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{2023.06}[foss/2021a] GROMACS v2021.3 #288

Merged
merged 4 commits into from
Jun 29, 2023
Merged

{2023.06}[foss/2021a] GROMACS v2021.3 #288

merged 4 commits into from
Jun 29, 2023

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laraPPr
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@laraPPr laraPPr commented Jun 28, 2023

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eessi-bot bot commented Jun 28, 2023

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

  • arch x86_64/generic for repo eessi-2021.12
  • arch x86_64/generic for repo eessi-2023.06-compat
  • arch x86_64/generic for repo eessi-2023.06-software
  • arch x86_64/intel/haswell for repo eessi-2021.12
  • arch x86_64/intel/haswell for repo eessi-2023.06-compat
  • arch x86_64/intel/haswell for repo eessi-2023.06-software
  • arch x86_64/intel/skylake_avx512 for repo eessi-2021.12
  • arch x86_64/intel/skylake_avx512 for repo eessi-2023.06-compat
  • arch x86_64/intel/skylake_avx512 for repo eessi-2023.06-software
  • arch x86_64/amd/zen2 for repo eessi-2021.12
  • arch x86_64/amd/zen2 for repo eessi-2023.06-compat
  • arch x86_64/amd/zen2 for repo eessi-2023.06-software
  • arch x86_64/amd/zen3 for repo eessi-2021.12
  • arch x86_64/amd/zen3 for repo eessi-2023.06-compat
  • arch x86_64/amd/zen3 for repo eessi-2023.06-software
  • arch aarch64/generic for repo eessi-2021.12
  • arch aarch64/generic for repo eessi-2023.06-compat
  • arch aarch64/generic for repo eessi-2023.06-software
  • arch aarch64/neoverse_n1 for repo eessi-2021.12
  • arch aarch64/neoverse_n1 for repo eessi-2023.06-compat
  • arch aarch64/neoverse_n1 for repo eessi-2023.06-software
  • arch aarch64/neoverse_v1 for repo eessi-2021.12
  • arch aarch64/neoverse_v1 for repo eessi-2023.06-compat
  • arch aarch64/neoverse_v1 for repo eessi-2023.06-software

@laraPPr laraPPr changed the title Add gromacs {2023.06}[foss/2021a] GROMACS v2021.3 Jun 28, 2023
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laraPPr commented Jun 28, 2023

bot: build arch:x86_64/generic repo:eessi-2023.06-software

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

  • received bot command build arch:x86_64/generic repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:x86_64/generic repository:eessi-2023.06-software

  • handling command build architecture:x86_64/generic repository:eessi-2023.06-software resulted in:

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New job on instance eessi-bot-citc-aws for architecture x86_64-generic for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5631

date job status comment
Jun 28 07:58:01 UTC 2023 submitted job id 5631 awaits release by job manager
Jun 28 07:58:26 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 07:59:34 UTC 2023 running job 5631 is running
Jun 28 09:31:48 UTC 2023 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-5631.out
❌ found message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
✅ found message(s) matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-x86_64-generic-1687944635.tar.gzsize: 159 MiB (166806039 bytes)
entries: 9318
modules under 2023.06/software/linux/x86_64/generic/modules/all
Eigen/3.3.9-GCCcore-10.3.0.lua
GROMACS/2021.3-foss-2021a.lua
hypothesis/6.13.1-GCCcore-10.3.0.lua
networkx/2.5.1-foss-2021a.lua
pybind11/2.6.2-GCCcore-10.3.0.lua
scikit-build/0.11.1-GCCcore-10.3.0.lua
SciPy-bundle/2021.05-foss-2021a.lua
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GROMACS/2021.3-foss-2021a
hypothesis/6.13.1-GCCcore-10.3.0
networkx/2.5.1-foss-2021a
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.lmod/cache/timestamp
Jun 29 07:03:52 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-x86_64-generic-1687944635.tar.gz to S3 bucket succeeded

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laraPPr commented Jun 28, 2023

bot: build arch:x86_64/generic repo:eessi-2023.06-software

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

  • received bot command build arch:x86_64/generic repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:x86_64/generic repository:eessi-2023.06-software

  • handling command build architecture:x86_64/generic repository:eessi-2023.06-software resulted in:

