{2023.06}[foss/2023a] GROMACS v2023.3 by boegel · Pull Request #401 · EESSI/software-layer

boegel · 2023-11-26T20:55:20Z

~~Should first deploy & merge:~~

{2023.06}[foss/2023a] SciPy-bundle v2023.07 #403

1 out of 58 required modules missing:

* GROMACS/2023.3-foss-2023a (GROMACS-2023.3-foss-2023a.eb)
* ```

boegel · 2023-11-26T20:55:42Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2023-11-26T20:55:44Z

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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 1294, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 1295, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2023-11-26T20:55:48Z

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/2023.11/pr_401/1294

date	job status	comment
Nov 26 20:55:47 UTC 2023	submitted	job id `1294` awaits release by job manager
Nov 26 20:56:38 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 26 20:57:42 UTC 2023	running	job `1294` is running
Nov 26 20:59:47 UTC 2023	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job1294.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Nov 26 20:59:47 UTC 2023	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job1294.test` does not exist in job directory or reading it failed.

eessi-bot · 2023-11-26T20:55:52Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1295

date	job status	comment
Nov 26 20:55:51 UTC 2023	submitted	job id `1295` awaits release by job manager
Nov 26 20:56:37 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 26 20:57:40 UTC 2023	running	job `1295` is running
Nov 26 20:59:45 UTC 2023	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job1295.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Nov 26 20:59:45 UTC 2023	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job1295.test` does not exist in job directory or reading it failed.

boegel · 2023-11-26T20:59:15Z

Doesn't work yet, mpi4py is also needed, I'll get builds to work in easybuilders/easybuild-easyconfigs#19321 first.

I'll manually cancel the build jobs.

…io_GROMACS-foss-2023a

boegel · 2023-11-28T08:49:09Z

bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2023-11-28T08:49:12Z

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

received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 1417, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2023-11-28T08:49:17Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1417

date	job status	comment
Nov 28 08:49:16 UTC 2023	submitted	job id `1417` awaits release by job manager
Nov 28 08:49:21 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 08:53:56 UTC 2023	running	job `1417` is running
Nov 28 10:24:32 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-1417.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-neoverse_v1-1701166746.tar.gz` size: 975 MiB (1022832879 bytes) entries: 25002 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `Catch2/2.13.9.lua` `cffi/1.15.1-GCCcore-12.3.0.lua` `CMake/3.18.4-GCCcore-10.2.0.lua` `cryptography/41.0.1-GCCcore-12.3.0.lua` `cURL/7.72.0-GCCcore-10.2.0.lua` `Eigen/3.4.0-GCCcore-12.3.0.lua` `expat/2.5.0-GCCcore-12.3.0.lua` `flit/3.9.0-GCCcore-12.3.0.lua` `GCCcore/10.2.0.lua` `gfbf/2023a.lua` `git/2.41.0-GCCcore-12.3.0-nodocs.lua` `hatchling/1.18.0-GCCcore-12.3.0.lua` `hypothesis/6.82.0-GCCcore-12.3.0.lua` `libarchive/3.4.3-GCCcore-10.2.0.lua` `Meson/1.1.1-GCCcore-12.3.0.lua` `mpi4py/3.1.4-gompi-2023a.lua` `poetry/1.5.1-GCCcore-12.3.0.lua` `pybind11/2.11.1-GCCcore-12.3.0.lua` `Python-bundle-PyPI/2023.06-GCCcore-12.3.0.lua` `scikit-build/0.17.6-GCCcore-12.3.0.lua` `setuptools-rust/1.6.0-GCCcore-12.3.0.lua` `virtualenv/20.23.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `Catch2/2.13.9` `cffi/1.15.1-GCCcore-12.3.0` `CMake/3.18.4-GCCcore-10.2.0` `cryptography/41.0.1-GCCcore-12.3.0` `cURL/7.72.0-GCCcore-10.2.0` `Eigen/3.4.0-GCCcore-12.3.0` `expat/2.5.0-GCCcore-12.3.0` `flit/3.9.0-GCCcore-12.3.0` `GCCcore/10.2.0` `gfbf/2023a` `git/2.41.0-GCCcore-12.3.0-nodocs` `hatchling/1.18.0-GCCcore-12.3.0` `hypothesis/6.82.0-GCCcore-12.3.0` `libarchive/3.4.3-GCCcore-10.2.0` `Meson/1.1.1-GCCcore-12.3.0` `mpi4py/3.1.4-gompi-2023a` `poetry/1.5.1-GCCcore-12.3.0` `pybind11/2.11.1-GCCcore-12.3.0` `Python-bundle-PyPI/2023.06-GCCcore-12.3.0` `scikit-build/0.17.6-GCCcore-12.3.0` `setuptools-rust/1.6.0-GCCcore-12.3.0` `virtualenv/20.23.1-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_v1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 10:24:32 UTC 2023	test result	(no tests yet)

boegel · 2023-11-28T10:46:55Z

Hooks are missing to work around test failures with scipy on neoverse_v1, see also #403 (comment)

boegel · 2023-11-28T10:47:06Z

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

eessi-bot · 2023-11-28T10:47:09Z

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 boegel
- 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 1426, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2023-11-28T10:47:13Z

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/2023.11/pr_401/1426

