{2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369

kErica · 2023-10-19T14:35:46Z

adding BWA 0.7.17 with GCCcore-11.3.0 to EESSI pilot 2023.06 2022a toolchain

eessi-bot · 2023-10-19T14:35:51Z

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/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/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/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/zen3 for repo eessi-hpc.org-2023.06-compat
arch x86_64/amd/zen3 for repo eessi-hpc.org-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/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_v1 for repo eessi-hpc.org-2023.06-compat
arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-software

kErica · 2023-10-19T14:39:14Z

bot: help

eessi-bot · 2023-10-19T14:39:17Z

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

account kErica has NO permission to send commands to the bot

boegel · 2023-10-19T15:45:19Z

@kErica Documentation on how to proceed is available at http://www.eessi.io/docs/software_layer/adding_software/, let us know if you need any help...

kErica · 2023-10-26T10:49:16Z

@kErica Documentation on how to proceed is available at http://www.eessi.io/docs/software_layer/adding_software/, let us know if you need any help...

Hi @boegel, I checked the docs and no references on how to make my account able to use the bot. Can you give me a hand? or a link ;) with instructions

eessi-bot · 2023-10-26T10:49:18Z

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

account kErica has NO permission to send commands to the bot

kErica · 2023-11-07T13:01:39Z

bot: help

eessi-bot · 2023-11-07T13:01:42Z

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

received bot command help from kErica
- expanded format: help
handling command help resulted in:
How to send commands to bot instances
- Commands must be sent with a new comment (edits of existing comments are ignored).
- A comment may contain multiple commands, one per line.
- Every command begins at the start of a line and has the syntax bot: COMMAND [ARGUMENTS]*
- Currently supported COMMANDs are: help, build, show_config
For more information, see https://www.eessi.io/docs/bot

kErica · 2023-11-07T13:04:24Z

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

eessi-bot · 2023-11-07T13:04:26Z

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

received bot command build arch:x86_64/generic repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build architecture:x86_64/generic repository:eessi-hpc.org-2023.06-software
handling command build architecture:x86_64/generic repository:eessi-hpc.org-2023.06-software resulted in:
- submitted job 436, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)

eessi-bot · 2023-11-07T13:04:30Z

New job on instance eessi-bot-mc-aws for architecture x86_64-generic for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/436

date	job status	comment
Nov 07 13:04:29 UTC 2023	submitted	job id `436` awaits release by job manager
Nov 07 13:04:39 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 07 14:28:31 UTC 2023	running	job `436` is running
Nov 07 14:32:35 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-436.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-1699367488.tar.gz` size: 0 MiB (653074 bytes) entries: 53 modules under 2023.06/software/linux/x86_64/generic/modules/all `BWA/0.7.17-GCCcore-11.3.0.lua` software under 2023.06/software/linux/x86_64/generic/software `BWA/0.7.17-GCCcore-11.3.0` other under 2023.06/software/linux/x86_64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`

kErica · 2023-11-07T16:17:22Z

bot: build arch:aarch64/generic repo:eessi-hpc.org-2023.06-software

eessi-bot · 2023-11-07T16:17:25Z

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

received bot command build arch:aarch64/generic repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build architecture:aarch64/generic repository:eessi-hpc.org-2023.06-software
handling command build architecture:aarch64/generic repository:eessi-hpc.org-2023.06-software resulted in:
- submitted job 515, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)

eessi-bot · 2023-11-07T16:17:31Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/515

date	job status	comment
Nov 07 16:17:30 UTC 2023	submitted	job id `515` awaits release by job manager
Nov 07 16:17:47 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 07 16:18:49 UTC 2023	running	job `515` is running
Nov 07 16:39:10 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-515.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.