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New job on instance eessi-bot-citc-aws for architecture x86_64-generic for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5644

date job status comment
Jun 28 11:10:03 UTC 2023 submitted job id 5644 awaits release by job manager
Jun 28 11:10:52 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 11:13:58 UTC 2023 running job 5644 is running
Jun 28 12:35:09 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5644.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-1687955624.tar.gzsize: 159 MiB (166802857 bytes)
entries: 9318
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laraPPr commented Jun 28, 2023

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

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

  • received bot command build arch:x86_64/intel/haswell repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:x86_64/intel/haswell repository:eessi-2023.06-software

  • received bot command build arch:x86_64/intel/skylake_avx512 repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:x86_64/intel/skylake_avx512 repository:eessi-2023.06-software

  • received bot command build arch:x86_64/amd/zen2 repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:x86_64/amd/zen2 repository:eessi-2023.06-software

  • received bot command build arch:x86_64/amd/zen3 repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:x86_64/amd/zen3 repository:eessi-2023.06-software

  • received bot command build arch:aarch64/generic repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:aarch64/generic repository:eessi-2023.06-software

  • received bot command build arch:aarch64/neoverse_n1 repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:aarch64/neoverse_n1 repository:eessi-2023.06-software

  • received bot command build arch:aarch64/neoverse_v1 repo:eessi-2023.06-software from laraPPr

    • expanded format: build architecture:aarch64/neoverse_v1 repository:eessi-2023.06-software

  • handling command build architecture:x86_64/intel/haswell repository:eessi-2023.06-software resulted in:

  • handling command build architecture:x86_64/intel/skylake_avx512 repository:eessi-2023.06-software resulted in:

  • handling command build architecture:x86_64/amd/zen2 repository:eessi-2023.06-software resulted in:

  • handling command build architecture:x86_64/amd/zen3 repository:eessi-2023.06-software resulted in:

  • handling command build architecture:aarch64/generic repository:eessi-2023.06-software resulted in:

  • handling command build architecture:aarch64/neoverse_n1 repository:eessi-2023.06-software resulted in:

  • handling command build architecture:aarch64/neoverse_v1 repository:eessi-2023.06-software resulted in:

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New job on instance eessi-bot-citc-aws for architecture x86_64-intel-haswell for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5645

date job status comment
Jun 28 12:40:12 UTC 2023 submitted job id 5645 awaits release by job manager
Jun 28 12:41:29 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:42:31 UTC 2023 running job 5645 is running
Jun 28 14:14:19 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5645.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-haswell-1687961545.tar.gzsize: 162 MiB (170117961 bytes)
entries: 9318
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GROMACS/2021.3-foss-2021a.lua
hypothesis/6.13.1-GCCcore-10.3.0.lua
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.lmod/cache/timestamp
Jun 29 07:03:11 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-x86_64-intel-haswell-1687961545.tar.gz to S3 bucket succeeded

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New job on instance eessi-bot-citc-aws for architecture x86_64-intel-skylake_avx512 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5646

date job status comment
Jun 28 12:40:20 UTC 2023 submitted job id 5646 awaits release by job manager
Jun 28 12:41:26 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:44:44 UTC 2023 running job 5646 is running
Jun 28 13:59:29 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5646.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_avx512-1687960696.tar.gzsize: 160 MiB (168368072 bytes)
entries: 9318
modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all
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GROMACS/2021.3-foss-2021a.lua
hypothesis/6.13.1-GCCcore-10.3.0.lua
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SciPy-bundle/2021.05-foss-2021a.lua
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hypothesis/6.13.1-GCCcore-10.3.0
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Jun 29 07:03:41 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1687960696.tar.gz to S3 bucket succeeded

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New job on instance eessi-bot-citc-aws for architecture x86_64-amd-zen2 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5647

date job status comment
Jun 28 12:40:27 UTC 2023 submitted job id 5647 awaits release by job manager
Jun 28 12:41:24 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:44:42 UTC 2023 running job 5647 is running
Jun 28 14:01:39 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5647.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-zen2-1687960841.tar.gzsize: 162 MiB (170067580 bytes)
entries: 9318
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Jun 29 07:03:21 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-x86_64-amd-zen2-1687960841.tar.gz to S3 bucket succeeded

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New job on instance eessi-bot-citc-aws for architecture x86_64-amd-zen3 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5648

date job status comment
Jun 28 12:40:33 UTC 2023 submitted job id 5648 awaits release by job manager
Jun 28 12:41:22 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:44:40 UTC 2023 running job 5648 is running
Jun 28 13:47:32 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5648.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-zen3-1687959967.tar.gzsize: 162 MiB (170052600 bytes)
entries: 9318
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Jun 29 07:04:01 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-x86_64-amd-zen3-1687959967.tar.gz to S3 bucket succeeded

