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{2023.06}[foss/2023a] OpenFOAM v2312 #563

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@boegel boegel commented May 7, 2024

2 out of 113 required modules missing:

* KaHIP/3.16-gompi-2023a (KaHIP-3.16-gompi-2023a.eb)
* OpenFOAM/v2312-foss-2023a (OpenFOAM-v2312-foss-2023a.eb)

@boegel boegel added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label May 7, 2024
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  • arch x86_64/generic for repo eessi.io-2023.06-compat
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  • arch x86_64/intel/haswell for repo eessi.io-2023.06-compat
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  • arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-software
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  • arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-software
  • arch x86_64/amd/zen2 for repo eessi.io-2023.06-compat
  • arch x86_64/amd/zen2 for repo eessi.io-2023.06-software
  • arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-software
  • arch x86_64/amd/zen3 for repo eessi.io-2023.06-compat
  • arch x86_64/amd/zen3 for repo eessi.io-2023.06-software
  • arch aarch64/generic for repo eessi-hpc.org-2023.06-compat
  • arch aarch64/generic for repo eessi-hpc.org-2023.06-software
  • arch aarch64/generic for repo eessi.io-2023.06-compat
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Instance eessi-bot-mc-azure is configured to build:

  • arch x86_64/amd/zen4 for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/amd/zen4 for repo eessi-hpc.org-2023.06-software
  • arch x86_64/amd/zen4 for repo eessi.io-2023.06-compat
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boegel commented May 7, 2024

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

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    • expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3
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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/2024.05/pr_563/10305

date job status comment
May 07 13:23:44 UTC 2024 submitted job id 10305 awaits release by job manager
May 07 13:24:28 UTC 2024 released job awaits launch by Slurm scheduler
May 07 13:29:56 UTC 2024 running job 10305 is running
May 07 14:50:10 UTC 2024 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-10305.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-zen3-1715092555.tar.gzsize: 11 MiB (11585324 bytes)
entries: 44
modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all
KaHIP/3.16-gompi-2023a.lua
software under 2023.06/software/linux/x86_64/amd/zen3/software
KaHIP/3.16-gompi-2023a
other under 2023.06/software/linux/x86_64/amd/zen3
no other files in tarball
May 07 14:50:10 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-10305.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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bedroge commented Jun 7, 2024

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

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date job status comment
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Details
✅ job output file slurm-12272.out
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bedroge commented Jun 7, 2024

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

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date job status comment
Jun 07 12:27:57 UTC 2024 submitted job id 12274 awaits release by job manager
Jun 07 12:29:00 UTC 2024 released job awaits launch by Slurm scheduler
Jun 07 12:30:05 UTC 2024 running job 12274 is running
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✅ job output file slurm-12274.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-zen3-1717767335.tar.gzsize: 11 MiB (11586200 bytes)
entries: 44
modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all
KaHIP/3.16-gompi-2023a.lua
software under 2023.06/software/linux/x86_64/amd/zen3/software
KaHIP/3.16-gompi-2023a
other under 2023.06/software/linux/x86_64/amd/zen3
no other files in tarball
Jun 07 13:41:59 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-12274.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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bedroge commented Jun 7, 2024

Sanity check is failing because of missing binaries (e.g. boundaryFoam and engineFoam). They should be in OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/bin, but they're not, while the same version on generoso does have them:

$ ls -1 /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/bin/ | wc -l
133

$ ls -1 /project/boegelbot/Rocky8/haswell/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/bin | wc -l
316
$ 

But I can't find any explanation for this in the logs...

