{2023.06}[foss/2022a] CMSeq V1.0.4 #190

TopRichard · 2023-10-08T12:49:49Z

Trying to build CMSeq/1.0.4-foss-2022a as a step forward for getting closer to the current available HPC software stack.

Will install the following packages:

Pysam/0.19.1-GCC-11.3.0 (Pysam-0.19.1-GCC-11.3.0.eb)
pkgconfig/1.5.5-GCCcore-11.3.0-python (pkgconfig-1.5.5-GCCcore-11.3.0-python.eb)
Biopython/1.79-foss-2022a (Biopython-1.79-foss-2022a.eb)
bcbio-gff/0.7.0-foss-2022a (bcbio-gff-0.7.0-foss-2022a.eb)
h5py/3.7.0-foss-2022a (h5py-3.7.0-foss-2022a.eb)
biom-format/2.1.14-foss-2022a (biom-format-2.1.14-foss-2022a.eb)
CMSeq/1.0.4-foss-2022a (CMSeq-1.0.4-foss-2022a.eb)

nessi-bot · 2023-10-08T12:49:53Z

Instance AWS-NESSI is configured to build:

arch x86_64/generic for repo nessi-2022.11-swl-deb10
arch x86_64/generic for repo nessi-2023.06-cl
arch x86_64/generic for repo nessi-2023.06-swl-deb10
arch x86_64/generic for repo nessi-2023.06-swl-deb11
arch x86_64/intel/skylake_avx512 for repo nessi-2022.11-swl-deb10
arch x86_64/intel/skylake_avx512 for repo nessi-2023.06-cl
arch x86_64/intel/skylake_avx512 for repo nessi-2023.06-swl-deb10
arch x86_64/intel/skylake_avx512 for repo nessi-2023.06-swl-deb11
arch x86_64/intel/cascadelake for repo nessi-2022.11-swl-deb10
arch x86_64/intel/cascadelake for repo nessi-2023.06-cl
arch x86_64/intel/cascadelake for repo nessi-2023.06-swl-deb10
arch x86_64/intel/cascadelake for repo nessi-2023.06-swl-deb11
arch x86_64/amd/zen2 for repo nessi-2022.11-swl-deb10
arch x86_64/amd/zen2 for repo nessi-2023.06-cl
arch x86_64/amd/zen2 for repo nessi-2023.06-swl-deb10
arch x86_64/amd/zen2 for repo nessi-2023.06-swl-deb11
arch aarch64/generic for repo nessi-2022.11-swl-deb10
arch aarch64/generic for repo nessi-2023.06-cl
arch aarch64/generic for repo nessi-2023.06-swl-deb10
arch aarch64/generic for repo nessi-2023.06-swl-deb11

nessi-bot · 2023-10-08T12:49:53Z

Instance Saga-NESSI is configured to build:

arch x86_64/intel/cascadelake for repo nessi-2022.11-swl-deb10
arch x86_64/intel/cascadelake for repo nessi-2023.06-cl
arch x86_64/intel/cascadelake for repo nessi-2023.06-swl-deb10
arch x86_64/intel/cascadelake for repo nessi-2023.06-swl-deb11
arch x86_64/intel/skylake_avx512 for repo nessi-2022.11-swl-deb10
arch x86_64/intel/skylake_avx512 for repo nessi-2023.06-cl
arch x86_64/intel/skylake_avx512 for repo nessi-2023.06-swl-deb10
arch x86_64/intel/skylake_avx512 for repo nessi-2023.06-swl-deb11
arch x86_64/generic for repo nessi-2022.11-swl-deb10
arch x86_64/generic for repo nessi-2023.06-cl
arch x86_64/generic for repo nessi-2023.06-swl-deb10
arch x86_64/generic for repo nessi-2023.06-swl-deb11

nessi-bot · 2023-10-08T12:49:53Z

Instance Fram-NESSI is configured to build:

