add Lmod hook to set `$OMPI_MCA_btl` to `^smcuda` when loading OpenMPI module to work around bug #473

boegel · 2024-02-12T20:51:24Z

Temporary workaround for hangs/crashes in OpenMPI due to a bug, cfr. https://gitlab.com/eessi/support/-/issues/41

Tested, works like a charm, for example:

$ module load foss/2023a
Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI (see https://gitlab.com/eessi/support/-/issues/41)

$ echo $OMPI_MCA_btl
^smcuda

eessi-bot-aws · 2024-02-12T20:51:28Z

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

arch x86_64/generic for repo eessi-hpc.org-2023.06-compat
arch x86_64/generic for repo eessi-hpc.org-2023.06-software
arch x86_64/generic for repo eessi.io-2023.06-compat
arch x86_64/generic for repo eessi.io-2023.06-software
arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-compat
arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-software
arch x86_64/intel/haswell for repo eessi.io-2023.06-compat
arch x86_64/intel/haswell for repo eessi.io-2023.06-software
arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-compat
arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-software
arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-compat
arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-software
arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-compat
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
arch aarch64/generic for repo eessi.io-2023.06-software
arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-compat
arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-software
arch aarch64/neoverse_n1 for repo eessi.io-2023.06-compat
arch aarch64/neoverse_n1 for repo eessi.io-2023.06-software
arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-compat
arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-software
arch aarch64/neoverse_v1 for repo eessi.io-2023.06-compat
arch aarch64/neoverse_v1 for repo eessi.io-2023.06-software

…module

boegel · 2024-02-12T20:53:31Z

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

eessi-bot-aws · 2024-02-12T20:53:34Z

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 5835, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)

eessi-bot-aws · 2024-02-12T20:53:38Z

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_473/5835

date	job status	comment
Feb 12 20:53:37 UTC 2024	submitted	job id `5835` awaits release by job manager
Feb 12 20:53:46 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 20:57:05 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5835.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_v1-1707771408.tar.gz` size: 0 MiB (162071 bytes) entries: 4 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all no module files in tarball software under 2023.06/software/linux/aarch64/neoverse_v1/software no software packages in tarball other under 2023.06/software/linux/aarch64/neoverse_v1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 20:57:05 UTC 2024	test result	(no tests yet)
Feb 13 10:43:08 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-neoverse_v1-1707771408.tar.gz` to S3 bucket succeeded

boegel · 2024-02-12T21:29:30Z

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

eessi-bot-aws · 2024-02-12T21:29:33Z

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
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 5836, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 5837, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 5838, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 5839, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 5840, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 5841, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 5842, for details & status see add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473 (comment)

eessi-bot-aws · 2024-02-12T21:29:37Z

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_473/5836

date	job status	comment
Feb 12 21:29:36 UTC 2024	submitted	job id `5836` awaits release by job manager
Feb 12 21:30:18 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 21:36:29 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5836.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-1707773740.tar.gz` size: 0 MiB (162292 bytes) entries: 4 modules under 2023.06/software/linux/x86_64/generic/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/generic/software no software packages in tarball other under 2023.06/software/linux/x86_64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 21:36:29 UTC 2024	test result	(no tests yet)
Feb 13 10:43:27 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-generic-1707773740.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2024-02-12T21:29:40Z

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_473/5837

date	job status	comment
Feb 12 21:29:39 UTC 2024	submitted	job id `5837` awaits release by job manager
Feb 12 21:30:20 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 21:35:27 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5837.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-1707773711.tar.gz` size: 0 MiB (162538 bytes) entries: 4 modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/intel/haswell/software no software packages in tarball other under 2023.06/software/linux/x86_64/intel/haswell `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 21:35:27 UTC 2024	test result	(no tests yet)
Feb 13 10:43:47 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-haswell-1707773711.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2024-02-12T21:29:44Z

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_473/5838

date	job status	comment
Feb 12 21:29:43 UTC 2024	submitted	job id `5838` awaits release by job manager
Feb 12 21:30:22 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 21:36:30 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5838.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_avx512-1707773768.tar.gz` size: 0 MiB (162854 bytes) entries: 4 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software no software packages in tarball other under 2023.06/software/linux/x86_64/intel/skylake_avx512 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 21:36:30 UTC 2024	test result	(no tests yet)
Feb 13 10:44:06 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1707773768.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2024-02-12T21:29:48Z

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_473/5839

date	job status	comment
Feb 12 21:29:47 UTC 2024	submitted	job id `5839` awaits release by job manager
Feb 12 21:30:15 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 21:35:24 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5839.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-zen2-1707773684.tar.gz` size: 0 MiB (162383 bytes) entries: 4 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/amd/zen2/software no software packages in tarball other under 2023.06/software/linux/x86_64/amd/zen2 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 21:35:24 UTC 2024	test result	(no tests yet)
Feb 13 10:44:25 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen2-1707773684.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2024-02-12T21:29:51Z

