{2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658

TopRichard · 2024-08-05T07:02:23Z

BioPerl build process tries to copy perlmodule.py once again after sanity check which results in :

Failed to copy file /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.2/lib/python3.11/site-packages/easybuild/easyblocks/generic/perlmodule.py to .../reprod_20240802080341_2187/e
asyblocks/perlmodule.py: [Errno 13] Permission') (at easybuild/main.py:178 in build_and_install_software)

BioPerl hook adds user write permission after sanity check to allow copying the easyblock file.

Missing packages:

BioPerl/1.7.8-GCCcore-12.2.0
BioPerl/1.7.8-GCCcore-12.3.0
DB/18.1.40-GCCcore-12.3.0
DB_File/1.859-GCCcore-12.3.0
groff/1.22.4-GCCcore-12.3.0
Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0
XML-LibXML/2.0208-GCCcore-12.2.0
XML-LibXML/2.0209-GCCcore-12.3.0

eessi-bot · 2024-08-05T07:02:27Z

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

architectures: x86_64/generic, x86_64/intel/haswell, x86_64/intel/skylake_avx512, x86_64/amd/zen2, x86_64/amd/zen3, aarch64/generic, aarch64/neoverse_n1, aarch64/neoverse_v1
repositories: eessi.io-2023.06-compat, eessi-hpc.org-2023.06-software, eessi-hpc.org-2023.06-compat, eessi.io-2023.06-software

eessi-bot · 2024-08-05T07:02:28Z

Instance eessi-bot-mc-azure is configured to build for:

architectures: x86_64/amd/zen4
repositories: eessi.io-2023.06-compat, eessi-hpc.org-2023.06-compat, eessi-hpc.org-2023.06-software, eessi.io-2023.06-software

TopRichard · 2024-08-05T07:03:00Z

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

eessi-bot · 2024-08-05T07:03:02Z

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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 15694, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 15695, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 15696, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 15697, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 15698, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 15699, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 15700, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 15701, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)

eessi-bot · 2024-08-05T07:03:03Z

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

account TopRichard has NO permission to send commands to the bot

eessi-bot · 2024-08-05T07:03:07Z

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/2024.08/pr_658/15694

date	job status	comment
Aug 05 07:03:06 UTC 2024	submitted	job id `15694` awaits release by job manager
Aug 05 07:04:04 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:11:26 UTC 2024	running	job `15694` is running
Aug 05 08:09:33 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15694.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-1722844373.tar.gz` size: 98 MiB (102826648 bytes) entries: 20705 modules under 2023.06/software/linux/x86_64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/generic `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:09:33 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15694.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:11Z

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/2024.08/pr_658/15695

date	job status	comment
Aug 05 07:03:10 UTC 2024	submitted	job id `15695` awaits release by job manager
Aug 05 07:04:06 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:11:28 UTC 2024	running	job `15695` is running
Aug 05 08:10:38 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15695.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-1722844427.tar.gz` size: 98 MiB (102884253 bytes) entries: 20705 modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/intel/haswell/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/intel/haswell `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:10:38 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15695.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:16Z

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/2024.08/pr_658/15696

date	job status	comment
Aug 05 07:03:14 UTC 2024	submitted	job id `15696` awaits release by job manager
Aug 05 07:04:08 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:11:29 UTC 2024	running	job `15696` is running
Aug 05 08:07:22 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15696.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_avx512-1722844287.tar.gz` size: 98 MiB (102855988 bytes) entries: 20705 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:07:22 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15696.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:20Z

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/2024.08/pr_658/15697

date	job status	comment
Aug 05 07:03:19 UTC 2024	submitted	job id `15697` awaits release by job manager
Aug 05 07:04:00 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:10:18 UTC 2024	running	job `15697` is running
Aug 05 08:13:46 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15697.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-zen2-1722844628.tar.gz` size: 98 MiB (102900065 bytes) entries: 20705 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen2 `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:13:46 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15697.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:24Z