date	job status	comment
Nov 28 10:47:13 UTC 2023	submitted	job id `1426` awaits release by job manager
Nov 28 10:47:56 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 10:52:38 UTC 2023	running	job `1426` is running
Nov 28 13:04:06 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-1426.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-zen3-1701176402.tar.gz` size: 1203 MiB (1261698462 bytes) entries: 39173 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `Catch2/2.13.9.lua` `cffi/1.15.1-GCCcore-12.3.0.lua` `CMake/3.18.4-GCCcore-10.2.0.lua` `cryptography/41.0.1-GCCcore-12.3.0.lua` `cURL/7.72.0-GCCcore-10.2.0.lua` `Eigen/3.4.0-GCCcore-12.3.0.lua` `expat/2.5.0-GCCcore-12.3.0.lua` `flit/3.9.0-GCCcore-12.3.0.lua` `GCCcore/10.2.0.lua` `gfbf/2023a.lua` `git/2.41.0-GCCcore-12.3.0-nodocs.lua` `GROMACS/2023.3-foss-2023a.lua` `hatchling/1.18.0-GCCcore-12.3.0.lua` `hypothesis/6.82.0-GCCcore-12.3.0.lua` `libarchive/3.4.3-GCCcore-10.2.0.lua` `Meson/1.1.1-GCCcore-12.3.0.lua` `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` `poetry/1.5.1-GCCcore-12.3.0.lua` `pybind11/2.11.1-GCCcore-12.3.0.lua` `Python-bundle-PyPI/2023.06-GCCcore-12.3.0.lua` `scikit-build/0.17.6-GCCcore-12.3.0.lua` `SciPy-bundle/2023.07-gfbf-2023a.lua` `setuptools-rust/1.6.0-GCCcore-12.3.0.lua` `virtualenv/20.23.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `Catch2/2.13.9` `cffi/1.15.1-GCCcore-12.3.0` `CMake/3.18.4-GCCcore-10.2.0` `cryptography/41.0.1-GCCcore-12.3.0` `cURL/7.72.0-GCCcore-10.2.0` `Eigen/3.4.0-GCCcore-12.3.0` `expat/2.5.0-GCCcore-12.3.0` `flit/3.9.0-GCCcore-12.3.0` `GCCcore/10.2.0` `gfbf/2023a` `git/2.41.0-GCCcore-12.3.0-nodocs` `GROMACS/2023.3-foss-2023a` `hatchling/1.18.0-GCCcore-12.3.0` `hypothesis/6.82.0-GCCcore-12.3.0` `libarchive/3.4.3-GCCcore-10.2.0` `Meson/1.1.1-GCCcore-12.3.0` `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` `poetry/1.5.1-GCCcore-12.3.0` `pybind11/2.11.1-GCCcore-12.3.0` `Python-bundle-PyPI/2023.06-GCCcore-12.3.0` `scikit-build/0.17.6-GCCcore-12.3.0` `SciPy-bundle/2023.07-gfbf-2023a` `setuptools-rust/1.6.0-GCCcore-12.3.0` `virtualenv/20.23.1-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen3 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 13:04:06 UTC 2023	test result	(no tests yet)

…io_GROMACS-foss-2023a

boegel · 2023-11-28T16:00:36Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/generic
bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell
bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3
bot: build repo:eessi.io-2023.06-software arch:aarch64/generic
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2023-11-28T16:00:39Z

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/generic from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 1427, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 1428, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 1429, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 1430, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 1431, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 1432, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 1433, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 1434, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2023-11-28T16:00:44Z

New job on instance eessi-bot-mc-aws for architecture x86_64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1427

date	job status	comment
Nov 28 16:00:43 UTC 2023	submitted	job id `1427` awaits release by job manager
Nov 28 16:01:35 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:10:06 UTC 2023	running	job `1427` is running
Nov 28 16:58:28 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-1427.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-generic-1701190678.tar.gz` size: 45 MiB (48144328 bytes) entries: 2256 modules under 2023.06/software/linux/x86_64/generic/modules/all `GROMACS/2023.3-foss-2023a.lua` `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/x86_64/generic/software `GROMACS/2023.3-foss-2023a` `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/x86_64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:58:28 UTC 2023	test result	(no tests yet)

eessi-bot · 2023-11-28T16:00:49Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-haswell for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1428

date	job status	comment
Nov 28 16:00:48 UTC 2023	submitted	job id `1428` awaits release by job manager
Nov 28 16:01:38 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:11:15 UTC 2023	running	job `1428` is running
Nov 29 16:11:14 UTC 2023	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job1428.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Nov 29 16:11:14 UTC 2023	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job1428.test` does not exist in job directory or reading it failed.

eessi-bot · 2023-11-28T16:00:54Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-skylake_avx512 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1429