arch x86_64/generic for repo nessi-2022.11-swl-deb10
arch x86_64/generic for repo nessi-2023.06-cl
arch x86_64/generic for repo nessi-2023.06-swl-deb10
arch x86_64/generic for repo nessi-2023.06-swl-deb11
arch x86_64/intel/broadwell for repo nessi-2022.11-swl-deb10
arch x86_64/intel/broadwell for repo nessi-2023.06-cl
arch x86_64/intel/broadwell for repo nessi-2023.06-swl-deb10
arch x86_64/intel/broadwell for repo nessi-2023.06-swl-deb11

nessi-bot · 2023-10-08T12:49:53Z

Instance eX3-NESSI is configured to build:

arch x86_64/amd/zen2 for repo nessi-2022.11-swl-deb10
arch x86_64/amd/zen2 for repo nessi-2023.06-cl
arch x86_64/amd/zen2 for repo nessi-2023.06-swl-deb10
arch x86_64/amd/zen2 for repo nessi-2023.06-swl-deb11
arch aarch64/generic for repo nessi-2022.11-swl-deb10
arch aarch64/generic for repo nessi-2023.06-cl
arch aarch64/generic for repo nessi-2023.06-swl-deb10
arch aarch64/generic for repo nessi-2023.06-swl-deb11

TopRichard · 2023-10-08T12:50:59Z

bot: build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/generic
bot: build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/cascadelake
bot: build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/skylake
bot: build inst:AWS repo:nessi-2023.06-swl-deb10 arch:zen2
bot: build inst:Fram-NESSI repo:nessi-2023.06-swl-deb10 arch:x86_64/intel/broadwell

nessi-bot · 2023-10-08T12:51:01Z

Updates by the bot instance eX3-NESSI (click for details)

received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/generic from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/cascadelake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/skylake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb10 arch:zen2 from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2
received bot command build inst:Fram-NESSI repo:nessi-2023.06-swl-deb10 arch:x86_64/intel/broadwell from TopRichard
- expanded format: build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2 resulted in:
- no jobs were submitted
handling command build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell resulted in:
- no jobs were submitted

nessi-bot · 2023-10-08T12:51:01Z

Updates by the bot instance Fram-NESSI (click for details)

received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/generic from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/cascadelake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/skylake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb10 arch:zen2 from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2
received bot command build inst:Fram-NESSI repo:nessi-2023.06-swl-deb10 arch:x86_64/intel/broadwell from TopRichard
- expanded format: build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2 resulted in:
- no jobs were submitted
handling command build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell resulted in:
- submitted job 5425376, for details & status see {2023.06}[foss/2022a] CMSeq V1.0.4 #190 (comment)

nessi-bot · 2023-10-08T12:51:01Z

Updates by the bot instance Saga-NESSI (click for details)

received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/generic from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/cascadelake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/skylake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb10 arch:zen2 from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2
received bot command build inst:Fram-NESSI repo:nessi-2023.06-swl-deb10 arch:x86_64/intel/broadwell from TopRichard
- expanded format: build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake resulted in:
- no jobs were submitted
handling command build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2 resulted in:
- no jobs were submitted
handling command build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell resulted in:
- no jobs were submitted

nessi-bot · 2023-10-08T12:51:01Z

Updates by the bot instance AWS-NESSI (click for details)

received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/generic from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/cascadelake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb11 arch:x86_64/intel/skylake from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake
received bot command build inst:AWS repo:nessi-2023.06-swl-deb10 arch:zen2 from TopRichard
- expanded format: build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2
received bot command build inst:Fram-NESSI repo:nessi-2023.06-swl-deb10 arch:x86_64/intel/broadwell from TopRichard
- expanded format: build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/generic resulted in:
- submitted job 7870, for details & status see {2023.06}[foss/2022a] CMSeq V1.0.4 #190 (comment)
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/cascadelake resulted in:
- submitted job 7871, for details & status see {2023.06}[foss/2022a] CMSeq V1.0.4 #190 (comment)
handling command build instance:AWS repository:nessi-2023.06-swl-deb11 architecture:x86_64/intel/skylake resulted in:
- submitted job 7872, for details & status see {2023.06}[foss/2022a] CMSeq V1.0.4 #190 (comment)
handling command build instance:AWS repository:nessi-2023.06-swl-deb10 architecture:zen2 resulted in:
- submitted job 7873, for details & status see {2023.06}[foss/2022a] CMSeq V1.0.4 #190 (comment)
handling command build instance:Fram-NESSI repository:nessi-2023.06-swl-deb10 architecture:x86_64/intel/broadwell resulted in:
- no jobs were submitted

