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{2023.06}[2023a,sapphire_rapids] First batch of (bioinformatics) apps from EB 4.9.2 2023a easystack #896

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merged 3 commits into from
Jan 26, 2025
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{2023.06}[2023a,sapphire_rapids] First batch of (bioinformatics) apps from EB 4.9.2 2023a easystack #896

merged 3 commits into from
Jan 26, 2025

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bedroge
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@bedroge bedroge commented Jan 26, 2025 

2 out of 8 required modules missing:

* HTSlib/1.18-GCC-12.3.0 (HTSlib-1.18-GCC-12.3.0.eb)
* BCFtools/1.18-GCC-12.3.0 (BCFtools-1.18-GCC-12.3.0.eb)


1 out of 3 required modules missing:

* BWA/0.7.18-GCCcore-12.3.0 (BWA-0.7.18-GCCcore-12.3.0.eb)


1 out of 2 required modules missing:

* CapnProto/1.0.1-GCCcore-12.3.0 (CapnProto-1.0.1-GCCcore-12.3.0.eb)


1 out of 10 required modules missing:

* DendroPy/4.6.1-GCCcore-12.3.0 (DendroPy-4.6.1-GCCcore-12.3.0.eb)


1 out of 8 required modules missing:

* DIAMOND/2.1.8-GCC-12.3.0 (DIAMOND-2.1.8-GCC-12.3.0.eb)


2 out of 12 required modules missing:

* ISA-L/2.30.0-GCCcore-12.3.0 (ISA-L-2.30.0-GCCcore-12.3.0.eb)
* fastp/0.23.4-GCC-12.3.0 (fastp-0.23.4-GCC-12.3.0.eb)

1 out of 24 required modules missing:

* HMMER/3.4-gompi-2023a (HMMER-3.4-gompi-2023a.eb)

2 out of 34 required modules missing:

* LSD2/2.4.1-GCCcore-12.3.0 (LSD2-2.4.1-GCCcore-12.3.0.eb)
* IQ-TREE/2.3.5-gompi-2023a (IQ-TREE-2.3.5-gompi-2023a.eb)

1 out of 3 required modules missing:

* KronaTools/2.8.1-GCCcore-12.3.0 (KronaTools-2.8.1-GCCcore-12.3.0.eb)

1 out of 7 required modules missing:

* LSD2/2.4.1-GCCcore-12.3.0 (LSD2-2.4.1-GCCcore-12.3.0.eb)

1 out of 3 required modules missing:

* MAFFT/7.520-GCC-12.3.0-with-extensions (MAFFT-7.520-GCC-12.3.0-with-extensions.eb)

1 out of 29 required modules missing:

* ncbi-vdb/3.0.10-gompi-2023a (ncbi-vdb-3.0.10-gompi-2023a.eb)

Looks like there is some overlap with #895 (ISA-L), so that one needs to be ingested first.

@bedroge bedroge added 2023.06-software.eessi.io 2023.06 version of software.eessi.io sapphire_rapids labels Jan 26, 2025
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eessi-bot bot commented Jan 26, 2025

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

  • architectures: x86_64/generic, x86_64/intel/haswell, x86_64/intel/sapphire_rapids, 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-software, eessi.io-2023.06-compat

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eessi-bot bot commented Jan 26, 2025

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

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

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bedroge commented Jan 26, 2025

I've removed the ones that have some overlap with #895 for now, so we can start the build here.

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

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eessi-bot bot commented Jan 26, 2025 •
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Updates by the bot instance eessi-bot-mc-aws (click for details)

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eessi-bot bot commented Jan 26, 2025 •
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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/intel/sapphire_rapids from bedroge

    • expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/sapphire_rapids

  • handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/sapphire_rapids resulted in:

    • no jobs were submitted

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eessi-bot bot commented Jan 26, 2025 •
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New job on instance eessi-bot-mc-aws for CPU micro-architecture x86_64-intel-sapphire_rapids for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2025.01/pr_896/42800

date job status comment
Jan 26 15:09:06 UTC 2025 submitted job id 42800 awaits release by job manager
Jan 26 15:09:36 UTC 2025 released job awaits launch by Slurm scheduler
Jan 26 15:15:38 UTC 2025 running job 42800 is running
Jan 26 15:43:04 UTC 2025 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-42800.out
✅ no message matching FATAL:
✅ 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-sapphire_rapids-1737905660.tar.gzsize: 48 MiB (51266938 bytes)
entries: 1631
modules under 2023.06/software/linux/x86_64/intel/sapphire_rapids/modules/all
BCFtools/1.18-GCC-12.3.0.lua
BWA/0.7.18-GCCcore-12.3.0.lua
CapnProto/1.0.1-GCCcore-12.3.0.lua
DendroPy/4.6.1-GCCcore-12.3.0.lua
FastME/2.1.6.3-GCC-12.3.0.lua
HMMER/3.4-gompi-2023a.lua
HTSlib/1.18-GCC-12.3.0.lua
IQ-TREE/2.3.5-gompi-2023a.lua
KronaTools/2.8.1-GCCcore-12.3.0.lua
LSD2/2.4.1-GCCcore-12.3.0.lua
MAFFT/7.520-GCC-12.3.0-with-extensions.lua
ncbi-vdb/3.0.10-gompi-2023a.lua
software under 2023.06/software/linux/x86_64/intel/sapphire_rapids/software
BCFtools/1.18-GCC-12.3.0
BWA/0.7.18-GCCcore-12.3.0
CapnProto/1.0.1-GCCcore-12.3.0
DendroPy/4.6.1-GCCcore-12.3.0
FastME/2.1.6.3-GCC-12.3.0
HMMER/3.4-gompi-2023a
HTSlib/1.18-GCC-12.3.0
IQ-TREE/2.3.5-gompi-2023a
KronaTools/2.8.1-GCCcore-12.3.0
LSD2/2.4.1-GCCcore-12.3.0
MAFFT/7.520-GCC-12.3.0-with-extensions
ncbi-vdb/3.0.10-gompi-2023a
other under 2023.06/software/linux/x86_64/intel/sapphire_rapids
no other files in tarball
Jan 26 15:43:04 UTC 2025 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ OK ] (1/9) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:x86-64-intel-srapids-node+default
P: perf: 663.229 timesteps/s (r:0, l:None, u:None)
[ OK ] (2/9) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /775175bf @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 1.82 us (r:0, l:None, u:None)
[ OK ] (3/9) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /52707c40 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 1.72 us (r:0, l:None, u:None)
[ OK ] (4/9) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /b1aacda9 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 3.81 us (r:0, l:None, u:None)
[ OK ] (5/9) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /c6bad193 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 7.91 us (r:0, l:None, u:None)
[ OK ] (6/9) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /15cad6c4 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 0.38 us (r:0, l:None, u:None)
[ OK ] (7/9) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /6672deda @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 0.38 us (r:0, l:None, u:None)
[ OK ] (8/9) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /2a9a47b1 @BotBuildTests:x86-64-intel-srapids-node+default
P: bandwidth: 13326.06 MB/s (r:0, l:None, u:None)
[ OK ] (9/9) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /1b24ab8e @BotBuildTests:x86-64-intel-srapids-node+default
P: bandwidth: 13340.5 MB/s (r:0, l:None, u:None)
[ PASSED ] Ran 9/9 test case(s) from 9 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-42800.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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boegel commented Jan 26, 2025

FastME/2.1.6.3-GCC-12.3.0 is also included in #895, so rebuild should be done here once that is deployed...

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bedroge commented Jan 26, 2025

FastME/2.1.6.3-GCC-12.3.0 is also included in #895, so rebuild should be done here once that is deployed...

I thought I had removed that one too, but apparently not...

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bedroge commented Jan 26, 2025

I've readded the ones that have some overlap with #895, and also added a few more apps. This build can be triggered when #895 has been ingested/merged.

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bedroge commented Jan 26, 2025

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

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eessi-bot bot commented Jan 26, 2025 •
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Updates by the bot instance eessi-bot-mc-aws (click for details)

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eessi-bot bot commented Jan 26, 2025 •
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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/intel/sapphire_rapids from bedroge

    • expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/intel/sapphire_rapids

  • handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/sapphire_rapids resulted in:

    • no jobs were submitted

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eessi-bot bot commented Jan 26, 2025 •
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New job on instance eessi-bot-mc-aws for CPU micro-architecture x86_64-intel-sapphire_rapids for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2025.01/pr_896/42801

date job status comment
Jan 26 16:55:43 UTC 2025 submitted job id 42801 awaits release by job manager
Jan 26 16:56:12 UTC 2025 released job awaits launch by Slurm scheduler
Jan 26 17:02:15 UTC 2025 running job 42801 is running
Jan 26 19:00:12 UTC 2025 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-42801.out
✅ no message matching FATAL:
✅ 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-sapphire_rapids-1737915069.tar.gzsize: 4103 MiB (4303071987 bytes)
entries: 3737
modules under 2023.06/software/linux/x86_64/intel/sapphire_rapids/modules/all
BCFtools/1.18-GCC-12.3.0.lua
BWA/0.7.18-GCCcore-12.3.0.lua
CapnProto/1.0.1-GCCcore-12.3.0.lua
DendroPy/4.6.1-GCCcore-12.3.0.lua
f90wrap/0.2.13-foss-2023a.lua
fastp/0.23.4-GCC-12.3.0.lua
HMMER/3.4-gompi-2023a.lua
HTSlib/1.18-GCC-12.3.0.lua
IQ-TREE/2.3.5-gompi-2023a.lua
KronaTools/2.8.1-GCCcore-12.3.0.lua
LSD2/2.4.1-GCCcore-12.3.0.lua
MAFFT/7.520-GCC-12.3.0-with-extensions.lua
Meson/1.3.1-GCCcore-12.3.0.lua
meson-python/0.15.0-GCCcore-12.3.0.lua
MetalWalls/21.06.1-foss-2023a.lua
ncbi-vdb/3.0.10-gompi-2023a.lua
QuantumESPRESSO/7.3.1-foss-2023a.lua
software under 2023.06/software/linux/x86_64/intel/sapphire_rapids/software
BCFtools/1.18-GCC-12.3.0
BWA/0.7.18-GCCcore-12.3.0
CapnProto/1.0.1-GCCcore-12.3.0
DendroPy/4.6.1-GCCcore-12.3.0
f90wrap/0.2.13-foss-2023a
fastp/0.23.4-GCC-12.3.0
HMMER/3.4-gompi-2023a
HTSlib/1.18-GCC-12.3.0
IQ-TREE/2.3.5-gompi-2023a
KronaTools/2.8.1-GCCcore-12.3.0
LSD2/2.4.1-GCCcore-12.3.0
MAFFT/7.520-GCC-12.3.0-with-extensions
Meson/1.3.1-GCCcore-12.3.0
meson-python/0.15.0-GCCcore-12.3.0
MetalWalls/21.06.1-foss-2023a
ncbi-vdb/3.0.10-gompi-2023a
QuantumESPRESSO/7.3.1-foss-2023a
other under 2023.06/software/linux/x86_64/intel/sapphire_rapids
no other files in tarball
Jan 26 19:00:12 UTC 2025 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ OK ] ( 1/11) EESSI_QuantumESPRESSO_PW %ecut=50 %nbnd=10 %scale=1_node %module_name=QuantumESPRESSO/7.3.1-foss-2023a %device_type=cpu /1bfec028 @BotBuildTests:x86-64-intel-srapids-node+default
P: extract_report_time: 0 s (r:0, l:None, u:None)
P: PWSCF_cpu: 10.08 s (r:0, l:None, u:None)
P: PWSCF_wall: 7.13 s (r:0, l:None, u:None)
P: electrons_cpu: 8.89 s (r:0, l:None, u:None)
P: electrons_wall: 5.45 s (r:0, l:None, u:None)
P: c_bands_cpu: 7.65 s (r:0, l:None, u:None)
P: c_bands_wall: 4.77 s (r:0, l:None, u:None)
P: cegterg_cpu: 7.49 s (r:0, l:None, u:None)
P: cegterg_wall: 4.65 s (r:0, l:None, u:None)
P: calbec_cpu: 1.37 s (r:0, l:None, u:None)
P: calbec_wall: 0.31 s (r:0, l:None, u:None)
P: fft_cpu: 0.24 s (r:0, l:None, u:None)
P: fft_wall: 0.23 s (r:0, l:None, u:None)
P: ffts_cpu: 0.0 s (r:0, l:None, u:None)
P: ffts_wall: 0.0 s (r:0, l:None, u:None)
P: fftw_cpu: 4.57 s (r:0, l:None, u:None)
P: fftw_wall: 3.38 s (r:0, l:None, u:None)
[ OK ] ( 2/11) EESSI_QuantumESPRESSO_PW %ecut=50 %nbnd=10 %scale=1_node %module_name=QuantumESPRESSO/7.2-foss-2022b %device_type=cpu /685466f4 @BotBuildTests:x86-64-intel-srapids-node+default
P: extract_report_time: 0 s (r:0, l:None, u:None)
P: PWSCF_cpu: 7.7 s (r:0, l:None, u:None)
P: PWSCF_wall: 4.71 s (r:0, l:None, u:None)
P: electrons_cpu: 6.47 s (r:0, l:None, u:None)
P: electrons_wall: 3.44 s (r:0, l:None, u:None)
P: c_bands_cpu: 5.27 s (r:0, l:None, u:None)
P: c_bands_wall: 2.75 s (r:0, l:None, u:None)
P: cegterg_cpu: 5.1 s (r:0, l:None, u:None)