date	job status	comment
Nov 28 16:00:52 UTC 2023	submitted	job id `1429` awaits release by job manager
Nov 28 16:01:40 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:11:17 UTC 2023	running	job `1429` is running
Nov 28 16:53:16 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-1429.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-intel-skylake_avx512-1701190282.tar.gz` size: 47 MiB (49936350 bytes) entries: 2256 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `GROMACS/2023.3-foss-2023a.lua` `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `GROMACS/2023.3-foss-2023a` `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:53:16 UTC 2023	test result	(no tests yet)

eessi-bot · 2023-11-28T16:00:58Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen2 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1430

date	job status	comment
Nov 28 16:00:57 UTC 2023	submitted	job id `1430` awaits release by job manager
Nov 28 16:01:31 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:10:02 UTC 2023	running	job `1430` is running
Nov 28 16:52:08 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-1430.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-x86_64-amd-zen2-1701190237.tar.gz` size: 7 MiB (7595789 bytes) entries: 1491 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/x86_64/amd/zen2 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:52:08 UTC 2023	test result	(no tests yet)

eessi-bot · 2023-11-28T16:01:03Z

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/2023.11/pr_401/1431

date	job status	comment
Nov 28 16:01:02 UTC 2023	submitted	job id `1431` awaits release by job manager
Nov 28 16:01:33 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:08:56 UTC 2023	running	job `1431` is running
Nov 28 16:44:21 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-1431.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-x86_64-amd-zen3-1701189825.tar.gz` size: 7 MiB (7596192 bytes) entries: 1491 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/x86_64/amd/zen3 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:44:21 UTC 2023	test result	(no tests yet)

eessi-bot · 2023-11-28T16:01:07Z

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/2023.11/pr_401/1432

date	job status	comment
Nov 28 16:01:06 UTC 2023	submitted	job id `1432` awaits release by job manager
Nov 28 16:01:23 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:06:43 UTC 2023	running	job `1432` is running
Nov 28 16:53:12 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-1432.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-aarch64-generic-1701190319.tar.gz` size: 39 MiB (41334155 bytes) entries: 2256 modules under 2023.06/software/linux/aarch64/generic/modules/all `GROMACS/2023.3-foss-2023a.lua` `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/aarch64/generic/software `GROMACS/2023.3-foss-2023a` `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/aarch64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:53:12 UTC 2023	test result	(no tests yet)

eessi-bot · 2023-11-28T16:01:13Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_n1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1433

date	job status	comment
Nov 28 16:01:12 UTC 2023	submitted	job id `1433` awaits release by job manager
Nov 28 16:01:26 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:06:45 UTC 2023	running	job `1433` is running
Nov 28 16:53:14 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-1433.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-aarch64-neoverse_n1-1701190321.tar.gz` size: 44 MiB (46166200 bytes) entries: 2256 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `GROMACS/2023.3-foss-2023a.lua` `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `GROMACS/2023.3-foss-2023a` `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/aarch64/neoverse_n1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:53:14 UTC 2023	test result	(no tests yet)

eessi-bot · 2023-11-28T16:01:17Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_401/1434

date	job status	comment
Nov 28 16:01:16 UTC 2023	submitted	job id `1434` awaits release by job manager
Nov 28 16:01:29 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 28 16:06:47 UTC 2023	running	job `1434` is running
Nov 28 16:38:42 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-1434.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-neoverse_v1-1701189476.tar.gz` size: 7 MiB (7559081 bytes) entries: 1491 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `mpi4py/3.1.4-gompi-2023a.lua` `networkx/3.1-gfbf-2023a.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `mpi4py/3.1.4-gompi-2023a` `networkx/3.1-gfbf-2023a` other under 2023.06/software/linux/aarch64/neoverse_v1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Nov 28 16:38:42 UTC 2023	test result	(no tests yet)

boegel · 2023-11-28T17:45:29Z

Test suite failed on neoverse_v1 (job 1434), some failure-related output:

45/85 Test #45: SimdUnitTests ................................***Failed    0.03 sec

80/85 Test #80: MdrunFEPTests ................................***Failed    1.12 sec

The following tests FAILED:
         15 - GmxlibTests (Subprocess aborted)
         45 - SimdUnitTests (Failed)
         80 - MdrunFEPTests (Failed)

boegel · 2023-11-28T17:46:48Z

On zen3 and zen2:

99% tests passed, 1 tests failed out of 87
...
The following tests FAILED:
          2 - GmxapiMpiTests (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:74: CMakeFiles/run-ctest-nophys] Error 8

edit: this (partially) matches failing test build in generoso test cluster in easyconfig PR, see here

…io_GROMACS-foss-2023a

boegel · 2024-02-01T17:35:18Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/generic
bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell
bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3
bot: build repo:eessi.io-2023.06-software arch:aarch64/generic
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2024-02-01T17:35:23Z

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/generic from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 5150, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 5151, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 5152, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 5153, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 5154, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 5155, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 5156, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 5157, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2024-02-01T17:35:27Z

New job on instance eessi-bot-mc-aws for architecture x86_64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5150

date	job status	comment
Feb 01 17:35:26 UTC 2024	submitted	job id `5150` awaits release by job manager
Feb 01 17:36:27 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:43:53 UTC 2024	running	job `5150` is running
Feb 01 18:30:42 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5150.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-generic-1706812155.tar.gz` size: 38 MiB (40712707 bytes) entries: 768 modules under 2023.06/software/linux/x86_64/generic/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/x86_64/generic/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/x86_64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 01 18:30:42 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T17:35:31Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-haswell for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5151

date	job status	comment
Feb 01 17:35:30 UTC 2024	submitted	job id `5151` awaits release by job manager
Feb 01 17:36:29 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:45:07 UTC 2024	running	job `5151` is running
Feb 01 20:58:54 UTC 2024	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job5151.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Feb 01 20:58:54 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job5151.test` does not exist in job directory or reading it failed.

eessi-bot · 2024-02-01T17:35:34Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-skylake_avx512 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5152

date	job status	comment
Feb 01 17:35:33 UTC 2024	submitted	job id `5152` awaits release by job manager
Feb 01 17:36:31 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:43:56 UTC 2024	running	job `5152` is running
Feb 01 18:25:27 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5152.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-intel-skylake_avx512-1706811859.tar.gz` size: 40 MiB (42519237 bytes) entries: 768 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 01 18:25:27 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T17:35:38Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen2 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5153

date	job status	comment
Feb 01 17:35:37 UTC 2024	submitted	job id `5153` awaits release by job manager
Feb 01 17:36:22 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:43:49 UTC 2024	running	job `5153` is running
Feb 01 18:26:33 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5153.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-zen2-1706811963.tar.gz` size: 41 MiB (43356438 bytes) entries: 768 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/x86_64/amd/zen2 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 01 18:26:33 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T17:35:42Z

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/2024.02/pr_401/5154

date	job status	comment
Feb 01 17:35:41 UTC 2024	submitted	job id `5154` awaits release by job manager
Feb 01 17:36:25 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:43:51 UTC 2024	running	job `5154` is running
Feb 01 18:19:49 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-5154.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 Details No artefacts were created or found.