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/2024.08/pr_658/15698

date	job status	comment
Aug 05 07:03:23 UTC 2024	submitted	job id `15698` awaits release by job manager
Aug 05 07:04:02 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:10:20 UTC 2024	running	job `15698` is running
Aug 05 08:02:56 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15698.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-zen3-1722844092.tar.gz` size: 98 MiB (102860821 bytes) entries: 20705 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen3 `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:02:56 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15698.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:29Z

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/2024.08/pr_658/15699

date	job status	comment
Aug 05 07:03:28 UTC 2024	submitted	job id `15699` awaits release by job manager
Aug 05 07:03:54 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:09:10 UTC 2024	running	job `15699` is running
Aug 05 08:29:14 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15699.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-1722844332.tar.gz` size: 97 MiB (102754007 bytes) entries: 20705 modules under 2023.06/software/linux/aarch64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/generic `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:29:14 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15699.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:33Z

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/2024.08/pr_658/15700

date	job status	comment
Aug 05 07:03:32 UTC 2024	submitted	job id `15700` awaits release by job manager
Aug 05 07:03:56 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:09:12 UTC 2024	running	job `15700` is running
Aug 05 08:27:12 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15700.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_n1-1722844275.tar.gz` size: 98 MiB (102788714 bytes) entries: 20705 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_n1 `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:27:12 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15700.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-05T07:03:37Z

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/2024.08/pr_658/15701

date	job status	comment
Aug 05 07:03:36 UTC 2024	submitted	job id `15701` awaits release by job manager
Aug 05 07:03:58 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 07:09:14 UTC 2024	running	job `15701` is running
Aug 05 08:08:28 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15701.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_v1-1722843773.tar.gz` size: 98 MiB (102763644 bytes) entries: 20705 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_v1 `2023.06/init/easybuild/eb_hooks.py`
Aug 05 08:08:28 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 16/16 test case(s) from 16 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15701.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

ocaisa · 2024-08-05T12:31:31Z

eb_hooks.py

@@ -647,6 +647,16 @@ def post_sanitycheck_hook(self, *args, **kwargs):
 POST_SANITYCHECK_HOOKS[self.name](self, *args, **kwargs)


+def post_sanitycheck_bioperl(self, *args, **kwargs):


Why is this needed, this seems like a generic issue

If this is really an issue with the permissions of the easyblock then it needs generic fixing in EasyBuild (in framework, so it doesn't happen again)

I will remove the hook and initiate a build process

TopRichard · 2024-08-05T12:43:28Z

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

eessi-bot · 2024-08-05T12:43:31Z

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 TopRichard
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 15702, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)

eessi-bot · 2024-08-05T12:43:31Z

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

account TopRichard has NO permission to send commands to the bot

eessi-bot · 2024-08-05T12:43:35Z

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/2024.08/pr_658/15702

date	job status	comment
Aug 05 12:43:34 UTC 2024	submitted	job id `15702` awaits release by job manager
Aug 05 12:43:37 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 05 12:48:39 UTC 2024	running	job `15702` is running
Aug 05 13:50:43 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15702.out` ❌ found message matching `ERROR:` ❌ found 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-1722864713.tar.gz` size: 97 MiB (102499925 bytes) entries: 20684 modules under 2023.06/software/linux/x86_64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/generic no other files in tarball
Aug 05 13:50:43 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15702.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

TopRichard · 2024-08-06T10:07:04Z

After removing the hook, the build fails :

