{2023.06}[foss/2023a] GROMACS v2023.4 #463

bedroge · 2024-01-26T12:25:50Z

No description provided.

eessi-bot · 2024-01-26T12:25:54Z

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

bedroge · 2024-01-26T12:26:09Z

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

eessi-bot · 2024-01-26T12:26:12Z

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 bedroge
- 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 4815, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)

eessi-bot · 2024-01-26T12:26:16Z

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/2024.01/pr_463/4815

date	job status	comment
Jan 26 12:26:15 UTC 2024	submitted	job id `4815` awaits release by job manager
Jan 26 12:27:07 UTC 2024	released	job awaits launch by Slurm scheduler
Jan 26 12:32:09 UTC 2024	running	job `4815` is running
Jan 26 13:07:40 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-4815.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 No artefacts were created or found.
Jan 26 13:07:40 UTC 2024	test result	(no tests yet)

bedroge · 2024-01-26T13:17:47Z

While I was debugging #401 interactively, I also tried installing 2023.4, and then that version did work fine. But now the build with the bot does show the same test failure again 😞

-------------------------------------------------------
Program:     gmxapi-mpi-test, version 2023.4-EasyBuild_4.9.0
Source file: src/gromacs/utility/futil.cpp (line 454)
MPI rank:    1 (out of 2)

File input/output error:
/tmp/bot/easybuild/build/GROMACS/2023.4/foss-2023a/easybuild_obj/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.trr

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------

-------------------------------------------------------
Program:     gmxapi-mpi-test, version 2023.4-EasyBuild_4.9.0
Source file: src/gromacs/utility/futil.cpp (line 454)
MPI rank:    0 (out of 2)

File input/output error:
/tmp/bot/easybuild/build/GROMACS/2023.4/foss-2023a/easybuild_obj/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.trr

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------

boegel · 2024-01-26T15:03:32Z

@bedroge Some time to blame fuse-overlayfs? Or doesn't that come into play here yet (since this is pre-install test suite)?

bedroge · 2024-01-26T15:46:45Z

@bedroge Some time to blame fuse-overlayfs? Or doesn't that come into play here yet (since this is pre-install test suite)?

It's using /tmp inside the container, which shouldn't use fuse-overlayfs. I'm not entirely sure which host directory is bind mounted as /tmp, but if that's a shared filesystem (not entirely sure, but don't think that's the case?), it could explain things.

boegel · 2024-01-26T15:50:22Z

@bedroge Some time to blame fuse-overlayfs? Or doesn't that come into play here yet (since this is pre-install test suite)?

It's using /tmp inside the container, which shouldn't use fuse-overlayfs. I'm not entirely sure which host directory is bind mounted as /tmp, but if that's a shared filesystem (not entirely sure, but don't think that's the case?), it could explain things.

A unique subdirectory of /tmp is bind-mounted as /tmp in the build container I think, definitely not a shared filesystem (we would've seen problems already in that case).

bedroge · 2024-01-26T15:52:01Z

I've tried building this version a few more times now, and it's failing all the time on that same test. For some reason, it worked the very first time, though 😕

TopRichard · 2024-02-07T12:31:05Z

@bedroge @boegel Gromacs v2023.4 works for NESSI: NorESSI#273 but with deb10 container on certain architectures.

bedroge · 2024-02-09T12:35:45Z

@bedroge @boegel Gromacs v2023.4 works for NESSI: NorESSI#273 but with deb10 container on certain architectures.

Oh, that's really interesting... Now we did have weird behaviour for both 2023.3 and 2023.4, where it occasionally does work, but for e.g. haswell it's failing (almost) all the time, I think. Doesn't look like NESSI builds for haswell (?), so maybe I can try doing that interactively with our old debian10 container.

bedroge · 2024-02-09T15:48:14Z

@bedroge @boegel Gromacs v2023.4 works for NESSI: NorESSI#273 but with deb10 container on certain architectures.

Oh, that's really interesting... Now we did have weird behaviour for both 2023.3 and 2023.4, where it occasionally does work, but for e.g. haswell it's failing (almost) all the time, I think. Doesn't look like NESSI builds for haswell (?), so maybe I can try doing that interactively with our old debian10 container.

@TopRichard I tried it on a haswell node with our old Debian 10 build container (https://github.com/EESSI/filesystem-layer/pkgs/container/build-node/40951724?tag=debian10), but it has been stuck in the test step for several hours now, so I think it hangs (and we saw the same thing before). Is there any other significant difference in your Debian 10 container compared to the Debian 11 container?