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bedroge commented Jun 7, 2024

Oh, actually, it looks like the build step did fail, even though EB says it completed. In the log file of the build step itself I see lots of errors near the bottom, most of them are like this:

/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: insertFeaturePoints.C:(.text+0xc19): undefined reference to `__gmpn_mul'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFO
AM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `mpfr_get_emin'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFO
AM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `__gmpn_com'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFO
AM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `__gmpq_swap'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFO
AM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `__gmpq_init'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `__gmpn_copyi'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `mpfr_set_q'
/cvmfs/software.eessi.io/versions/2023.06/compat/linux/x86_64/usr/bin/ld.bfd: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libconformalVoronoiMesh.so: undefined reference to `__gmpn_add_n'

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ocaisa commented Jun 7, 2024

Ah, GMP is not included in the list of dependencies but it clearly is one

@bedroge
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bedroge commented Jun 7, 2024

Ah, GMP is not included in the list of dependencies but it clearly is one

Yep, and MPFR.

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bedroge commented Jun 7, 2024

Doing an interactive build now with both of them added to the deps:

    ('GMP', '6.2.1'),
    ('MPFR', '4.2.0'),

It's worrying though that the build actually failed, but apparently this Allwmake command returned with an exit code 0?

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boegel commented Jun 7, 2024

Doing an interactive build now with both of them added to the deps:

    ('GMP', '6.2.1'),
    ('MPFR', '4.2.0'),

It's worrying though that the build actually failed, but apparently this Allwmake command returned with an exit code 0?

If I remember correctly this was one of the motivations for implementing the sanity check concept in EasyBuild :)

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bedroge commented Jun 7, 2024

Adding those dependencies didn't help, still getting the same issue/errors.

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bedroge commented Jun 7, 2024

It's probably related to CGAL, which could previously be built in different ways. Since version 5 it's header-only, but when using this with OpenFOAM, it looks like MPFR and GMP are still required. There seems to be functionality in OpenFOAM that should detect which variant of CGAL you have, but I find lots of similar issues, e.g. this one with Spack: https://develop.openfoam.com/Development/openfoam/-/issues/3101.

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bedroge commented Jun 11, 2024

Confirmed, it's related to CGAL. In Spack they even stick to CGAL 4, probably because of similar issues:
https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/openfoam/package.py#L372

I suspect it pops up now because we're filtering $LD_LIBRARY_PATH. As a sort of a quick/dirty workaround I've added a command to preconfigopts that injects the MPFR and GMP directories to CGAL_LIBS somewhere, and that allowed the build to complete. I'll clean this up and make a PR for it.

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bedroge commented Jun 19, 2024

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
bot: build repo:eessi.io-2023.06-software arch:x86_64/generic
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:x86_64/intel/haswell
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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/2024.06/pr_563/13044

date job status comment
Jun 19 10:03:25 UTC 2024 submitted job id 13044 awaits release by job manager
Jun 19 10:04:12 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:05:37 UTC 2024 running job 13044 is running
Jun 19 12:06:38 UTC 2024 finished
😁 SUCCESS (click triangle for details)
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✅ job output file slurm-13044.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-1718797312.tar.gzsize: 527 MiB (552641970 bytes)
entries: 65533
modules under 2023.06/software/linux/aarch64/generic/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/aarch64/generic/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/aarch64/generic
no other files in tarball
Jun 19 12:06:38 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13044.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13045

date job status comment
Jun 19 10:03:29 UTC 2024 submitted job id 13045 awaits release by job manager
Jun 19 10:04:15 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:09:04 UTC 2024 running job 13045 is running
Jun 19 12:12:07 UTC 2024 finished
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✅ job output file slurm-13045.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_n1-1718797678.tar.gzsize: 528 MiB (553793208 bytes)
entries: 65533
modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/aarch64/neoverse_n1/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/aarch64/neoverse_n1
no other files in tarball
Jun 19 12:12:07 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13045.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13046

date job status comment
Jun 19 10:03:33 UTC 2024 submitted job id 13046 awaits release by job manager
Jun 19 10:04:17 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:09:08 UTC 2024 running job 13046 is running
Jun 19 11:37:14 UTC 2024 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-13046.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_v1-1718796057.tar.gzsize: 528 MiB (553730757 bytes)
entries: 65533
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/aarch64/neoverse_v1/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/aarch64/neoverse_v1
no other files in tarball
Jun 19 11:37:14 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13046.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13047