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_473/5840

date	job status	comment
Feb 12 21:29:50 UTC 2024	submitted	job id `5840` awaits release by job manager
Feb 12 21:30:16 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 21:35:26 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5840.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-zen3-1707773683.tar.gz` size: 0 MiB (162378 bytes) entries: 4 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/amd/zen3/software no software packages in tarball other under 2023.06/software/linux/x86_64/amd/zen3 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 21:35:26 UTC 2024	test result	(no tests yet)
Feb 13 10:44:45 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen3-1707773683.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2024-02-12T21:29:55Z

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_473/5841

date	job status	comment
Feb 12 21:29:54 UTC 2024	submitted	job id `5841` awaits release by job manager
Feb 12 21:30:11 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 22:36:37 UTC 2024	running	job `5841` is running
Feb 12 22:37:38 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5841.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-1707777406.tar.gz` size: 0 MiB (162055 bytes) entries: 4 modules under 2023.06/software/linux/aarch64/generic/modules/all no module files in tarball software under 2023.06/software/linux/aarch64/generic/software no software packages in tarball other under 2023.06/software/linux/aarch64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 22:37:38 UTC 2024	test result	(no tests yet)
Feb 13 10:45:04 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-generic-1707777406.tar.gz` to S3 bucket succeeded

eessi-bot-aws · 2024-02-12T21:29:58Z

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_473/5842

date	job status	comment
Feb 12 21:29:58 UTC 2024	submitted	job id `5842` awaits release by job manager
Feb 12 21:30:13 UTC 2024	released	job awaits launch by Slurm scheduler
Feb 12 21:35:23 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5842.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_n1-1707773691.tar.gz` size: 0 MiB (162081 bytes) entries: 4 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all no module files in tarball software under 2023.06/software/linux/aarch64/neoverse_n1/software no software packages in tarball other under 2023.06/software/linux/aarch64/neoverse_n1 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp` `.lmod/lmodrc.lua`
Feb 12 21:35:23 UTC 2024	test result	(no tests yet)
Feb 13 10:45:24 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-neoverse_n1-1707773691.tar.gz` to S3 bucket succeeded

bedroge

Lgtm

bedroge · 2024-02-13T12:18:43Z

The staging PRs have been merged, tarballs have been injected, and this is now available on the Stratum servers.

Neves-P · 2024-02-14T10:56:00Z

Following up from #404 (comment) which still hangs, it appears the Lmod hook is not available to the bot. @bedroge found that the Lmod hook in LMOD_RC gets set in init/eessi_environment_variables, which the bot doesn't source (instead doing so for init/minimal_eessi_env). We would want the hook to apply in the build environment and also when the module is loaded. Should we also apply this to init/minimal_eessi_env, or do you think it's better to go with a different approach?

boegel · 2024-02-14T12:15:09Z

@Neves-P I don't mind moving the setting of $LMOD_RC to minimal_eessi_env, but since that requires $EESSI_SOFTWARE_PATH, I don't think that's going to be so easy.

Do note that eessi_environment_variables is being sourced in EESSI-install-software.sh, so that means that $LMOD_RC should be set correctly by the time that EasyBuild is being run, no?

boegel added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label Feb 12, 2024

add Lmod hook to set $OMPI_MCA_btl to '^smcuda' when loading OpenMPI …

0d03852

…module

boegel force-pushed the 2023.06-software.eessi.io_OpenMPI_disable_smcuda branch from c4dadde to 0d03852 Compare February 12, 2024 20:52

EESSI deleted a comment from eessi-bot-aws bot Feb 12, 2024

bedroge approved these changes Feb 13, 2024

View reviewed changes

bedroge added the bot:deploy Ask bot to deploy missing software installations to EESSI label Feb 13, 2024

boegel changed the title ~~add Lmod hook to set $OMPI_MCA_btl to '^smcuda' when loading OpenMPI module~~ add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug Feb 13, 2024

bedroge merged commit 3c00a95 into EESSI:2023.06-software.eessi.io Feb 13, 2024
33 checks passed

boegel deleted the 2023.06-software.eessi.io_OpenMPI_disable_smcuda branch February 13, 2024 12:54

boegel mentioned this pull request Feb 13, 2024

{2023.06}[foss/2023a] OpenFOAM v10 #404

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This was referenced Apr 2, 2024

add Lmod hook to set to ^smcuda when loading OpenMPI module to work around bug + renaming NorESSI/software-layer#293

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Syncing code-base and CVMFS repository with EESSI (April 2024) NorESSI/software-layer#294

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add Lmod hook to set `$OMPI_MCA_btl` to `^smcuda` when loading OpenMPI module to work around bug #473

add Lmod hook to set `$OMPI_MCA_btl` to `^smcuda` when loading OpenMPI module to work around bug #473

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boegel commented Feb 14, 2024

add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473

add Lmod hook to set $OMPI_MCA_btl to ^smcuda when loading OpenMPI module to work around bug #473

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bedroge commented Feb 13, 2024

Neves-P commented Feb 14, 2024

boegel commented Feb 14, 2024

add Lmod hook to set `$OMPI_MCA_btl` to `^smcuda` when loading OpenMPI module to work around bug #473

add Lmod hook to set `$OMPI_MCA_btl` to `^smcuda` when loading OpenMPI module to work around bug #473

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