Feb 01 18:19:49 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T17:35:45Z

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/2024.02/pr_401/5155

date	job status	comment
Feb 01 17:35:44 UTC 2024	submitted	job id `5155` awaits release by job manager
Feb 01 17:36:16 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:41:34 UTC 2024	running	job `5155` is running
Feb 01 18:25:25 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5155.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-aarch64-generic-1706811893.tar.gz` size: 32 MiB (33947616 bytes) entries: 768 modules under 2023.06/software/linux/aarch64/generic/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/aarch64/generic/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/aarch64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 01 18:25:25 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T17:35:49Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_n1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5156

date	job status	comment
Feb 01 17:35:48 UTC 2024	submitted	job id `5156` awaits release by job manager
Feb 01 17:36:18 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:41:36 UTC 2024	running	job `5156` is running
Feb 01 18:26:31 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5156.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-aarch64-neoverse_n1-1706811931.tar.gz` size: 36 MiB (38785569 bytes) entries: 768 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/aarch64/neoverse_n1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 01 18:26:31 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T17:35:52Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5157

date	job status	comment
Feb 01 17:35:52 UTC 2024	submitted	job id `5157` awaits release by job manager
Feb 01 17:36:20 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 17:41:38 UTC 2024	running	job `5157` is running
Feb 01 18:12:58 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-5157.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 Details No artefacts were created or found.
Feb 01 18:12:58 UTC 2024	test result	(no tests yet)

boegel · 2024-02-01T20:53:27Z

I re-triggered the build to try again using EasyBuild v4.9.0, because I didn't run into failures at all with a manual build (in EESSI build container/environment) on our AMD Rome (zen2) system...

failing tests for x86_64/amd/zen3 (job 5154):

99% tests passed, 1 tests failed out of 87
...
The following tests FAILED:
          2 - GmxapiMpiTests (Failed)

note that there were no failing tests for x86_64/amd/zen2 this time, while in a previous attempt GmxapiMpiTests also failed there (see #401 (comment))

failing tests for aarch64/neoverse_v1 (job 5157):

96% tests passed, 3 tests failed out of 85
...
The following tests FAILED:
         15 - GmxlibTests (SEGFAULT)
         45 - SimdUnitTests (Failed)
         80 - MdrunFEPTests (Failed)

on x86_64/intel/haswell, test step is hanging, so looks like it's just going to time out...

Details

bot         4069  0.0  0.0 222864  3304 ?        S    17:44   0:00 bash /var/spool/slurmd/job05151/slurm_script
bot         4070  0.0  0.0 223128  3556 ?        S    17:44   0:00  \_ bash bot/build.sh
bot         4267  0.0  0.0 223128  3652 ?        S    17:44   0:00      \_ /bin/bash ./eessi_container.sh --verbose --access rw --mode run --container docker://ghcr.io/eessi/build-node:debian11 --repository eessi.io-2023.06-software --save /project/60006/SHARED/jobs/2024.02/pr_401/event_4577dd40-c128-11ee-9720-d3d6dffc6b6e/run_001/linux_x86_64_intel_haswell/eessi.io-2023.06-software/previous_tmp/build_step --storage /tmp/bot/EESSI --nvidia all --host-injections /project/def-users/bot/shared/host-injections -- ./install_software_layer.sh --build-logs-dir /project/def-users/SHARED/build-logs --shared-fs-path /project/def-users/bot/shared
bot         4640  0.0  0.1 1223036 32088 ?       Sl   17:44   0:00      |   \_ Apptainer runtime parent
bot         4667  0.0  0.0 1152192 29912 ?       Sl   17:44   0:00      |       \_ appinit
bot         4702  0.0  0.1 533640 40320 ?        Sl   17:44   0:00      |       |   \_ cvmfs2 cvmfs-config.cern.ch /dev/fd/3 -f
bot         4703  0.8  0.2 951000 65176 ?        Sl   17:44   1:37      |       |   \_ cvmfs2 software.eessi.io /dev/fd/3 -f
bot         4705  0.7  0.0  27712 27100 ?        S    17:44   1:26      |       |   \_ fuse-overlayfs -o lowerdir=/cvmfs_ro/software.eessi.io -o upperdir=/tmp/overlay-upper -o workdir=/tmp/overlay-work /dev/fd/3 -f
bot         4706  0.0  0.0   3824  2832 ?        S    17:44   0:00      |       |   \_ /bin/bash /project/60006/SHARED/jobs/2024.02/pr_401/event_4577dd40-c128-11ee-9720-d3d6dffc6b6e/run_001/linux_x86_64_intel_haswell/eessi.io-2023.06-software/install_software_layer.sh --build-logs-dir /project/def-users/SHARED/build-logs --shared-fs-path /project/def-users/bot/shared