kErica · 2023-11-08T10:05:00Z

bot: build repo:eessi-hpc.org-2023.06-software

eessi-bot · 2023-11-08T10:05:03Z

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

received bot command build repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build repository:eessi-hpc.org-2023.06-software

kErica · 2023-11-10T09:45:19Z

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

eessi-bot · 2023-11-10T09:45:22Z

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

received bot command build repo:eessi-2023.06-software arch:x86_64/intel/haswell from kErica
- expanded format: build repository:eessi-2023.06-software architecture:x86_64/intel/haswell
received bot command build repo:eessi-2023.06-software arch:x86_64/intel/skylake_avx512 from kErica
- expanded format: build repository:eessi-2023.06-software architecture:x86_64/intel/skylake_avx512
received bot command build repo:eessi-2023.06-software arch:x86_64/amd/zen2 from kErica
- expanded format: build repository:eessi-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi-2023.06-software arch:x86_64/amd/zen3 from kErica
- expanded format: build repository:eessi-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi-2023.06-software architecture:x86_64/intel/haswell resulted in:
- no jobs were submitted
handling command build repository:eessi-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- no jobs were submitted
handling command build repository:eessi-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- no jobs were submitted
handling command build repository:eessi-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted

kErica · 2023-11-10T10:25:09Z

bot: build arch:x86_64/amd/zen2 repo:eessi-hpc.org-2023.06-software

eessi-bot · 2023-11-10T10:25:11Z

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

received bot command build arch:x86_64/amd/zen2 repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build architecture:x86_64/amd/zen2 repository:eessi-hpc.org-2023.06-software

boegel · 2023-11-10T12:23:05Z

@trz42 Do you have a minute to check why the bot isn't doing what it should be here?

trz42 · 2023-11-10T19:50:03Z

@trz42 Do you have a minute to check why the bot isn't doing what it should be here?

Sorry, for late reply. It's the same issue as in #360 (comment)

boegel · 2023-11-11T12:19:25Z

@kErica The problems with the bot seem to be resolved, please try again

kErica · 2023-11-13T09:37:40Z

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

eessi-bot · 2023-11-13T09:37:44Z

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

received bot command build repo:eessi-2023.06-software arch:x86_64/intel/haswell from kErica
- expanded format: build repository:eessi-2023.06-software architecture:x86_64/intel/haswell
handling command build repository:eessi-2023.06-software architecture:x86_64/intel/haswell resulted in:
- no jobs were submitted

kErica · 2023-11-13T09:41:32Z

bot: build arch:aarch64/generic repo:eessi-hpc.org-2023.06-software

eessi-bot · 2023-11-13T09:41:36Z

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

received bot command build arch:aarch64/generic repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build architecture:aarch64/generic repository:eessi-hpc.org-2023.06-software
handling command build architecture:aarch64/generic repository:eessi-hpc.org-2023.06-software resulted in:
- submitted job 579, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)

eessi-bot · 2023-11-13T09:41:39Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/579

date	job status	comment
Nov 13 09:41:38 UTC 2023	submitted	job id `579` awaits release by job manager
Nov 13 09:42:18 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 13 09:47:21 UTC 2023	running	job `579` is running
Nov 13 10:08:00 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-579.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.

kErica · 2023-11-13T09:45:36Z

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

eessi-bot · 2023-11-13T09:45:39Z

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

received bot command build arch:x86_64/intel/haswell repo:eessi-2023.06-software from kErica
- expanded format: build architecture:x86_64/intel/haswell repository:eessi-2023.06-software
handling command build architecture:x86_64/intel/haswell repository:eessi-2023.06-software resulted in:
- no jobs were submitted

kErica · 2023-11-13T09:50:46Z

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

eessi-bot · 2023-11-13T09:50:49Z

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

received bot command build arch:x86_64/intel/haswell repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build architecture:x86_64/intel/haswell repository:eessi-hpc.org-2023.06-software
handling command build architecture:x86_64/intel/haswell repository:eessi-hpc.org-2023.06-software resulted in:
- submitted job 580, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)

eessi-bot · 2023-11-13T09:50:53Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-haswell for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/580

date	job status	comment
Nov 13 09:50:52 UTC 2023	submitted	job id `580` awaits release by job manager
Nov 13 09:51:26 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 13 09:57:36 UTC 2023	running	job `580` is running
Nov 13 10:15:10 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-580.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-1699870432.tar.gz` size: 0 MiB (675461 bytes) entries: 53 modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all `BWA/0.7.17-GCCcore-11.3.0.lua` software under 2023.06/software/linux/x86_64/intel/haswell/software `BWA/0.7.17-GCCcore-11.3.0` other under 2023.06/software/linux/x86_64/intel/haswell `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`

kErica · 2023-11-13T10:27:22Z

bot: build repo:eessi-hpc.org-2023.06-software arch:x86_64/intel/skylake_avx512
bot: build repo:eessi-hpc.org-2023.06-software arch:x86_64/amd/zen2
bot: build repo:eessi-hpc.org-2023.06-software arch:x86_64/amd/zen3