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New job on instance eessi-bot-citc-aws for architecture aarch64-generic for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5649

date job status comment
Jun 28 12:40:40 UTC 2023 submitted job id 5649 awaits release by job manager
Jun 28 12:41:20 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:44:38 UTC 2023 running job 5649 is running
Jun 28 14:18:26 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5649.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-1687961815.tar.gzsize: 151 MiB (159012598 bytes)
entries: 9318
modules under 2023.06/software/linux/aarch64/generic/modules/all
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Jun 29 07:03:00 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-aarch64-generic-1687961815.tar.gz to S3 bucket succeeded

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eessi-bot bot commented Jun 28, 2023 •
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New job on instance eessi-bot-citc-aws for architecture aarch64-neoverse_n1 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5650

date job status comment
Jun 28 12:40:47 UTC 2023 submitted job id 5650 awaits release by job manager
Jun 28 12:41:16 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:44:36 UTC 2023 running job 5650 is running
Jun 28 14:15:22 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5650.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_n1-1687961646.tar.gzsize: 155 MiB (163424793 bytes)
entries: 9318
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hypothesis/6.13.1-GCCcore-10.3.0.lua
networkx/2.5.1-foss-2021a.lua
pybind11/2.6.2-GCCcore-10.3.0.lua
scikit-build/0.11.1-GCCcore-10.3.0.lua
SciPy-bundle/2021.05-foss-2021a.lua
software under 2023.06/software/linux/aarch64/neoverse_n1/software
Eigen/3.3.9-GCCcore-10.3.0
GROMACS/2021.3-foss-2021a
hypothesis/6.13.1-GCCcore-10.3.0
networkx/2.5.1-foss-2021a
pybind11/2.6.2-GCCcore-10.3.0
scikit-build/0.11.1-GCCcore-10.3.0
SciPy-bundle/2021.05-foss-2021a
other under 2023.06/software/linux/aarch64/neoverse_n1
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp
Jun 29 07:02:51 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-aarch64-neoverse_n1-1687961646.tar.gz to S3 bucket succeeded

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eessi-bot bot commented Jun 28, 2023 •
edited
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New job on instance eessi-bot-citc-aws for architecture aarch64-neoverse_v1 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.06/pr_288/5651

date job status comment
Jun 28 12:40:55 UTC 2023 submitted job id 5651 awaits release by job manager
Jun 28 12:41:13 UTC 2023 released job awaits launch by Slurm scheduler
Jun 28 12:44:34 UTC 2023 running job 5651 is running
Jun 28 13:47:30 UTC 2023 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-5651.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_v1-1687959990.tar.gzsize: 157 MiB (165172891 bytes)
entries: 9318
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
Eigen/3.3.9-GCCcore-10.3.0.lua
GROMACS/2021.3-foss-2021a.lua
hypothesis/6.13.1-GCCcore-10.3.0.lua
networkx/2.5.1-foss-2021a.lua
pybind11/2.6.2-GCCcore-10.3.0.lua
scikit-build/0.11.1-GCCcore-10.3.0.lua
SciPy-bundle/2021.05-foss-2021a.lua
software under 2023.06/software/linux/aarch64/neoverse_v1/software
Eigen/3.3.9-GCCcore-10.3.0
GROMACS/2021.3-foss-2021a
hypothesis/6.13.1-GCCcore-10.3.0
networkx/2.5.1-foss-2021a
pybind11/2.6.2-GCCcore-10.3.0
scikit-build/0.11.1-GCCcore-10.3.0
SciPy-bundle/2021.05-foss-2021a
other under 2023.06/software/linux/aarch64/neoverse_v1
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp
Jun 29 07:03:31 UTC 2023 uploaded transfer of eessi-2023.06-software-linux-aarch64-neoverse_v1-1687959990.tar.gz to S3 bucket succeeded

@laraPPr laraPPr added the ready-to-deploy Mark a PR as ready to deploy label Jun 28, 2023
@boegel boegel added bot:deploy Ask bot to deploy missing software installations to EESSI and removed ready-to-deploy Mark a PR as ready to deploy labels Jun 29, 2023
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boegel commented Jun 29, 2023

Ingestion triggered for all 8 tarballs...