== permissions...
== ... (took < 1 sec)
== packaging...
== ... (took < 1 sec)
== FAILED: Installation ended unsuccessfully (build directory: /tmp/bot/easybuild/build/BioPerl/1.7.8/GCCcore-12.2.0): build failed (first 300 chars): Failed to copy file /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/EasyBuild/4.9.2/lib/python3.11/site-packages/easybuild/easyblocks/generic/perlmodule.py to /tmp/eb-fftevtnk/eb-ak3d7syr/reprod_20240805124945_346/easyblocks/perlmodule.py: [Errno 13] Permission denie (took 1 min 36 secs)
== Results of the build can be found in the log file(s) /tmp/eb-fftevtnk/eb-ak3d7syr/easybuild-BioPerl-1.7.8-20240805.124945.bGmIN.log
0:02:13  1 out of 2 easyconfigs done: XML-LibXML/2.0208-GCCcore-12.2.0 (OK)ERROR: Build of /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/EasyBuild/4.9.2/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb failed (err: 'build failed (first 300 chars): Failed to copy file /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/EasyBuild/4.9.2/lib/python3.11/site-packages/easybuild/easyblocks/generic/perlmodule.py to /tmp/eb-fftevtnk/eb-ak3d7syr/reprod_20240805124945_346/easyblocks/perlmodule.py: [Errno 13] Permission denie')
Last EasyBuild log file copied from /tmp/eb-fftevtnk/easybuild-48ln20pb.log to /project/60006/SHARED/jobs/2024.08/pr_658/event_50dd1c80-5328-11ef-93bd-58a74643a660/run_000/linux_x86_64_generic/eessi.io-2023.06-software
EasyBuild log file /tmp/eb-fftevtnk/easybuild-48ln20pb.log copied to /project/def-users/SHARED/build-logs/jobs/15702/easybuild-48ln20pb.log (with context appended)
Using /project/60006/SHARED/jobs/2024.08/pr_658/event_50dd1c80-5328-11ef-93bd-58a74643a660/run_000/linux_x86_64_generic/eessi.io-2023.06-software/658.diff to give create exceptions for PR filtering of easystack

ocaisa · 2024-08-06T10:12:20Z

So this seems like the file exists already for whatever reason, and an overwriting copy fails. This sounds like an EasyBuild framework problem, it should

check if the file exists
- if it does, check if the contents are the same. If they are don't bother trying to copy, if they are not error out
- if it does not, make the copy
  It sounds like a side-effect of our read-only install setting.

ocaisa · 2024-08-06T10:17:59Z

I think you can probably cheat your way around it by using --include-easyblocks-from-commit=89ea2e4737d792055de828e18f38bccee26b76cf (latest commit to easyblock repo), that will prefer the easyblocks from that repo which won't have these restrictive permissions.

An issue should still be opened in the EasyBuild framework

TopRichard · 2024-08-06T11:32:45Z

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

eessi-bot · 2024-08-06T11:32:48Z

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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- 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 TopRichard
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 15755, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 15756, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 15757, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 15758, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 15759, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 15760, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 15761, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 15762, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)

eessi-bot · 2024-08-06T11:32:49Z

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

account TopRichard has NO permission to send commands to the bot

eessi-bot · 2024-08-06T11:32:53Z

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/2024.08/pr_658/15755

date	job status	comment
Aug 06 11:32:52 UTC 2024	submitted	job id `15755` awaits release by job manager
Aug 06 11:33:53 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:42:23 UTC 2024	running	job `15755` is running
Aug 06 12:43:38 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15755.out` ❌ found message matching `ERROR:` ❌ found 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-1722947120.tar.gz` size: 97 MiB (102514145 bytes) entries: 20684 modules under 2023.06/software/linux/x86_64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/generic no other files in tarball
Aug 06 12:43:38 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15755.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:32:57Z

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/2024.08/pr_658/15756

date	job status	comment
Aug 06 11:32:56 UTC 2024	submitted	job id `15756` awaits release by job manager
Aug 06 11:33:55 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:42:25 UTC 2024	running	job `15756` is running
Aug 06 12:43:39 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15756.out` ❌ found message matching `ERROR:` ❌ found 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-1722947047.tar.gz` size: 97 MiB (102548930 bytes) entries: 20684 modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/intel/haswell/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/intel/haswell no other files in tarball
Aug 06 12:43:39 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15756.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:33:01Z

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/2024.08/pr_658/15757

date	job status	comment
Aug 06 11:33:00 UTC 2024	submitted	job id `15757` awaits release by job manager
Aug 06 11:33:57 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:42:27 UTC 2024	running	job `15757` is running
Aug 06 12:42:33 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15757.out` ❌ found message matching `ERROR:` ❌ found 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_avx512-1722947068.tar.gz` size: 97 MiB (102563605 bytes) entries: 20684 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 no other files in tarball
Aug 06 12:42:33 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15757.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:33:05Z