TopRichard · 2024-02-09T17:08:05Z

@bedroge we are using the same containers of EESSI , and our stack doesn’t have haswell, so that i try building GROMACS for haswell within NESSI stack, i will figure out a way to further help in this.

bedroge · 2024-03-27T07:04:21Z

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

eessi-bot · 2024-03-27T07:04:24Z

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 bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3

eessi-bot · 2024-03-27T07:04:27Z

error: patch failed: easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml:11 error: easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml: patch does not apply Unable to download or merge changes between the source branch and the destination branch.Tip: This can usually be resolved by syncing your branch and resolving any merge conflicts.

Alternative formattings (edited manually):

error: patch failed: easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml:11
error: easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml: patch does not apply

Unable to download or merge changes between the source branch and the destination branch.
Tip: This can usually be resolved by syncing your branch and resolving any merge conflicts.

or

Unable to download or merge changes between the source branch and the destination branch.

error: patch failed: easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml:11
error: easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml: patch does not apply

Tip: This can usually be resolved by syncing your branch and resolving any merge conflicts.

bedroge · 2024-03-27T07:35:44Z

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

eessi-bot · 2024-03-27T07:35:47Z

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 bedroge
- 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 8659, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)

eessi-bot · 2024-03-27T07:35:51Z

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/2024.03/pr_463/8659

date	job status	comment
Mar 27 07:35:50 UTC 2024	submitted	job id `8659` awaits release by job manager
Mar 27 07:36:00 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 27 07:40:01 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-8659.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts No artefacts were created or found.
Mar 27 07:40:01 UTC 2024	test result	😁 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-8659.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

…-layer into gromacs_2023.4

bedroge · 2024-03-27T15:46:09Z

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

eessi-bot · 2024-03-27T15:46:12Z

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 bedroge
- 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 8677, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)

eessi-bot · 2024-03-27T15:46:16Z

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/2024.03/pr_463/8677

date	job status	comment
Mar 27 15:46:15 UTC 2024	submitted	job id `8677` awaits release by job manager
Mar 27 15:46:57 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 27 15:51:59 UTC 2024	running	job `8677` is running
Mar 27 16:43:57 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8677.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no 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-zen3-1711557102.tar.gz` size: 41 MiB (43225941 bytes) entries: 765 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `GROMACS/2023.4-foss-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `GROMACS/2023.4-foss-2023a` other under 2023.06/software/linux/x86_64/amd/zen3 no other files in tarball
Mar 27 16:43:57 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8677.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-03-28T09:11:15Z

This actually completed:

== COMPLETED: Installation ended successfully (took 36 mins 48 secs)
== Results of the build can be found in the log file(s) /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen3/software/GROMACS/2023.4-foss-2023a/easybuild/easybuild-GROMACS-2023.4-20240327.162926.log.bz2
== Build succeeded for 1 out of 1

But then failed in the missing software check (I guess because the easyconfig hasn't been merged yet?):

ERROR: One or more files not found: GROMACS-2023.4-foss-2023a.eb (search paths: /tmp/tmp.LSEuf7NgOB/easyconfigs/easybuild/easyconfigs)

So, let's try building for the other architectures as well.

bedroge · 2024-03-28T09:11:32Z

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

eessi-bot · 2024-03-28T09:11:36Z

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

received bot command build repo:eessi.io-2023.06-software arch:aarch64/generic from bedroge
- 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 bedroge
- 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 bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
received bot command build repo:eessi.io-2023.06-software arch:x86_64/generic from bedroge
- 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/amd/zen2 from bedroge
- 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/intel/haswell from bedroge
- 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 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:aarch64/generic resulted in:
- submitted job 8719, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 8720, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 8721, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 8722, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 8723, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 8724, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 8725, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)

eessi-bot · 2024-03-28T09:11:49Z

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/2024.03/pr_463/8719

date	job status	comment
Mar 28 09:11:48 UTC 2024	submitted	job id `8719` awaits release by job manager
Mar 28 09:12:31 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:16:11 UTC 2024	running	job `8719` is running
Mar 28 10:13:47 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8719.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-generic-1711620187.tar.gz` size: 32 MiB (33811112 bytes) entries: 765 modules under 2023.06/software/linux/aarch64/generic/modules/all `GROMACS/2023.4-foss-2023a.lua` software under 2023.06/software/linux/aarch64/generic/software `GROMACS/2023.4-foss-2023a` other under 2023.06/software/linux/aarch64/generic no other files in tarball
Mar 28 10:13:47 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8719.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-03-28T09:11:56Z