nessi-bot · 2023-10-08T12:51:08Z

New job on instance AWS-NESSI for architecture x86_64-generic for repository nessi-2023.06-swl-deb11 in job dir /mnt/shared/home/nessibot/pilot.nessi.no/PR155/jobs/2023.10/pr_190/7870

date	job status	comment
Oct 08 12:51:08 PM UTC 2023	submitted	job id `7870` awaits release by job manager
Oct 08 12:51:46 PM UTC 2023	released	job awaits launch by Slurm scheduler
Oct 08 12:56:07 PM UTC 2023	running	job `7870` is running
Oct 08 01:21:37 PM UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-7870.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-1696771202.tar.gz` size: 32 MiB (34440088 bytes) entries: 1806 modules under 2023.06/software/linux/x86_64/generic/modules/all `bcbio-gff/0.7.0-foss-2022a.lua` `biom-format/2.1.14-foss-2022a.lua` `Biopython/1.79-foss-2022a.lua` `CMSeq/1.0.4-foss-2022a.lua` `h5py/3.7.0-foss-2022a.lua` `pkgconfig/1.5.5-GCCcore-11.3.0-python.lua` `Pysam/0.19.1-GCC-11.3.0.lua` software under 2023.06/software/linux/x86_64/generic/software `bcbio-gff/0.7.0-foss-2022a` `biom-format/2.1.14-foss-2022a` `Biopython/1.79-foss-2022a` `CMSeq/1.0.4-foss-2022a` `h5py/3.7.0-foss-2022a` `pkgconfig/1.5.5-GCCcore-11.3.0-python` `Pysam/0.19.1-GCC-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`
Oct 08 06:31:19 PM UTC 2023	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-generic-1696771202.tar.gz` to S3 bucket succeeded
Oct 08 06:39:57 PM UTC 2023	staged	tarball `eessi-2023.06-software-linux-x86_64-generic-1696771202.tar.gz` downloaded to Stratum-0
Oct 08 06:45:56 PM UTC 2023	pr_opened	merge PR https://github.com/NorESSI/staging/pull/613 to approve ingest
Oct 08 06:53:28 PM UTC 2023	approved	👍 tarball `eessi-2023.06-software-linux-x86_64-generic-1696771202.tar.gz` approved, see PR https://github.com/NorESSI/staging/pull/613
Oct 08 06:57:50 PM UTC 2023	ingested	🎉 tarball `eessi-2023.06-software-linux-x86_64-generic-1696771202.tar.gz` successfully ingested at `2023.06/software/linux/x86_64/generic/`

nessi-bot · 2023-10-08T12:51:10Z

New job on instance Fram-NESSI for architecture x86_64-intel-broadwell for repository nessi-2023.06-swl-deb10 in job dir /cluster/projects/nn9992k/pilot.nessi.no/PR155/jobs/2023.10/pr_190/5425376