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/2024.08/pr_658/15758

date	job status	comment
Aug 06 11:33:04 UTC 2024	submitted	job id `15758` awaits release by job manager
Aug 06 11:33:49 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:41:11 UTC 2024	running	job `15758` is running
Aug 06 12:44:43 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15758.out` ❌ found message matching `ERROR:` ❌ found 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-zen2-1722947236.tar.gz` size: 97 MiB (102585772 bytes) entries: 20684 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen2 no other files in tarball
Aug 06 12:44:43 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15758.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:33:09Z

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/2024.08/pr_658/15759

date	job status	comment
Aug 06 11:33:08 UTC 2024	submitted	job id `15759` awaits release by job manager
Aug 06 11:33:51 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:41:12 UTC 2024	running	job `15759` is running
Aug 06 12:34:41 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15759.out` ❌ found message matching `ERROR:` ❌ found 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-zen3-1722946739.tar.gz` size: 97 MiB (102540617 bytes) entries: 20684 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen3 no other files in tarball
Aug 06 12:34:41 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15759.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:33:13Z

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/2024.08/pr_658/15760

date	job status	comment
Aug 06 11:33:12 UTC 2024	submitted	job id `15760` awaits release by job manager
Aug 06 11:33:43 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:38:59 UTC 2024	running	job `15760` is running
Aug 06 13:00:16 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15760.out` ❌ found message matching `ERROR:` ❌ found 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-1722946921.tar.gz` size: 97 MiB (102410641 bytes) entries: 20684 modules under 2023.06/software/linux/aarch64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/generic no other files in tarball
Aug 06 13:00:16 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15760.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:33:17Z

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/2024.08/pr_658/15761

date	job status	comment
Aug 06 11:33:16 UTC 2024	submitted	job id `15761` awaits release by job manager
Aug 06 11:33:45 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:40:04 UTC 2024	running	job `15761` is running
Aug 06 13:01:17 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15761.out` ❌ found message matching `ERROR:` ❌ found 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_n1-1722946968.tar.gz` size: 97 MiB (102426966 bytes) entries: 20684 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_n1 no other files in tarball
Aug 06 13:01:17 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15761.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-08-06T11:33:21Z

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/2024.08/pr_658/15762

date	job status	comment
Aug 06 11:33:20 UTC 2024	submitted	job id `15762` awaits release by job manager
Aug 06 11:33:47 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 11:39:01 UTC 2024	running	job `15762` is running
Aug 06 12:40:19 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-15762.out` ❌ found message matching `ERROR:` ❌ found 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_v1-1722946394.tar.gz` size: 97 MiB (102381643 bytes) entries: 20684 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_v1 no other files in tarball
Aug 06 12:40:19 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15762.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

boegel · 2024-08-06T11:56:21Z

I think you can probably cheat your way around it by using --include-easyblocks-from-commit=89ea2e4737d792055de828e18f38bccee26b76cf (latest commit to easyblock repo), that will prefer the easyblocks from that repo which won't have these restrictive permissions.

An issue should still be opened in the EasyBuild framework

I'm not a big fan of using a workaround like this...

I'm also puzzled: why does this only occur with BioPerl, which is a pretty standard easyconfig using the PerlModule easyblock? Is it because the top-level easyblock being used is PerlModule, and then the extensions are also installed with that same easyblock (which is kind of weird)?

ocaisa · 2024-08-06T11:59:36Z

I've left a comment in easybuilders/easybuild-framework#4602 (comment) about (at least one place) where I think this could be resolved in framework, but that won't help us here as that would need a new release for us to leverage.

TopRichard · 2024-08-06T12:35:41Z

I think you can probably cheat your way around it by using --include-easyblocks-from-commit=89ea2e4737d792055de828e18f38bccee26b76cf (latest commit to easyblock repo), that will prefer the easyblocks from that repo which won't have these restrictive permissions.