eessi-bot · 2023-11-13T10:27:25Z

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

received bot command build repo:eessi-hpc.org-2023.06-software arch:x86_64/intel/skylake_avx512 from kErica
- expanded format: build repository:eessi-hpc.org-2023.06-software architecture:x86_64/intel/skylake_avx512
received bot command build repo:eessi-hpc.org-2023.06-software arch:x86_64/amd/zen2 from kErica
- expanded format: build repository:eessi-hpc.org-2023.06-software architecture:x86_64/amd/zen2
received bot command build repo:eessi-hpc.org-2023.06-software arch:x86_64/amd/zen3 from kErica
- expanded format: build repository:eessi-hpc.org-2023.06-software architecture:x86_64/amd/zen3
handling command build repository:eessi-hpc.org-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 581, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)
handling command build repository:eessi-hpc.org-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 582, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)
handling command build repository:eessi-hpc.org-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 583, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)

eessi-bot · 2023-11-13T10:27:29Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-skylake_avx512 for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/581

date	job status	comment
Nov 13 10:27:28 UTC 2023	submitted	job id `581` awaits release by job manager
Nov 13 10:28:19 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 13 10:33:27 UTC 2023	running	job `581` is running
Nov 13 10:50:29 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-581.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_avx512-1699872591.tar.gz` size: 0 MiB (668948 bytes) entries: 53 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `BWA/0.7.17-GCCcore-11.3.0.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `BWA/0.7.17-GCCcore-11.3.0` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`

eessi-bot · 2023-11-13T10:27:32Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen2 for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/582

date	job status	comment
Nov 13 10:27:31 UTC 2023	submitted	job id `582` awaits release by job manager
Nov 13 10:28:14 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 13 10:33:21 UTC 2023	running	job `582` is running
Nov 13 10:50:28 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-582.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-zen2-1699872549.tar.gz` size: 0 MiB (670469 bytes) entries: 53 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `BWA/0.7.17-GCCcore-11.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `BWA/0.7.17-GCCcore-11.3.0` other under 2023.06/software/linux/x86_64/amd/zen2 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`

eessi-bot · 2023-11-13T10:27:36Z

New job on instance eessi-bot-mc-aws for architecture x86_64-amd-zen3 for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.11/pr_369/583

date	job status	comment
Nov 13 10:27:35 UTC 2023	submitted	job id `583` awaits release by job manager
Nov 13 10:28:17 UTC 2023	released	job awaits launch by Slurm scheduler
Nov 13 10:33:24 UTC 2023	running	job `583` is running
Nov 13 10:49:26 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-583.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-zen3-1699872544.tar.gz` size: 0 MiB (670629 bytes) entries: 53 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `BWA/0.7.17-GCCcore-11.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `BWA/0.7.17-GCCcore-11.3.0` other under 2023.06/software/linux/x86_64/amd/zen3 `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`

bedroge · 2023-11-21T13:47:04Z

I just inspected the build log for the failing aarch64 build, and it's failing due to:

ksw.c:29:10: fatal error: emmintrin.h: No such file or directory
   29 | #include <emmintrin.h>
      |          ^~~~~~~~~~~~~
compilation terminated.

That's happening on this line https://github.com/lh3/bwa/blob/v0.7.17/ksw.c#L29, and this basically isn't supported on Arm systems. This has been fixed on their master branch though (by this PR: lh3/bwa#359), but it looks like they're not really releasing new versions anymore... also see lh3/bwa#401.

@kErica do you need this for a particular use case? In that case, maybe it's best to open an issue in our support portal, and we can work on and keep track of a solution. We could take the fix from the PR, add it as a patch file to the easybuild-easyconfigs repo, and then try again.

kErica · 2023-11-22T09:48:50Z

Hi @bedroge,
I saw the same error - checking on the github repo from BWA the latest commit (from last year) should help with the compatibility to ARM.

I saw there is a PR (easybuilders/easybuild-easyconfigs#19273) to upgrade the toolchain and I asked the author to change the source to the latest commit and see if that will work.