date	job status	comment
Oct 08 12:51:09 UTC 2023	submitted	job id `5425376` awaits release by job manager
Oct 08 12:55:55 UTC 2023	released	job awaits launch by Slurm scheduler
Oct 08 13:00:58 UTC 2023	running	job `5425376` is running
Oct 08 13:16:07 UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-5425376.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-broadwell-1696770729.tar.gz` size: 32 MiB (34578787 bytes) entries: 1806 modules under 2023.06/software/linux/x86_64/intel/broadwell/modules/all `bcbio-gff/0.7.0-foss-2022a.lua` `biom-format/2.1.14-foss-2022a.lua` `Biopython/1.79-foss-2022a.lua` `CMSeq/1.0.4-foss-2022a.lua` `h5py/3.7.0-foss-2022a.lua` `pkgconfig/1.5.5-GCCcore-11.3.0-python.lua` `Pysam/0.19.1-GCC-11.3.0.lua` software under 2023.06/software/linux/x86_64/intel/broadwell/software `bcbio-gff/0.7.0-foss-2022a` `biom-format/2.1.14-foss-2022a` `Biopython/1.79-foss-2022a` `CMSeq/1.0.4-foss-2022a` `h5py/3.7.0-foss-2022a` `pkgconfig/1.5.5-GCCcore-11.3.0-python` `Pysam/0.19.1-GCC-11.3.0` other under 2023.06/software/linux/x86_64/intel/broadwell `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Oct 08 18:31:18 UTC 2023	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-broadwell-1696770729.tar.gz` to S3 bucket succeeded
Oct 08 06:40:00 PM UTC 2023	staged	tarball `eessi-2023.06-software-linux-x86_64-intel-broadwell-1696770729.tar.gz` downloaded to Stratum-0
Oct 08 06:46:01 PM UTC 2023	pr_opened	merge PR https://github.com/NorESSI/staging/pull/614 to approve ingest
Oct 08 06:53:31 PM UTC 2023	approved	👍 tarball `eessi-2023.06-software-linux-x86_64-intel-broadwell-1696770729.tar.gz` approved, see PR https://github.com/NorESSI/staging/pull/614
Oct 08 06:58:29 PM UTC 2023	ingested	🎉 tarball `eessi-2023.06-software-linux-x86_64-intel-broadwell-1696770729.tar.gz` successfully ingested at `2023.06/software/linux/x86_64/intel/broadwell/`

nessi-bot · 2023-10-08T12:51:16Z

New job on instance AWS-NESSI for architecture x86_64-intel-cascadelake for repository nessi-2023.06-swl-deb11 in job dir /mnt/shared/home/nessibot/pilot.nessi.no/PR155/jobs/2023.10/pr_190/7871

date	job status	comment
Oct 08 12:51:15 PM UTC 2023	submitted	job id `7871` awaits release by job manager
Oct 08 12:51:43 PM UTC 2023	released	job awaits launch by Slurm scheduler
Oct 08 01:50:36 PM UTC 2023	running	job `7871` is running
Oct 08 02:13:05 PM UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-7871.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-cascadelake-1696774343.tar.gz` size: 32 MiB (34484722 bytes) entries: 1806 modules under 2023.06/software/linux/x86_64/intel/cascadelake/modules/all `bcbio-gff/0.7.0-foss-2022a.lua` `biom-format/2.1.14-foss-2022a.lua` `Biopython/1.79-foss-2022a.lua` `CMSeq/1.0.4-foss-2022a.lua` `h5py/3.7.0-foss-2022a.lua` `pkgconfig/1.5.5-GCCcore-11.3.0-python.lua` `Pysam/0.19.1-GCC-11.3.0.lua` software under 2023.06/software/linux/x86_64/intel/cascadelake/software `bcbio-gff/0.7.0-foss-2022a` `biom-format/2.1.14-foss-2022a` `Biopython/1.79-foss-2022a` `CMSeq/1.0.4-foss-2022a` `h5py/3.7.0-foss-2022a` `pkgconfig/1.5.5-GCCcore-11.3.0-python` `Pysam/0.19.1-GCC-11.3.0` other under 2023.06/software/linux/x86_64/intel/cascadelake `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Oct 08 06:31:42 PM UTC 2023	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-cascadelake-1696774343.tar.gz` to S3 bucket succeeded
Oct 08 06:40:03 PM UTC 2023	staged	tarball `eessi-2023.06-software-linux-x86_64-intel-cascadelake-1696774343.tar.gz` downloaded to Stratum-0
Oct 08 06:46:06 PM UTC 2023	pr_opened	merge PR https://github.com/NorESSI/staging/pull/615 to approve ingest
Oct 08 06:53:34 PM UTC 2023	approved	👍 tarball `eessi-2023.06-software-linux-x86_64-intel-cascadelake-1696774343.tar.gz` approved, see PR https://github.com/NorESSI/staging/pull/615
Oct 08 06:59:11 PM UTC 2023	ingested	🎉 tarball `eessi-2023.06-software-linux-x86_64-intel-cascadelake-1696774343.tar.gz` successfully ingested at `2023.06/software/linux/x86_64/intel/cascadelake/`