bot         4720  0.0  0.0   3956  2776 ?        S    17:44   0:00      |       |   |   \_ /bin/bash ./run_in_compat_layer_env.sh ./EESSI-install-software.sh --build-logs-dir /project/def-users/SHARED/build-logs --shared-fs-path /project/def-users/bot/shared
bot         4823  0.0  0.0   7344  3624 ?        S    17:44   0:00      |       |   |       \_ /cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/bin/bash /cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/startprefix
bot         4838  0.0  0.0   4320  3132 ?        S    17:44   0:00      |       |   |           \_ /cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/bin/bash -l
bot         4872  0.0  0.0   4080  2932 ?        S    17:44   0:00      |       |   |               \_ /bin/bash ./EESSI-install-software.sh --build-logs-dir /project/def-users/SHARED/build-logs --shared-fs-path /project/def-users/bot/shared
bot         5087  0.0  0.3 181068 108108 ?       Sl   17:44   0:08      |       |   |                   \_ /cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/lib/python-exec/python3.11/python -m easybuild.main --easystack /project/60006/SHARED/jobs/2024.02/pr_401/event_4577dd40-c128-11ee-9720-d3d6dffc6b6e/run_001/linux_x86_64_intel_haswell/eessi.io-2023.06-software/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml --robot
bot        32567  0.0  0.0   6284  3020 ?        S    17:51   0:00      |       |   |                       \_ make check -j 16
bot        32570  0.0  0.0   6700  3464 ?        S    17:51   0:00      |       |   |                           \_ make -f CMakeFiles/Makefile2 check
bot        32574  0.0  0.0   8812  5416 ?        S    17:51   0:00      |       |   |                               \_ make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all
bot        32764  0.0  0.0   6156  2820 ?        S    17:51   0:00      |       |   |                                   \_ make -f python_packaging/gmxapi/test/CMakeFiles/gmxapi_pytest.dir/build.make python_packaging/gmxapi/test/CMakeFiles/gmxapi_pytest.dir/build
bot        32765  0.0  0.0   2592   628 ?        S    17:51   0:00      |       |   |                                   |   \_ /bin/sh -c cd /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/easybuild_obj/python_packaging/gmxapi/gmxapi_staging && /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/CMake/3.26.3-GCCcore-12.3.0/bin/cmake -E env --unset=OMP_NUM_THREADS /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pytest -rA -l --log-cli-level ERROR /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/gromacs-2023.3/python_packaging/gmxapi/test
bot        32766  0.0  0.0  24600  8920 ?        S    17:51   0:00      |       |   |                                   |       \_ /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/CMake/3.26.3-GCCcore-12.3.0/bin/cmake -E env --unset=OMP_NUM_THREADS /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pytest -rA -l --log-cli-level ERROR /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/gromacs-2023.3/python_packaging/gmxapi/test
bot        32770  0.0  0.1 199420 40188 ?        Sl   17:51   0:00      |       |   |                                   |           \_ /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pytest -rA -l --log-cli-level ERROR /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/gromacs-2023.3/python_packaging/gmxapi/test
bot        32778  0.0  0.0 158016 21880 ?        Ssl  17:51   0:00      |       |   |                                   |               \_ orted --hnp --set-sid --report-uri 14 --singleton-died-pipe 15 -mca state_novm_select 1 -mca ess hnp -mca pmix ^s1,s2,cray,isolated
bot        32774  0.0  0.0   6156  2916 ?        S    17:51   0:00      |       |   |                                   \_ make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_pytest.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_pytest.dir/build
bot        32775  0.0  0.0   2592   692 ?        S    17:51   0:00      |       |   |                                       \_ /bin/sh -c cd /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/easybuild_obj/python_packaging/gmxapi/gmxapi_staging && /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/CMake/3.26.3-GCCcore-12.3.0/bin/cmake -E env --unset=OMP_NUM_THREADS LD_LIBRARY_PATH= PYTHONPATH=/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/mpi4py/3.1.4-gompi-2023a/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/networkx/3.1-gfbf-2023a/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/pybind11/2.11.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python-bundle-PyPI/2023.06-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/virtualenv/20.23.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/cryptography/41.0.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/cffi/1.15.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/easybuild/python:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/scikit-build/0.17.6-GCCcore-12.3.0/lib/python3.11/site-packages:/tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/easybuild_obj/python_packaging/gmxapi/gmxapi_staging:/tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/easybuild_obj/lib /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pytest --log-cli-level ERROR /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/gromacs-2023.3/python_packaging/sample_restraint/tests