I will open an issue in the support portal to track it - eessi/support - issue23

There is no specific use case, I want to start add genomic related apps to EESSI, which are missing at the moment, so that more users can use EESSI provided apps ;)

ocaisa · 2023-11-22T11:47:35Z

Patch that should solve ARM support is at lh3/bwa#359

boegel · 2023-11-23T05:31:08Z

To get actual patch file that you can try to apply to 0.7.17 release, use this URL https://github.com/lh3/bwa/pull/359.diff

The 0.7.17 releases is from 2017 though, so I wouldn't hold my breath for a new release.

Maybe we should switch to datestamp of latest commit for BWA (and tweak the PACKAGE_VERSION bit in main.c, see https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/main.c#L33)?

testing the latest commit in ARM on pilot - without the EESSI#390 patch

kErica · 2023-12-18T09:53:35Z

bot: build repo:eessi-hpc.org-2023.06-software arch:x86_64/intel/skylake_avx512
bot: build arch:aarch64/generic repo:eessi-hpc.org-2023.06-software

eessi-bot · 2023-12-18T09:53:38Z

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

received bot command build repo:eessi-hpc.org-2023.06-software arch:x86_64/intel/skylake_avx512 from kErica
- expanded format: build repository:eessi-hpc.org-2023.06-software architecture:x86_64/intel/skylake_avx512
received bot command build arch:aarch64/generic repo:eessi-hpc.org-2023.06-software from kErica
- expanded format: build architecture:aarch64/generic repository:eessi-hpc.org-2023.06-software
handling command build repository:eessi-hpc.org-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 2559, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)
handling command build architecture:aarch64/generic repository:eessi-hpc.org-2023.06-software resulted in:
- submitted job 2560, for details & status see {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369 (comment)

eessi-bot · 2023-12-18T09:53:42Z

New job on instance eessi-bot-mc-aws for architecture x86_64-intel-skylake_avx512 for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.12/pr_369/2559

date	job status	comment
Dec 18 09:53:41 UTC 2023	submitted	job id `2559` awaits release by job manager
Dec 18 09:54:21 UTC 2023	released	job awaits launch by Slurm scheduler
Dec 18 09:59:35 UTC 2023	running	job `2559` is running
Dec 18 10:01:44 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-2559.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_avx512-1702893636.tar.gz` size: 0 MiB (250070 bytes) entries: 3 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`
Dec 18 10:01:44 UTC 2023	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job2559.test` does not exist in job directory or reading it failed.

eessi-bot · 2023-12-18T09:53:46Z

New job on instance eessi-bot-mc-aws for architecture aarch64-generic for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.12/pr_369/2560

date	job status	comment
Dec 18 09:53:45 UTC 2023	submitted	job id `2560` awaits release by job manager
Dec 18 09:54:19 UTC 2023	released	job awaits launch by Slurm scheduler
Dec 18 09:58:29 UTC 2023	running	job `2560` is running
Dec 18 10:01:42 UTC 2023	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-2560.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-1702893665.tar.gz` size: 0 MiB (248911 bytes) entries: 3 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`
Dec 18 10:01:42 UTC 2023	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job2560.test` does not exist in job directory or reading it failed.

kErica · 2023-12-18T10:11:54Z

closing PR: new PR #429

latest commit from BWA
newer toolchain
patch for ARM

…023a-CUDA-12.1.1 {2023.06}[foss/2023a] PyTorch v2.1.2 with CUDA/12.1.1

adding BWA 0.7.17 with GCC/11.3.0 to EESSI pilot 2023.06

9f3a15f

kErica changed the title ~~BWA-0.7.17-GCCcore-11.3.0~~ {2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 Oct 26, 2023

boegel added the pilot-2023.06 label Nov 7, 2023

boegel changed the base branch from 2023.06 to pilot.eessi-hpc.org-2023.06 November 21, 2023 21:20

Update eessi-2023.06-eb-4.8.1-2022a.yml

cdff55d

testing the latest commit in ARM on pilot - without the EESSI#390 patch

kErica closed this Dec 18, 2023

trz42 pushed a commit to trz42/software-layer that referenced this pull request May 30, 2024

Merge pull request EESSI#369 from trz42/nessi-2023.06-PyTorch-2.1.2-2…

edf8e0a

…023a-CUDA-12.1.1 {2023.06}[foss/2023a] PyTorch v2.1.2 with CUDA/12.1.1

{2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369

{2023.06}[GCCcore/11.3.0] BWA-0.7.17-GCCcore-11.3.0 #369

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