An issue should still be opened in the EasyBuild framework

The workaround doesn't work

ocaisa · 2024-08-06T13:52:48Z

Ok, I found the problem, the easyconfigs are using the PerlModule easyblock and so are the extensions: https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb (edit: @boegel already saw this, wish I had read his comment in full!)
That's a departure from previous easyconfigs

ocaisa · 2024-08-06T14:02:34Z

Fix in easybuilders/easybuild-easyconfigs#21136

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml

ocaisa · 2024-08-06T14:17:28Z

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

eessi-bot · 2024-08-06T14:17:31Z

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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 15766, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 15767, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 15768, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 15769, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 15770, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 15771, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 15772, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 15773, for details & status see {2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658 (comment)

eessi-bot · 2024-08-06T14:17:32Z

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/generic from ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- 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 ocaisa
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted

eessi-bot · 2024-08-06T14:17:35Z

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/2024.08/pr_658/15766

date	job status	comment
Aug 06 14:17:34 UTC 2024	submitted	job id `15766` awaits release by job manager
Aug 06 14:18:38 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:26:13 UTC 2024	running	job `15766` is running
Aug 06 15:24:02 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15766.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-1722956731.tar.gz` size: 98 MiB (102828286 bytes) entries: 20706 modules under 2023.06/software/linux/x86_64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/generic no other files in tarball
Aug 06 15:24:02 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15766.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:42:59 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-generic-1722956731.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:17:39Z

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/2024.08/pr_658/15767

date	job status	comment
Aug 06 14:17:38 UTC 2024	submitted	job id `15767` awaits release by job manager
Aug 06 14:18:41 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:27:24 UTC 2024	running	job `15767` is running
Aug 06 15:24:04 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15767.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-1722956799.tar.gz` size: 98 MiB (102869409 bytes) entries: 20706 modules under 2023.06/software/linux/x86_64/intel/haswell/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/intel/haswell/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/intel/haswell no other files in tarball
Aug 06 15:24:04 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15767.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:43:20 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-haswell-1722956799.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:17:43Z

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/2024.08/pr_658/15768

date	job status	comment
Aug 06 14:17:42 UTC 2024	submitted	job id `15768` awaits release by job manager
Aug 06 14:18:43 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:27:26 UTC 2024	running	job `15768` is running
Aug 06 15:22:56 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15768.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_avx512-1722956773.tar.gz` size: 98 MiB (102864791 bytes) entries: 20706 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/intel/skylake_avx512 no other files in tarball
Aug 06 15:22:56 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15768.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:43:41 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1722956773.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:17:48Z

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/2024.08/pr_658/15769

date	job status	comment
Aug 06 14:17:47 UTC 2024	submitted	job id `15769` awaits release by job manager
Aug 06 14:18:33 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:25:02 UTC 2024	running	job `15769` is running
Aug 06 15:27:17 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15769.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-zen2-1722956968.tar.gz` size: 98 MiB (102899658 bytes) entries: 20706 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen2 no other files in tarball
Aug 06 15:27:17 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15769.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:44:02 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen2-1722956968.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:17:52Z

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/2024.08/pr_658/15770

date	job status	comment
Aug 06 14:17:51 UTC 2024	submitted	job id `15770` awaits release by job manager
Aug 06 14:18:36 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:25:04 UTC 2024	running	job `15770` is running
Aug 06 15:16:01 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15770.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-zen3-1722956460.tar.gz` size: 98 MiB (102875531 bytes) entries: 20706 modules under 2023.06/software/linux/x86_64/amd/zen3/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen3/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/x86_64/amd/zen3 no other files in tarball
Aug 06 15:16:01 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15770.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:44:22 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen3-1722956460.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:17:55Z

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/2024.08/pr_658/15771

date	job status	comment
Aug 06 14:17:54 UTC 2024	submitted	job id `15771` awaits release by job manager
Aug 06 14:18:26 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:19:45 UTC 2024	running	job `15771` is running
Aug 06 15:36:42 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15771.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-1722956367.tar.gz` size: 97 MiB (102739086 bytes) entries: 20706 modules under 2023.06/software/linux/aarch64/generic/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/generic no other files in tarball
Aug 06 15:36:42 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15771.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:44:43 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-generic-1722956367.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:17:59Z