nessi-bot · 2023-10-08T12:51:22Z

New job on instance AWS-NESSI for architecture x86_64-intel-skylake_avx512 for repository nessi-2023.06-swl-deb11 in job dir /mnt/shared/home/nessibot/pilot.nessi.no/PR155/jobs/2023.10/pr_190/7872

date	job status	comment
Oct 08 12:51:21 PM UTC 2023	submitted	job id `7872` awaits release by job manager
Oct 08 12:51:41 PM UTC 2023	released	job awaits launch by Slurm scheduler
Oct 08 12:56:05 PM UTC 2023	running	job `7872` is running
Oct 08 01:19:30 PM UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-7872.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_avx512-1696771114.tar.gz` size: 32 MiB (34489399 bytes) entries: 1806 modules under 2023.06/software/linux/x86_64/intel/skylake_avx512/modules/all `bcbio-gff/0.7.0-foss-2022a.lua` `biom-format/2.1.14-foss-2022a.lua` `Biopython/1.79-foss-2022a.lua` `CMSeq/1.0.4-foss-2022a.lua` `h5py/3.7.0-foss-2022a.lua` `pkgconfig/1.5.5-GCCcore-11.3.0-python.lua` `Pysam/0.19.1-GCC-11.3.0.lua` software under 2023.06/software/linux/x86_64/intel/skylake_avx512/software `bcbio-gff/0.7.0-foss-2022a` `biom-format/2.1.14-foss-2022a` `Biopython/1.79-foss-2022a` `CMSeq/1.0.4-foss-2022a` `h5py/3.7.0-foss-2022a` `pkgconfig/1.5.5-GCCcore-11.3.0-python` `Pysam/0.19.1-GCC-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`
Oct 08 06:31:08 PM UTC 2023	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1696771114.tar.gz` to S3 bucket succeeded
Oct 08 06:40:06 PM UTC 2023	staged	tarball `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1696771114.tar.gz` downloaded to Stratum-0
Oct 08 06:46:10 PM UTC 2023	pr_opened	merge PR https://github.com/NorESSI/staging/pull/616 to approve ingest
Oct 08 06:53:37 PM UTC 2023	approved	👍 tarball `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1696771114.tar.gz` approved, see PR https://github.com/NorESSI/staging/pull/616
Oct 08 06:59:48 PM UTC 2023	ingested	🎉 tarball `eessi-2023.06-software-linux-x86_64-intel-skylake_avx512-1696771114.tar.gz` successfully ingested at `2023.06/software/linux/x86_64/intel/skylake_avx512/`

nessi-bot · 2023-10-08T12:51:30Z

New job on instance AWS-NESSI for architecture x86_64-amd-zen2 for repository nessi-2023.06-swl-deb10 in job dir /mnt/shared/home/nessibot/pilot.nessi.no/PR155/jobs/2023.10/pr_190/7873