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/2024.03/pr_463/8720

date	job status	comment
Mar 28 09:11:55 UTC 2024	submitted	job id `8720` awaits release by job manager
Mar 28 09:12:33 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:17:21 UTC 2024	running	job `8720` is running
Mar 28 10:16:14 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8720.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no 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_n1-1711620306.tar.gz` size: 36 MiB (38656276 bytes) entries: 765 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `GROMACS/2023.4-foss-2023a.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `GROMACS/2023.4-foss-2023a` other under 2023.06/software/linux/aarch64/neoverse_n1 no other files in tarball
Mar 28 10:16:14 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8720.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-03-28T09:12:06Z

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/2024.03/pr_463/8721

date	job status	comment
Mar 28 09:12:05 UTC 2024	submitted	job id `8721` awaits release by job manager
Mar 28 09:12:35 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:17:23 UTC 2024	running	job `8721` is running
Mar 28 10:10:05 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8721.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 No artefacts were created or found.
Mar 28 10:10:05 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8721.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-03-28T09:12:14Z

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/2024.03/pr_463/8722

date	job status	comment
Mar 28 09:12:13 UTC 2024	submitted	job id `8722` awaits release by job manager
Mar 28 09:12:39 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:18:39 UTC 2024	running	job `8722` is running
Mar 28 10:23:22 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8722.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no 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-generic-1711620355.tar.gz` size: 38 MiB (40576204 bytes) entries: 765 modules under 2023.06/software/linux/x86_64/generic/modules/all `GROMACS/2023.4-foss-2023a.lua` software under 2023.06/software/linux/x86_64/generic/software `GROMACS/2023.4-foss-2023a` other under 2023.06/software/linux/x86_64/generic no other files in tarball
Mar 28 10:23:22 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8722.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-03-28T09:12:23Z

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/2024.03/pr_463/8723

date	job status	comment
Mar 28 09:12:22 UTC 2024	submitted	job id `8723` awaits release by job manager
Mar 28 09:12:37 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:17:25 UTC 2024	running	job `8723` is running
Mar 28 10:24:32 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8723.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 No artefacts were created or found.
Mar 28 10:24:32 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8723.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-03-28T09:12:32Z

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/2024.03/pr_463/8724

date	job status	comment
Mar 28 09:12:31 UTC 2024	submitted	job id `8724` awaits release by job manager
Mar 28 09:13:51 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:19:53 UTC 2024	running	job `8724` is running
Mar 28 11:51:30 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8724.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 No artefacts were created or found.
Mar 28 11:51:30 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8724.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-03-28T09:12:40Z

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/2024.03/pr_463/8725

date	job status	comment
Mar 28 09:12:39 UTC 2024	submitted	job id `8725` awaits release by job manager
Mar 28 09:13:54 UTC 2024	released	job awaits launch by Slurm scheduler
Mar 28 09:19:56 UTC 2024	running	job `8725` is running
Mar 28 10:17:26 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-8725.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no 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_avx512-1711620130.tar.gz` size: 40 MiB (42389834 bytes) entries: 765 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `GROMACS/2023.4-foss-2023a.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `GROMACS/2023.4-foss-2023a` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 no other files in tarball
Mar 28 10:17:26 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-8725.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-03-28T11:50:20Z

Quick summary of the status of the builds:

# Job 8721 on neoverse v1:
The following tests FAILED:
         15 - GmxlibTests (Subprocess aborted)
         45 - SimdUnitTests (Failed)
         80 - MdrunFEPTests (Failed)

# Job 8723 on zen2:
The following tests FAILED:
          2 - GmxapiMpiTests (Failed)

# Job 8724 on haswell:
Stuck, killed it manually

All the other ones actually completed successfully, but failed in the check for missing installations.

Regarding the haswell build, I saw the following processes running on the node:

bot        31437   31427  0 09:26 ?        00:00:00 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        31438   31436  0 09:26 ?        00:00:00 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'm guessing this may be a similar issue as what we are seeing in #508 and #456.

marconetto · 2024-03-29T21:23:57Z

Hi folks, I would like to use gromacs from the eessi prod repo. I understand this is the PR to generate gromacs in prod repo right?

bedroge · 2024-03-30T15:11:26Z

Hi folks, I would like to use gromacs from the eessi prod repo. I understand this is the PR to generate gromacs in prod repo right?