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/2024.08/pr_658/15772

date	job status	comment
Aug 06 14:17:59 UTC 2024	submitted	job id `15772` awaits release by job manager
Aug 06 14:18:29 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:23:54 UTC 2024	running	job `15772` is running
Aug 06 15:41:49 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15772.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_n1-1722956648.tar.gz` size: 97 MiB (102718960 bytes) entries: 20706 modules under 2023.06/software/linux/aarch64/neoverse_n1/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_n1/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_n1 no other files in tarball
Aug 06 15:41:49 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15772.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:45:04 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-neoverse_n1-1722956648.tar.gz` to S3 bucket succeeded

eessi-bot · 2024-08-06T14:18:04Z

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/2024.08/pr_658/15773

date	job status	comment
Aug 06 14:18:03 UTC 2024	submitted	job id `15773` awaits release by job manager
Aug 06 14:18:31 UTC 2024	released	job awaits launch by Slurm scheduler
Aug 06 14:23:56 UTC 2024	running	job `15773` is running
Aug 06 15:20:40 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-15773.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_v1-1722956087.tar.gz` size: 97 MiB (102688457 bytes) entries: 20706 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `BioPerl/1.7.8-GCCcore-12.2.0.lua` `BioPerl/1.7.8-GCCcore-12.3.0.lua` `DB/18.1.40-GCCcore-12.3.0.lua` `DB_File/1.859-GCCcore-12.3.0.lua` `groff/1.22.4-GCCcore-12.3.0.lua` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0.lua` `XML-LibXML/2.0208-GCCcore-12.2.0.lua` `XML-LibXML/2.0209-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `BioPerl/1.7.8-GCCcore-12.2.0` `BioPerl/1.7.8-GCCcore-12.3.0` `DB/18.1.40-GCCcore-12.3.0` `DB_File/1.859-GCCcore-12.3.0` `groff/1.22.4-GCCcore-12.3.0` `Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0` `XML-LibXML/2.0208-GCCcore-12.2.0` `XML-LibXML/2.0209-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_v1 no other files in tarball
Aug 06 15:20:40 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ PASSED ] Ran 17/17 test case(s) from 17 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-15773.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Aug 06 15:45:24 UTC 2024	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-neoverse_v1-1722956087.tar.gz` to S3 bucket succeeded

ocaisa

LGTM

{2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8

448f0ab

TopRichard added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label Aug 5, 2024

ocaisa reviewed Aug 5, 2024

View reviewed changes

removed BioPerl hook

4b37ea2

Richard Top added 2 commits August 6, 2024 11:28

Added --include-easyblock and an issue reference to EasyBuild framework

e194d2a

Sync local branch with remote

af1c845

ocaisa mentioned this pull request Aug 6, 2024

Ensure that recent BioPerl easyconfigs use Bundle easyblock easybuilders/easybuild-easyconfigs#21136

Merged

ocaisa requested changes Aug 6, 2024

View reviewed changes

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml Outdated Show resolved Hide resolved

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Apply suggestions from code review

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ocaisa approved these changes Aug 6, 2024

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ocaisa added the bot:deploy Ask bot to deploy missing software installations to EESSI label Aug 6, 2024

ocaisa merged commit 81d27c7 into EESSI:2023.06-software.eessi.io Aug 6, 2024
33 checks passed

TopRichard mentioned this pull request Aug 7, 2024

{2023.06,zen4}[2023a] BioPerl 1.7.8 #662

Merged

		@@ -647,6 +647,16 @@ def post_sanitycheck_hook(self, args, *kwargs):
		POST_SANITYCHECK_HOOKS[self.name](self, args, *kwargs)


		def post_sanitycheck_bioperl(self, args, *kwargs):

{2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658

{2023.06}[GCCcore/12.2.0][GCCcore/12.3.0] BioPerl v1.7.8 #658

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eessi-bot bot commented Aug 6, 2024 •

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eessi-bot bot commented Aug 6, 2024 •

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eessi-bot bot commented Aug 6, 2024 •

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eessi-bot bot commented Aug 6, 2024 •

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