bot        32776  0.0  0.0  24600  8908 ?        S    17:51   0:00      |       |   |                                           \_ /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/CMake/3.26.3-GCCcore-12.3.0/bin/cmake -E env --unset=OMP_NUM_THREADS LD_LIBRARY_PATH= PYTHONPATH=/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/mpi4py/3.1.4-gompi-2023a/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/networkx/3.1-gfbf-2023a/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/pybind11/2.11.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python-bundle-PyPI/2023.06-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/virtualenv/20.23.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/cryptography/41.0.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/cffi/1.15.1-GCCcore-12.3.0/lib/python3.11/site-packages:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/easybuild/python:/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/scikit-build/0.17.6-GCCcore-12.3.0/lib/python3.11/site-packages:/tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/easybuild_obj/python_packaging/gmxapi/gmxapi_staging:/tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/easybuild_obj/lib /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pytest --log-cli-level ERROR /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/gromacs-2023.3/python_packaging/sample_restraint/tests
bot        32777  0.0  0.1 203856 44732 ?        Sl   17:51   0:00      |       |   |                                               \_ /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/Python/3.11.3-GCCcore-12.3.0/bin/python -m pytest --log-cli-level ERROR /tmp/bot/easybuild/build/GROMACS/2023.3/foss-2023a/gromacs-2023.3/python_packaging/sample_restraint/tests
bot        32780  0.0  0.0 158020 18220 ?        Ssl  17:51   0:00      |       |   |                                                   \_ orted --hnp --set-sid --report-uri 14 --singleton-died-pipe 15 -mca state_novm_select 1 -mca ess hnp -mca pmix ^s1,s2,cray,isolated

I've killed job 5151 for haswell, let's re-try that one...

boegel · 2024-02-01T20:58:53Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2024-02-01T20:58:57Z

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/intel/haswell from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen2 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 5158, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 5159, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 5160, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2024-02-01T20:59:00Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-haswell for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5158

date	job status	comment
Feb 01 20:59:00 UTC 2024	submitted	job id `5158` awaits release by job manager
Feb 01 21:00:01 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 21:01:03 UTC 2024	running	job `5158` is running
Feb 02 21:01:04 UTC 2024	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job5158.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Feb 02 21:01:04 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job5158.test` does not exist in job directory or reading it failed.

eessi-bot · 2024-02-01T20:59:04Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen2 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5159

date	job status	comment
Feb 01 20:59:03 UTC 2024	submitted	job id `5159` awaits release by job manager
Feb 01 20:59:58 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 21:06:14 UTC 2024	running	job `5159` is running
Feb 01 21:48:32 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5159.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-zen2-1706824045.tar.gz` size: 41 MiB (43353599 bytes) entries: 768 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/x86_64/amd/zen2 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 01 21:48:32 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-01T20:59:07Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5160

date	job status	comment
Feb 01 20:59:07 UTC 2024	submitted	job id `5160` awaits release by job manager
Feb 01 20:59:56 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 01 21:05:09 UTC 2024	running	job `5160` is running
Feb 01 21:36:02 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-5160.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 Details No artefacts were created or found.
