add patch to recent LAMMPS easyconfigs to ensure that system Python packages are used and not updated in Python virtual environment by lorisercole · Pull Request #25127 · easybuilders/easybuild-easyconfigs

lorisercole · 2026-01-22T13:03:12Z

LAMMPS creates a virtual environment to build a python wheel of its python interface. The required packages are not pinned, causing possible future incompatibilities since pip downloads the latest versions. This patch ensures that the system packages installed by EasyBuild are used in the virtual environment whenever possible, and deactivates automatic updates by pip.

Furthermore, it constrains the dependency build<1.4 that would otherwise cause build errors for 2023a and 2023b toolchains.
Fixes #25089

LAMMPS creates a virtual environment to build a python wheel of its python interface. The required packages are not pinned, causing possible future incompatibilities since pip downloads the latest versions. This patch ensures that the system packages installed by EasyBuild are used in the virtual environment whenever possible, and deactivates automatic updates by pip. Furthermore, it constrains the dependency `build<1.4` that would otherwise cause build errors for `2023a` and `2023b` toolchains. Fixes easybuilders#25089 Signed-off-by: Loris Ercole <[email protected]>

laraPPr · 2026-01-26T14:32:32Z

@boegelbot please test @ jsc-zen3 EB_ARGS="LAMMPS-22Jul2025-foss-2024a-kokkos.eb LAMMPS-29Aug2024-foss-2023b-kokkos.eb LAMMPS-29Aug2024_update2-foss-2023a-kokkos.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb"

laraPPr · 2026-01-26T14:34:14Z

@boegelbot please test @ jsc-zen3-a100 EB_ARGS="LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-29Aug2024_update2-foss-2023b-kokkos-CUDA-12.4.0.eb LAMMPS-28Oct2024-foss-2023a-kokkos-mace-CUDA-12.1.1.eb LAMMPS-22Jul2025-foss-2024a-kokkos-CUDA-12.6.0.eb"

boegelbot · 2026-01-26T14:40:08Z

@laraPPr: 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=25127 EB_ARGS="LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-29Aug2024_update2-foss-2023b-kokkos-CUDA-12.4.0.eb LAMMPS-28Oct2024-foss-2023a-kokkos-mace-CUDA-12.1.1.eb LAMMPS-22Jul2025-foss-2024a-kokkos-CUDA-12.6.0.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25127 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9492

Test results coming soon (I hope)...

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boegelbot · 2026-01-26T21:34:04Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (total: 6 hours 53 mins 37 secs) (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 590.44.01, Python 3.9.23
See https://gist.github.com/boegelbot/31b64b3efad6e87f9135dddbb8a1d00a for a full test report.

laraPPr · 2026-01-27T08:50:55Z

@boegelbot please test @ jsc-zen3-a100 EB_ARGS="LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-29Aug2024_update2-foss-2023b-kokkos-CUDA-12.4.0.eb LAMMPS-28Oct2024-foss-2023a-kokkos-mace-CUDA-12.1.1.eb LAMMPS-22Jul2025-foss-2024a-kokkos-CUDA-12.6.0.eb"

boegelbot · 2026-01-27T09:00:08Z

@laraPPr: 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=25127 EB_ARGS="LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-29Aug2024_update2-foss-2023b-kokkos-CUDA-12.4.0.eb LAMMPS-28Oct2024-foss-2023a-kokkos-mace-CUDA-12.1.1.eb LAMMPS-22Jul2025-foss-2024a-kokkos-CUDA-12.6.0.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25127 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9498

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).

lorisercole · 2026-01-27T09:36:35Z

@boegelbot please test @ jsc-zen3-a100 EB_ARGS="LAMMPS-2Aug2023_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos-CUDA-12.6.0.eb LAMMPS-29Aug2024_update2-foss-2023b-kokkos-CUDA-12.4.0.eb LAMMPS-28Oct2024-foss-2023a-kokkos-mace-CUDA-12.1.1.eb LAMMPS-22Jul2025-foss-2024a-kokkos-CUDA-12.6.0.eb"

Looks like these have already been tested successfully by the bot...
The CPU ones are missing

laraPPr · 2026-01-27T09:40:38Z

Ah yes your correct. sorry thought only the CPU ran. will trigger the other command again.

laraPPr · 2026-01-27T09:40:48Z

@boegelbot please test @ jsc-zen3 EB_ARGS="LAMMPS-22Jul2025-foss-2024a-kokkos.eb LAMMPS-29Aug2024-foss-2023b-kokkos.eb LAMMPS-29Aug2024_update2-foss-2023a-kokkos.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb"

boegelbot · 2026-01-27T09:50:08Z

@laraPPr: 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=25127 EB_ARGS="LAMMPS-22Jul2025-foss-2024a-kokkos.eb LAMMPS-29Aug2024-foss-2023b-kokkos.eb LAMMPS-29Aug2024_update2-foss-2023a-kokkos.eb LAMMPS-29Aug2024_update2-foss-2024a-kokkos.eb LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25127 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9499

Test results coming soon (I hope)...