Hi @marconetto, yes, that's correct. Unfortunately, we're seeing weird test failures on a few CPU types, and these are quite hard to figure out. We'd really like to make GROMACS available, but we also really want to be sure that the builds are fine before we actually add them to the repository. So we'll keep working on them (we also have open PRs for version 2023.3 in #401 and 2024.1 in #499, but all with similar issues), and hopefully we will be able to resolve the issues soon.

marconetto · 2024-04-01T01:23:55Z

thanks @bedroge for the clarification!

bedroge · 2024-04-04T11:22:40Z

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

eessi-bot · 2024-04-04T11:22:43Z

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 bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 9013, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)

eessi-bot · 2024-04-04T11:22:47Z

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/2024.04/pr_463/9013

date	job status	comment
Apr 04 11:22:46 UTC 2024	submitted	job id `9013` awaits release by job manager
Apr 04 11:23:47 UTC 2024	released	job awaits launch by Slurm scheduler
Apr 04 11:27:49 UTC 2024	running	job `9013` is running
Apr 04 11:35:01 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-9013.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts No artefacts were created or found.
Apr 04 11:35:01 UTC 2024	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job9013.test` does not exist in job directory or reading it failed.

bedroge · 2024-04-04T11:34:41Z

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

eessi-bot · 2024-04-04T11:34:44Z

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/intel/haswell from bedroge
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 9014, for details & status see {2023.06}[foss/2023a] GROMACS v2023.4 #463 (comment)

eessi-bot · 2024-04-04T11:34:48Z

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/2024.04/pr_463/9014

date	job status	comment
Apr 04 11:34:47 UTC 2024	submitted	job id `9014` awaits release by job manager
Apr 04 11:35:00 UTC 2024	released	job awaits launch by Slurm scheduler
Apr 04 11:36:04 UTC 2024	running	job `9014` is running
Apr 04 12:17:47 UTC 2024	finished	😢 FAILURE (click triangle for details) Reason EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild? Details ✅ job output file `slurm-9014.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 No artefacts were created or found.
Apr 04 12:17:47 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-9014.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-04-04T12:45:02Z

The haswell build is not getting stuck anymore (because of the Lmod hook that we added to the bot environment), but it does still fail due to one failing test:

          2 - GmxapiMpiTests (Failed)

This is the actual error message for the failing test:

Test failures from rank 0:
/tmp/bot/easybuild/build/GROMACS/2023.4/foss-2023a/gromacs-2023.4/api/gmxapi/cpp/tests/stopsignaler.cpp:206: Failure
Expected equality of these values:
  nsteps
    Which is: 4
  gmx::roundToInt(restraint->timeElapsedSinceStart() / getTestStepSize())
    Which is: 0
Test failures from rank 1:
/tmp/bot/easybuild/build/GROMACS/2023.4/foss-2023a/gromacs-2023.4/api/gmxapi/cpp/tests/stopsignaler.cpp:206: Failure
Expected equality of these values:
  nsteps
    Which is: 4
  gmx::roundToInt(restraint->timeElapsedSinceStart() / getTestStepSize())
    Which is: 0
[  FAILED  ] GmxApiTest.ApiRunnerStopSignalClient (203 ms)

boegel · 2024-05-01T06:57:14Z

superseded by #499

bedroge · 2024-05-01T09:31:29Z

Hi folks, I would like to use gromacs from the eessi prod repo. I understand this is the PR to generate gromacs in prod repo right?

HI @marconetto, GROMACS 2024.1 is now available in the production repo. Does that version suit your needs, or did you have a specific need for version 2023.4?

marconetto · 2024-05-01T13:20:36Z

Hi @bedroge , this is great news! Thanks for you and your team by putting this together. This version is fine, thanks a lot! I will test it next week and let you know if something is not working as expected.

add GROMACS 2023.4

60b87b8

Merge branch '2023.06-software.eessi.io' into gromacs_2023.4

262a8e0

Merge branch '2023.06-software.eessi.io' of github.com:EESSI/software…

5a6d301

…-layer into gromacs_2023.4

boegel added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label Apr 2, 2024

bedroge mentioned this pull request Apr 30, 2024

{2023.06}[foss/2023b] GROMACS 2024.1 #499

Merged

boegel closed this May 1, 2024

bedroge deleted the gromacs_2023.4 branch May 1, 2024 07:04

{2023.06}[foss/2023a] GROMACS v2023.4 #463

{2023.06}[foss/2023a] GROMACS v2023.4 #463

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