Feb 01 21:36:02 UTC 2024	test result	(no tests yet)

boegel · 2024-02-06T09:13:38Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1

eessi-bot · 2024-02-06T09:13:41Z

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/intel/haswell from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen3 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_n1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 5436, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 5437, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 5438, for details & status see {2023.06}[foss/2023a] GROMACS v2023.3 #401 (comment)

eessi-bot · 2024-02-06T09:13:45Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-haswell for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5436

date	job status	comment
Feb 06 09:13:44 UTC 2024	submitted	job id `5436` awaits release by job manager
Feb 06 09:14:49 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 06 09:20:57 UTC 2024	running	job `5436` is running
Feb 07 09:20:34 UTC 2024	finished	🤷 UNKNOWN (click triangle for detailed information) Job results file `_bot_job5436.result` does not exist in job directory or reading it failed. No artefacts were found/reported.
Feb 07 09:20:34 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job5436.test` does not exist in job directory or reading it failed.

eessi-bot · 2024-02-06T09:13:49Z

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/2024.02/pr_401/5437

date	job status	comment
Feb 06 09:13:48 UTC 2024	submitted	job id `5437` awaits release by job manager
Feb 06 09:14:47 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 06 09:20:55 UTC 2024	running	job `5437` is running
Feb 06 09:56:19 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5437.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-zen3-1707213349.tar.gz` size: 41 MiB (43357430 bytes) entries: 768 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/x86_64/amd/zen3 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 06 09:56:19 UTC 2024	test result	(no tests yet)

eessi-bot · 2024-02-06T09:13:54Z

New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_n1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.02/pr_401/5438

date	job status	comment
Feb 06 09:13:53 UTC 2024	submitted	job id `5438` awaits release by job manager
Feb 06 09:14:45 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 06 09:19:52 UTC 2024	running	job `5438` is running
Feb 06 10:04:42 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5438.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-aarch64-neoverse_n1-1707213821.tar.gz` size: 36 MiB (38782896 bytes) entries: 768 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `GROMACS/2023.3-foss-2023a.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `GROMACS/2023.3-foss-2023a` other under 2023.06/software/linux/aarch64/neoverse_n1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Feb 06 10:04:42 UTC 2024	test result	(no tests yet)

boegel · 2024-05-01T06:57:06Z

superseded by #499

…on_for_failing_test_step Fix emoticon for failing test step

{2023.06}[foss/2023a] GROMACS v2023.06

4ec80b0

boegel added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label Nov 26, 2023

Merge branch '2023.06-software.eessi.io' into 2023.06-software.eessi.…

9156af4

…io_GROMACS-foss-2023a

bedroge changed the title ~~{2023.06}[foss/2023a] GROMACS v2023.06~~ {2023.06}[foss/2023a] GROMACS v2023.3 Nov 28, 2023

Merge branch '2023.06-software.eessi.io' into 2023.06-software.eessi.…

c6957ef

…io_GROMACS-foss-2023a

boegel marked this pull request as ready for review November 28, 2023 16:00

Merge branch '2023.06-software.eessi.io' into 2023.06-software.eessi.…

c391499

…io_GROMACS-foss-2023a

boegel force-pushed the 2023.06-software.eessi.io_GROMACS-foss-2023a branch from 4384975 to c391499 Compare February 1, 2024 14:36

boegel mentioned this pull request Feb 1, 2024

update CI workflow to use software.eessi.io EESSI/test-suite#107

Closed

EESSI deleted a comment from eessi-bot bot Feb 1, 2024

boegel closed this May 1, 2024

boegel deleted the 2023.06-software.eessi.io_GROMACS-foss-2023a branch May 1, 2024 06:57

TopRichard added a commit to TopRichard/software-layer that referenced this pull request Jun 11, 2024

Merge pull request EESSI#401 from TopRichard/nessi-2023.06-Fix_emotic…

11fcb4b

…on_for_failing_test_step Fix emoticon for failing test step

bedroge mentioned this pull request Nov 27, 2025

{2023.06}[2023b] Rebuild GROMACS 2024.1 + 2024.3 + 2024.4 #1316

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