date job status comment
Jun 19 10:03:38 UTC 2024 submitted job id 13047 awaits release by job manager
Jun 19 10:04:24 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:11:37 UTC 2024 running job 13047 is running
Jun 19 12:20:39 UTC 2024 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-13047.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-1718798102.tar.gzsize: 529 MiB (555660549 bytes)
entries: 65533
modules under 2023.06/software/linux/x86_64/generic/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/x86_64/generic/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/x86_64/generic
no other files in tarball
Jun 19 12:20:39 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13047.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13048

date job status comment
Jun 19 10:03:42 UTC 2024 submitted job id 13048 awaits release by job manager
Jun 19 10:04:19 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:11:31 UTC 2024 running job 13048 is running
Jun 19 12:32:00 UTC 2024 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-13048.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-zen2-1718798853.tar.gzsize: 531 MiB (557146732 bytes)
entries: 65533
modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/x86_64/amd/zen2/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/x86_64/amd/zen2
no other files in tarball
Jun 19 12:32:00 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13048.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13049

date job status comment
Jun 19 10:03:46 UTC 2024 submitted job id 13049 awaits release by job manager
Jun 19 10:04:21 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:11:34 UTC 2024 running job 13049 is running
Jun 19 12:08:51 UTC 2024 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-13049.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-zen3-1718797561.tar.gzsize: 531 MiB (557097477 bytes)
entries: 65533
modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/x86_64/amd/zen3/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/x86_64/amd/zen3
no other files in tarball
Jun 19 12:08:51 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13049.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13050

date job status comment
Jun 19 10:03:50 UTC 2024 submitted job id 13050 awaits release by job manager
Jun 19 10:04:26 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:12:53 UTC 2024 running job 13050 is running
Jun 19 12:24:50 UTC 2024 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-13050.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-1718798220.tar.gzsize: 531 MiB (557655917 bytes)
entries: 65533
modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/x86_64/intel/haswell/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/x86_64/intel/haswell
no other files in tarball
Jun 19 12:24:50 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13050.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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eessi-bot-aws bot commented Jun 19, 2024

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/2024.06/pr_563/13051

date job status comment
Jun 19 10:03:54 UTC 2024 submitted job id 13051 awaits release by job manager
Jun 19 10:04:28 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:12:56 UTC 2024 running job 13051 is running
Jun 19 10:45:32 UTC 2024 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-13051.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-intel-skylake_avx512-1718792346.tar.gzsize: 10 MiB (11356671 bytes)
entries: 44
modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all
KaHIP/3.16-gompi-2023a.lua
software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software
KaHIP/3.16-gompi-2023a
other under 2023.06/software/linux/x86_64/intel/skylake_avx512
no other files in tarball
Jun 19 10:45:32 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 12/12 test case(s) from 12 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-13051.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@bedroge
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bedroge commented Jun 20, 2024

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/2024.06/pr_563/13051

date job status comment
Jun 19 10:03:54 UTC 2024 submitted job id 13051 awaits release by job manager
Jun 19 10:04:28 UTC 2024 released job awaits launch by Slurm scheduler
Jun 19 10:12:56 UTC 2024 running job 13051 is running
Jun 19 10:45:32 UTC 2024 finished
😢 FAILURE (click triangle for details)
Jun 19 10:45:32 UTC 2024 test result
😁 SUCCESS (click triangle for details)

make: /bin/sh: Argument list too long
make: *** [/cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/skylake_avx512/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/wmake/makefiles/general:210: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/skylake_avx512/software/OpenFOAM/v2312-foss-2023a/OpenFOAM-v2312/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so] Error 127

Looks like the path for skylake is too long...

@marconetto
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HI, just to double check, once this is issue is fixed, will we be able to run OpenFoam on zen4?