Details

- notification for comment with ID 3804141008 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).

laraPPr · 2026-01-27T10:28:25Z

Test report by @laraPPr
SUCCESS
Build succeeded for 5 out of 5 (total: 1 hour 37 mins 54 secs) (5 easyconfigs in total)
node3537.doduo.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 7552 48-Core Processor, Python 3.9.21
See https://gist.github.com/laraPPr/b6116e6036fc6eaf5cc35b9a8d461bde for a full test report.

laraPPr

lgtm

boegelbot · 2026-01-27T12:22:27Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (total: 2 hours 29 mins 26 secs) (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/602b2bcb02dddebbbfde3fb12811d35f for a full test report.

laraPPr · 2026-01-27T13:05:51Z

Test report by @laraPPr
FAILED
Build succeeded for 5 out of 6 (6 easyconfigs in total)
node4303.litleo.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9454P 48-Core Processor, 1 x NVIDIA NVIDIA H100 NVL, 580.95.05, Python 3.9.21
See https://gist.github.com/laraPPr/239c3d1665baacd29609520cb21669f2 for a full test report.

lorisercole · 2026-01-27T13:17:15Z

Test report by @laraPPr FAILED Build succeeded for 5 out of 6 (6 easyconfigs in total) node4303.litleo.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9454P 48-Core Processor, 1 x NVIDIA NVIDIA H100 NVL, 580.95.05, Python 3.9.21 See https://gist.github.com/laraPPr/239c3d1665baacd29609520cb21669f2 for a full test report.

Weird that this time one test failed. But I notice that this time it used EasyBuild 5.1.2 instead of 5.2.1 or 5.2.0 like in the successful runs. Maybe that's the reason?

laraPPr · 2026-01-27T13:28:19Z

Ah forgot to update the easybuild version on that cluster, Thanks for pointing it out. I though it might have something to do with the core pinning on our cluster. So it is running again right now.

laraPPr · 2026-01-27T14:19:26Z

Test report by @laraPPr
SUCCESS
Build succeeded for 1 out of 1 (total: 48 mins 46 secs) (1 easyconfigs in total)
node4303.litleo.os - Linux RHEL 9.6 (Plow), x86_64, AMD EPYC 9454P 48-Core Processor, 1 x NVIDIA NVIDIA H100 NVL, 580.95.05, Python 3.9.21
See https://gist.github.com/laraPPr/88e8a45515b120a8930ab56413a8013c for a full test report.

laraPPr · 2026-01-27T14:41:07Z

Going in, thanks @lorisercole!

boegelbot · 2026-01-30T01:31:29Z

Test report by @boegelbot
SUCCESS
Build succeeded for 6 out of 6 (total: 6 hours 52 mins 50 secs) (6 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 590.44.01, Python 3.9.23
See https://gist.github.com/boegelbot/75636fb1513f292e78f871076a1cd0e8 for a full test report.

github-actions Bot added 2023a 2023b 2024a issues & PRs related to 2024a common toolchains change labels Jan 22, 2026

laraPPr reviewed Jan 23, 2026

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Comment thread easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_python_venv.patch

laraPPr mentioned this pull request Jan 23, 2026

don't depend on ScaFaCos in LAMMPS easyconfigs when building on Arm + add patch to disable failing test on Arm due to bug in kim-api #25133

Merged

1 task

Rename patches

1b9068c

lorisercole requested a review from laraPPr January 23, 2026 18:04

laraPPr approved these changes Jan 27, 2026

View reviewed changes

laraPPr added this to the next release (5.2.1?) milestone Jan 27, 2026

laraPPr merged commit 169646c into easybuilders:develop Jan 27, 2026
8 checks passed

boegel changed the title ~~Patch LAMMPS python venv setup~~ add patch to recent LAMMPS easyconfigs to ensure that system Python packages are used and not updated in Python virtual environment Feb 20, 2026

stevenvdb mentioned this pull request Mar 24, 2026

Use EasyBuild packages in venv for building pod5 wheel #25599

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