date	job status	comment
Oct 08 12:51:29 PM UTC 2023	submitted	job id `7873` awaits release by job manager
Oct 08 12:51:39 PM UTC 2023	released	job awaits launch by Slurm scheduler
Oct 08 12:53:58 PM UTC 2023	running	job `7873` is running
Oct 08 01:13:10 PM UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-7873.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-zen2-1696770684.tar.gz` size: 32 MiB (34552030 bytes) entries: 1806 modules under 2023.06/software/linux/x86_64/amd/zen2/modules/all `bcbio-gff/0.7.0-foss-2022a.lua` `biom-format/2.1.14-foss-2022a.lua` `Biopython/1.79-foss-2022a.lua` `CMSeq/1.0.4-foss-2022a.lua` `h5py/3.7.0-foss-2022a.lua` `pkgconfig/1.5.5-GCCcore-11.3.0-python.lua` `Pysam/0.19.1-GCC-11.3.0.lua` software under 2023.06/software/linux/x86_64/amd/zen2/software `bcbio-gff/0.7.0-foss-2022a` `biom-format/2.1.14-foss-2022a` `Biopython/1.79-foss-2022a` `CMSeq/1.0.4-foss-2022a` `h5py/3.7.0-foss-2022a` `pkgconfig/1.5.5-GCCcore-11.3.0-python` `Pysam/0.19.1-GCC-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`
Oct 08 06:31:31 PM UTC 2023	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-amd-zen2-1696770684.tar.gz` to S3 bucket succeeded
Oct 08 06:39:55 PM UTC 2023	staged	tarball `eessi-2023.06-software-linux-x86_64-amd-zen2-1696770684.tar.gz` downloaded to Stratum-0
Oct 08 06:45:52 PM UTC 2023	pr_opened	merge PR https://github.com/NorESSI/staging/pull/612 to approve ingest
Oct 08 06:53:25 PM UTC 2023	approved	👍 tarball `eessi-2023.06-software-linux-x86_64-amd-zen2-1696770684.tar.gz` approved, see PR https://github.com/NorESSI/staging/pull/612
Oct 08 06:57:11 PM UTC 2023	ingested	🎉 tarball `eessi-2023.06-software-linux-x86_64-amd-zen2-1696770684.tar.gz` successfully ingested at `2023.06/software/linux/x86_64/amd/zen2/`

TopRichard · 2023-10-08T15:25:07Z

bot: build inst:eX3 repo:nessi-2023.06-swl-deb11 arch:aarch64/generic

nessi-bot · 2023-10-08T15:25:10Z

Updates by the bot instance AWS-NESSI (click for details)

received bot command build inst:eX3 repo:nessi-2023.06-swl-deb11 arch:aarch64/generic from TopRichard
- expanded format: build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic
handling command build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic resulted in:
- no jobs were submitted

nessi-bot · 2023-10-08T15:25:10Z

Updates by the bot instance Fram-NESSI (click for details)

received bot command build inst:eX3 repo:nessi-2023.06-swl-deb11 arch:aarch64/generic from TopRichard
- expanded format: build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic
handling command build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic resulted in:
- no jobs were submitted

nessi-bot · 2023-10-08T15:25:10Z

Updates by the bot instance eX3-NESSI (click for details)

received bot command build inst:eX3 repo:nessi-2023.06-swl-deb11 arch:aarch64/generic from TopRichard
- expanded format: build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic
handling command build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic resulted in:
- submitted job 14101, for details & status see {2023.06}[foss/2022a] CMSeq V1.0.4 #190 (comment)

nessi-bot · 2023-10-08T15:25:11Z

Updates by the bot instance Saga-NESSI (click for details)

received bot command build inst:eX3 repo:nessi-2023.06-swl-deb11 arch:aarch64/generic from TopRichard
- expanded format: build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic
handling command build instance:eX3 repository:nessi-2023.06-swl-deb11 architecture:aarch64/generic resulted in:
- no jobs were submitted

nessi-bot · 2023-10-08T15:25:15Z

New job on instance eX3-NESSI for architecture aarch64-generic for repository nessi-2023.06-swl-deb11 in job dir /home/thomarob/pilot.nessi.no/PR155/jobs/2023.10/pr_190/14101