P: cegterg_wall: 2.63 s (r:0, l:None, u:None)
P: calbec_cpu: 1.07 s (r:0, l:None, u:None)
P: calbec_wall: 0.09 s (r:0, l:None, u:None)
P: fft_cpu: 0.25 s (r:0, l:None, u:None)
P: fft_wall: 0.24 s (r:0, l:None, u:None)
P: ffts_cpu: 0.0 s (r:0, l:None, u:None)
P: ffts_wall: 0.0 s (r:0, l:None, u:None)
P: fftw_cpu: 2.97 s (r:0, l:None, u:None)
P: fftw_wall: 2.0 s (r:0, l:None, u:None)
[ OK ] ( 3/11) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:x86-64-intel-srapids-node+default
P: perf: 703.075 timesteps/s (r:0, l:None, u:None)
[ OK ] ( 4/11) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /775175bf @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 1.85 us (r:0, l:None, u:None)
[ OK ] ( 5/11) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /52707c40 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 1.65 us (r:0, l:None, u:None)
[ OK ] ( 6/11) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node %device_type=cpu /b1aacda9 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 3.82 us (r:0, l:None, u:None)
[ OK ] ( 7/11) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node %device_type=cpu /c6bad193 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 3.79 us (r:0, l:None, u:None)
[ OK ] ( 8/11) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /15cad6c4 @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 0.41 us (r:0, l:None, u:None)
[ OK ] ( 9/11) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /6672deda @BotBuildTests:x86-64-intel-srapids-node+default
P: latency: 0.32 us (r:0, l:None, u:None)
[ OK ] (10/11) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /2a9a47b1 @BotBuildTests:x86-64-intel-srapids-node+default
P: bandwidth: 13557.95 MB/s (r:0, l:None, u:None)
[ OK ] (11/11) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /1b24ab8e @BotBuildTests:x86-64-intel-srapids-node+default
P: bandwidth: 13989.78 MB/s (r:0, l:None, u:None)
[ PASSED ] Ran 11/11 test case(s) from 11 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-42801.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case
Jan 26 19:19:27 UTC 2025 uploaded transfer of eessi-2023.06-software-linux-x86_64-intel-sapphire_rapids-1737915069.tar.gz to S3 bucket succeeded

@bedroge bedroge mentioned this pull request Jan 26, 2025
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@bedroge bedroge added the ready-to-deploy Mark a PR as ready to deploy label Jan 26, 2025
@boegel boegel added bot:deploy Ask bot to deploy missing software installations to EESSI and removed ready-to-deploy Mark a PR as ready to deploy labels Jan 26, 2025
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boegel commented Jan 26, 2025

tarball deployed, so merging...

@boegel boegel merged commit 54f8d0f into EESSI:2023.06-software.eessi.io Jan 26, 2025
49 checks passed
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eessi-bot bot commented Jan 26, 2025

PR merged! Moved ['/project/def-users/SHARED/jobs/2025.01/pr_896/42800', '/project/def-users/SHARED/jobs/2025.01/pr_896/42801'] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.01.26

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eessi-bot bot commented Jan 26, 2025

PR merged! Moved [] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.01.26

@bedroge bedroge deleted the sapphire_rapids_eb492_2023a branch January 26, 2025 19:59
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@boegel boegel boegel approved these changes

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2023.06-software.eessi.io 2023.06 version of software.eessi.io bot:deploy Ask bot to deploy missing software installations to EESSI sapphire_rapids
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