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laraPPr commented Jun 29, 2023

Something weird happened the bot says it ingested the failed tarball for arch:x86_64-generic and not the succesfull one
succefull tarball: eessi-2023.06-software-linux-x86_64-generic-1687955624.tar.gz
failed tarball: eessi-2023.06-software-linux-x86_64-generic-1687944635.tar.gz
ingested tarball: eessi-2023.06-software-linux-x86_64-generic-1687944635.tar.gz

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boegel commented Jun 29, 2023

Something weird happened the bot says it ingested the failed tarball for arch:x86_64-generic and not the succesfull one succefull tarball: eessi-2023.06-software-linux-x86_64-generic-1687955624.tar.gz failed tarball: eessi-2023.06-software-linux-x86_64-generic-1687944635.tar.gz ingested tarball: eessi-2023.06-software-linux-x86_64-generic-1687944635.tar.gz

eessi-2023.06-software-linux-x86_64-generic-1687955624.tar.gz was originally marked as failed because this PR originally also included an included entry to eessi-2023.06-eb-4.7.2-2021b.yml (and hence not all checks for the tarball passed).
Once that was removed from this PR, eessi-2023.06-software-linux-x86_64-generic-1687955624.tar.gz was actually correctly marked as SUCCESS when the check was performed during the deploy phase, since it actually included everything needed for GROMACS/2021.3-foss-2021a in x86_64/generic.

So, it looks weird, but it actually worked correctly. :)

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trz42 commented Jun 29, 2023

eessi-2023.06-software-linux-x86_64-generic-1687955624.tar.gz was originally marked as failed because this PR originally also included an included entry to eessi-2023.06-eb-4.7.2-2021b.yml (and hence not all checks for the tarball passed). Once that was removed from this PR, eessi-2023.06-software-linux-x86_64-generic-1687955624.tar.gz was actually correctly marked as SUCCESS when the check was performed during the deploy phase, since it actually included everything needed for GROMACS/2021.3-foss-2021a in x86_64/generic.

So, it looks weird, but it actually worked correctly. :)

Interesting case:

  • small typo in original PR, which should actually not be included $\Longrightarrow$ what if there was no typo?
  • leads to failed PR as a whole, but what it was intended to built succeeded
  • outdated/lacking code in bot deploy procedure leading it to be uploaded (albeit it seemed to have failed)

In NESSI we make an effort to detect such issues (not sure we would have catched this one) using a checklist before we set the bot:deploy label.

NESSI Checklist for building:

  • Check whether builds for all required architectures succeeded (SUCCESS message + reasonably sized tarball)
  • Check if the PR is up-to-date with the target branch nessi.no-2023.06 in the repository (if not what are the differences)
  • Assess if all requested changes are sound (checking files changed on github.com)
  • Verify that all easyconfig/s being built are included with the EB version used (if not why not)
  • Review changes (if any) needed to get the build(s) succeed (common changes for all architectures, changes for a single architecture, changes because of build environment specifics, etc.)

The third check might have revealed something is a bit off with the PR.

Some of the checks may be better performed before triggering the builds. Some tests could also be automated (check that there is no typo, pre-build analysis of missing packages).

Also, I try to force myself adding some description to a PR. May be a bit duplication / additional effort. However, may help in detecting issues as early as possible.

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boegel commented Jun 29, 2023

The typo in the easystack file could have been caught early by the bot, it could have done a eb --missing, which would have failed.

But if there was no typo, and just an accidental change in two rather than one easystack file, that's more difficult to catch automatically...
Unless we make it a policy that each PR should only touch one easystack file, not sure if that's too limiting for some edge cases.

No need to block this PR though, especially since these installations are deployed already, so I'll merge this.
We can open issues for things to improve either here in software-layer repo, or in the bot repo.

@boegel boegel merged commit ff10f4a into EESSI:2023.06 Jun 29, 2023
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trz42 commented Jun 29, 2023

No need to block this PR though, especially since these installations are deployed already, so I'll merge this.

Sure. More food for thought.

@laraPPr laraPPr deleted the add_gromacs branch July 3, 2023 10:32
@boegel boegel mentioned this pull request Jul 7, 2023
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@bedroge bedroge mentioned this pull request Jul 14, 2023
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@laraPPr laraPPr mentioned this pull request Aug 23, 2023
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trz42 pushed a commit to trz42/software-layer that referenced this pull request Mar 14, 2024
@poksumdo
Merge pull request EESSI#288 from trz42/nessi-23.06-Z3-4.12.2-foss-2023a
a5dcf8e 
{2023.06}[foss/2023a] Z3 v4.12.2
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