@ocaisa
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ocaisa commented Jun 27, 2024

@marconetto Yes and no, the Zen4 builds are happening separately as we still have to bring that stack in line with the other architectures. Having said that, zen4 can't go through without getting this PR over the line. It's not an easy one though as this is a difficult issue and will require a little design

@marconetto
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marconetto commented Jun 27, 2024

thanks for the clarification @ocaisa!

@bedroge
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bedroge commented Jul 5, 2024

Based on my comments in #296 (comment), I was hoping to fix this by only unsetting some environment variables. That didn't work though, and I'm still not fully sure why. The failing command does work fine when running it interactively, also with the same environment variables set as during the build. My only guess is that there's a bunch of makefiles calling/including other ones, which are also somehow increasing the size of the environment and apparently exceeding some limit.

While analyzing and debugging this, I came up with a workaround though. The failing command is compiling libOpenFOAM.so, and this needs to link together a whole bunch of object files. It uses the full path to these object files, but since the command is running in the build/installation directory, it can use relative paths. This greatly reduces the length of the command. The following hook uses that approach and worked on skylake (still need to be cleaned/extended a bit):

def pre_build_hook_openfoam(self, *args, **kwargs):
    if self.name == 'OpenFOAM':
        objects_regex = (
            r'(\$E \$\(LINKLIBSO\) \$\(FOAM_EXTRA_LDFLAGS\)) \$\(OBJECTS\) (-L\$\(LIB_PLATFORMS\))',
            r'\1 $(subst $(WM_PROJECT_DIR),$(shell realpath --relative-to=$(PWD) $(WM_PROJECT_DIR)),$(OBJECTS)) \2'
        )
        apply_regex_substitutions('wmake/makefiles/general', [objects_regex])

@boegel
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boegel commented Jul 5, 2024

@bedroge Awesome work!

Instead of implementing this in a hook, why don't we bake it into the OpenFOAM easyblock instead, since this should be a general fix, it's not specific to EESSI at all?

@bedroge
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bedroge commented Jul 5, 2024

@bedroge Awesome work!

Instead of implementing this in a hook, why don't we bake it into the OpenFOAM easyblock instead, since this should be a general fix, it's not specific to EESSI at all?

Yes, you're absolutely right. I can open a PR in the easyblocks repo.

@bedroge
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bedroge commented Jul 9, 2024

I've opened an easyblocks PR: easybuilders/easybuild-easyblocks#3388.
Let's give it a spin...

@bedroge
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bedroge commented Jul 9, 2024

bot: build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512

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eessi-bot-aws bot commented Jul 9, 2024

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/skylake_avx512 from bedroge

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

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eessi-bot-aws bot commented Jul 9, 2024

Updates by the bot instance eessi-bot-mc-azure (click for details)
  • received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/skylake_avx512 from bedroge

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

    • no jobs were submitted

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eessi-bot-aws bot commented Jul 9, 2024

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/2024.07/pr_563/14154

date job status comment
Jul 09 13:48:31 UTC 2024 submitted job id 14154 awaits release by job manager
Jul 09 13:49:03 UTC 2024 released job awaits launch by Slurm scheduler
Jul 09 13:55:06 UTC 2024 running job 14154 is running
Jul 09 15:49:48 UTC 2024 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-14154.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_avx512-1720539408.tar.gzsize: 531 MiB (556978919 bytes)
entries: 65535
modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all
KaHIP/3.16-gompi-2023a.lua
OpenFOAM/v2312-foss-2023a.lua
software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software
KaHIP/3.16-gompi-2023a
OpenFOAM/v2312-foss-2023a
other under 2023.06/software/linux/x86_64/intel/skylake_avx512
2023.06/init/easybuild/eb_hooks.py
Jul 09 15:49:48 UTC 2024 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ PASSED ] Ran 14/14 test case(s) from 14 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-14154.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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