date	job status	comment
Oct 08 03:24:49 PM UTC 2023	submitted	job id `14101` awaits release by job manager
Oct 08 05:53:02 PM UTC 2023	released	job awaits launch by Slurm scheduler
Oct 08 05:58:11 PM UTC 2023	running	job `14101` is running
Oct 08 06:23:34 PM UTC 2023	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-14101.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-1696789006.tar.gz` size: 32 MiB (34027219 bytes) entries: 1806 modules under 2023.06/software/linux/aarch64/generic/modules/all `bcbio-gff/0.7.0-foss-2022a.lua` `biom-format/2.1.14-foss-2022a.lua` `Biopython/1.79-foss-2022a.lua` `CMSeq/1.0.4-foss-2022a.lua` `h5py/3.7.0-foss-2022a.lua` `pkgconfig/1.5.5-GCCcore-11.3.0-python.lua` `Pysam/0.19.1-GCC-11.3.0.lua` software under 2023.06/software/linux/aarch64/generic/software `bcbio-gff/0.7.0-foss-2022a` `biom-format/2.1.14-foss-2022a` `Biopython/1.79-foss-2022a` `CMSeq/1.0.4-foss-2022a` `h5py/3.7.0-foss-2022a` `pkgconfig/1.5.5-GCCcore-11.3.0-python` `Pysam/0.19.1-GCC-11.3.0` other under 2023.06/software/linux/aarch64/generic `.lmod/cache/spiderT.lua` `.lmod/cache/spiderT.luac_5.1` `.lmod/cache/timestamp`
Oct 08 06:33:20 PM UTC 2023	uploaded	transfer of `eessi-2023.06-software-linux-aarch64-generic-1696789006.tar.gz` to S3 bucket succeeded
Oct 08 06:39:52 PM UTC 2023	staged	tarball `eessi-2023.06-software-linux-aarch64-generic-1696789006.tar.gz` downloaded to Stratum-0
Oct 08 06:45:48 PM UTC 2023	pr_opened	merge PR https://github.com/NorESSI/staging/pull/611 to approve ingest
Oct 08 06:53:22 PM UTC 2023	approved	👍 tarball `eessi-2023.06-software-linux-aarch64-generic-1696789006.tar.gz` approved, see PR https://github.com/NorESSI/staging/pull/611
Oct 08 06:56:17 PM UTC 2023	ingested	🎉 tarball `eessi-2023.06-software-linux-aarch64-generic-1696789006.tar.gz` successfully ingested at `2023.06/software/linux/aarch64/generic/`

TopRichard · 2023-10-08T18:29:51Z

Checklist for building CMSeq V1.0.4 :

Check whether builds for all required architectures succeed (SUCCESS message + reasonably sized tarball)
Check if the PR is up-to-date with the target branch nessi.no-2023.06 in the repository (if not what are the differences)
Assess if all requested changes are sound (checking files changed on GitHub.com)
Verify that all easyconfig/s being built are included with the EB version used (if not why not)
Review changes (if any) needed to get the build(s) succeed (common changes for all architectures, changes for a single architecture, changes because of build environment specifics, etc.)

TopRichard · 2023-10-08T19:13:35Z

Target architectures

x86_64-intel-broadwell
x86_64-intel-skylake_avx512
x86_64-intel-cascadelake
x86_64-amd-zen2
x86_64-generic
aarch64-generic

Checklist for deployment/ingestion

at least one tarball for each architecture has been uploaded
at least one tarball for each architecture has been staged
for each architecture one and only one tarball has been approved
for each architecture one and only one tarball was ingested
[] encountered issues in the ingestion, likely related to troubles interacting with GitHub via PyGithub …
[] all tests in the CI have succeeded (rerun failed tests ~ 10 mins after last ingest)
has the package become available via CernVM-FS for all architectures ingested (for lmod cache updates pay attention to timestamp of files)

command & log

command

cd /cvmfs/pilot.nessi.no/versions/2023.06/software/linux ; 
ls -l \
      x86_64/{generic,amd/zen2,intel/[bsc]*}/{software,modules/all}/CMSeq/1.0.4-foss-2022a* \
      aarch64/generic/{software,modules/all}/CMSeq/1.0.4-foss-2022a*

-rw-r--r--. 1 cvmfs cvmfs 1740 Oct  8 18:15 aarch64/generic/modules/all/CMSeq/1.0.4-foss-2022a.lua
-rw-r--r--. 1 cvmfs cvmfs 1740 Oct  8 13:10 x86_64/amd/zen2/modules/all/CMSeq/1.0.4-foss-2022a.lua
-rw-r--r--. 1 cvmfs cvmfs 1739 Oct  8 13:18 x86_64/generic/modules/all/CMSeq/1.0.4-foss-2022a.lua
-rw-rw-r--. 1 cvmfs cvmfs 1747 Oct  8 13:11 x86_64/intel/broadwell/modules/all/CMSeq/1.0.4-foss-2022a.lua
-rw-r--r--. 1 cvmfs cvmfs 1749 Oct  8 14:11 x86_64/intel/cascadelake/modules/all/CMSeq/1.0.4-foss-2022a.lua
-rw-r--r--. 1 cvmfs cvmfs 1752 Oct  8 13:17 x86_64/intel/skylake_avx512/modules/all/CMSeq/1.0.4-foss-2022a.lua

