7c082 Compare October 16, 2025 08:33

Merge branch 'easybuilders:develop' into remove-dup-exts

b94b6fe

Crivella approved these changes Oct 29, 2025

View reviewed changes

Crivella removed the change label Oct 29, 2025

Crivella merged commit 418a4d0 into easybuilders:develop Oct 29, 2025
8 checks passed

Flamefire deleted the remove-dup-exts branch October 29, 2025 09:20

boegel changed the title ~~Remove extensions added multiple times~~ Remove extensions that were added multiple times Dec 23, 2025

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