aarch64/generic/software/CMSeq/1.0.4-foss-2022a:
total 14
dr-xr-xr-x. 2 cvmfs cvmfs 4096 Oct  8 18:15 bin
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 18:15 easybuild
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 18:14 lib
lrwxrwxrwx. 1 cvmfs cvmfs    3 Oct  8 18:15 lib64 -> lib

x86_64/amd/zen2/software/CMSeq/1.0.4-foss-2022a:
total 14
dr-xr-xr-x. 2 cvmfs cvmfs 4096 Oct  8 13:10 bin
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:10 easybuild
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:10 lib
lrwxrwxrwx. 1 cvmfs cvmfs    3 Oct  8 13:10 lib64 -> lib

x86_64/generic/software/CMSeq/1.0.4-foss-2022a:
total 14
dr-xr-xr-x. 2 cvmfs cvmfs 4096 Oct  8 13:18 bin
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:18 easybuild
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:18 lib
lrwxrwxrwx. 1 cvmfs cvmfs    3 Oct  8 13:18 lib64 -> lib

x86_64/intel/broadwell/software/CMSeq/1.0.4-foss-2022a:
total 14
dr-xr-xr-x. 2 cvmfs cvmfs 4096 Oct  8 13:11 bin
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:11 easybuild
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:11 lib
lrwxrwxrwx. 1 cvmfs cvmfs    3 Oct  8 13:11 lib64 -> lib

x86_64/intel/cascadelake/software/CMSeq/1.0.4-foss-2022a:
total 14
dr-xr-xr-x. 2 cvmfs cvmfs 4096 Oct  8 14:11 bin
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 14:11 easybuild
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 14:11 lib
lrwxrwxrwx. 1 cvmfs cvmfs    3 Oct  8 14:11 lib64 -> lib

x86_64/intel/skylake_avx512/software/CMSeq/1.0.4-foss-2022a:
total 14
dr-xr-xr-x. 2 cvmfs cvmfs 4096 Oct  8 13:17 bin
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:17 easybuild
dr-xr-xr-x. 3 cvmfs cvmfs 4096 Oct  8 13:17 lib
lrwxrwxrwx. 1 cvmfs cvmfs    3 Oct  8 13:17 lib64 -> lib

{2023.06}[foss/2022a] CMSeq V1.0.4

82572f4

TopRichard added the NESSI/2023.06 label Oct 8, 2023

TopRichard added the bot:deploy label Oct 8, 2023

TopRichard added the ingested label Oct 8, 2023

TopRichard requested a review from justadejavu October 8, 2023 19:19

justadejavu approved these changes Oct 8, 2023

View reviewed changes

TopRichard merged commit b12c563 into NorESSI:nessi.no-2023.06 Oct 8, 2023
66 of 73 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

{2023.06}[foss/2022a] CMSeq V1.0.4 #190

{2023.06}[foss/2022a] CMSeq V1.0.4 #190

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

TopRichard commented Oct 8, 2023

TopRichard commented Oct 8, 2023

{2023.06}[foss/2022a] CMSeq V1.0.4 #190

{2023.06}[foss/2022a] CMSeq V1.0.4 #190

Conversation

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited by trz42 Loading

nessi-bot bot commented Oct 8, 2023 • edited by trz42 Loading

nessi-bot bot commented Oct 8, 2023 • edited by trz42 Loading

nessi-bot bot commented Oct 8, 2023 • edited by trz42 Loading

nessi-bot bot commented Oct 8, 2023 • edited by trz42 Loading

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited Loading

nessi-bot bot commented Oct 8, 2023 • edited by trz42 Loading

TopRichard commented Oct 8, 2023

TopRichard commented Oct 8, 2023

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited

Loading

nessi-bot bot commented Oct 8, 2023 •

edited by trz42

Loading