{2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785

boegel · 2024-10-12T14:10:37Z

If these two PRs can be deployed & merged first, then this PR could also be built for A64FX:

…suite 3.3.0, pytest-xdist 3.3.1, tensorstore 0.1.65 (AlphaFold dependencies)

eessi-bot · 2024-10-12T14:10:41Z

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-build-deploy-bot-deucalion · 2024-10-12T14:10:41Z

Instance boegel-bot-deucalion is configured to build for:

architectures: aarch64/a64fx
repositories: eessi.io-2023.06-software

eessi-bot · 2024-10-12T14:10:42Z

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

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

boegel · 2024-10-12T14:20:54Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/generic
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4
bot: build repo:eessi.io-2023.06-software arch:aarch64/a64fx

eessi-bot · 2024-10-12T14:20:57Z

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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
handling command build repository:eessi.io-2023.06-software architecture:x86_64/generic resulted in:
- submitted job 22849, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- no jobs were submitted

eessi-bot · 2024-10-12T14:20:57Z

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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
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/amd/zen4 resulted in:
- submitted job 1417, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- no jobs were submitted

eessi-build-deploy-bot-deucalion · 2024-10-12T14:20:57Z

Updates by the bot instance boegel-bot-deucalion (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/generic from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
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/amd/zen4 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- submitted job 164116, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)

boegel · 2024-10-12T16:22:21Z

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

eessi-bot · 2024-10-12T16:22:24Z

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

received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 22850, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)

eessi-build-deploy-bot-deucalion · 2024-10-12T16:22:24Z

Updates by the bot instance boegel-bot-deucalion (click for details)

received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted

eessi-bot · 2024-10-12T16:22:24Z

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

received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted

boegel · 2024-10-12T16:59:15Z

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

eessi-build-deploy-bot-deucalion · 2024-10-12T16:59:18Z

Updates by the bot instance boegel-bot-deucalion (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell from boegel
- 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 boegel
- 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 boegel
- 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 boegel
- 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 boegel
- 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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
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

eessi-bot · 2024-10-12T16:59:18Z

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

received bot command build repo:eessi.io-2023.06-software arch:x86_64/intel/haswell from boegel
- 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 boegel
- 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 boegel
- 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 boegel
- 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 boegel
- 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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/haswell resulted in:
- submitted job 22851, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/intel/skylake_avx512 resulted in:
- submitted job 22852, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen2 resulted in:
- submitted job 22853, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen3 resulted in:
- submitted job 22854, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/generic resulted in:
- submitted job 22855, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1 resulted in:
- submitted job 22856, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)

eessi-bot · 2024-10-12T16:59:18Z

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/haswell from boegel
- 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 boegel
- 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 boegel
- 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 boegel
- 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 boegel
- 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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_n1
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

boegel · 2024-10-12T18:03:37Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2024-10-12T18:03:46Z

New job on instance eessi-bot-mc-aws for CPU micro-architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/22857

date	job status	comment
Oct 12 18:03:45 UTC 2024	submitted	job id `22857` awaits release by job manager
Oct 12 18:04:08 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 12 18:11:11 UTC 2024	running	job `22857` is running
Oct 12 18:31:38 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-22857.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-neoverse_v1-1728757396.tar.gz` size: 69 MiB (72459469 bytes) entries: 1902 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `absl-py/2.1.0-GCCcore-12.3.0.lua` `dm-tree/0.1.8-GCCcore-12.3.0.lua` `HH-suite/3.3.0-gompi-2023a.lua` `Kalign/3.4.0-GCCcore-12.3.0.lua` `ml_dtypes/0.3.2-gfbf-2023a.lua` `OpenMM/8.0.0-foss-2023a.lua` `pytest/7.4.2-GCCcore-12.3.0.lua` `pytest-xdist/3.3.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `absl-py/2.1.0-GCCcore-12.3.0` `dm-tree/0.1.8-GCCcore-12.3.0` `HH-suite/3.3.0-gompi-2023a` `Kalign/3.4.0-GCCcore-12.3.0` `ml_dtypes/0.3.2-gfbf-2023a` `OpenMM/8.0.0-foss-2023a` `pytest/7.4.2-GCCcore-12.3.0` `pytest-xdist/3.3.1-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_v1 `2023.06/init/minimal_eessi_env`
Oct 12 18:31:38 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos /aeb2d9df @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 987.709 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos /04ff9ece @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 952.303 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /31ac6ab9 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.06 us (r:0, l:None, u:None) [ OK ] ( 4/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /f3be40a2 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.2 us (r:0, l:None, u:None) [ OK ] ( 5/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /10e66fba @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 4.7 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /5be57ae7 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 4.36 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /c8c9aff5 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.38 us (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /9795e491 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.37 us (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /48da21c5 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 28640.4 MB/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /1b8c1ca2 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 28622.6 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-22857.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

boegel · 2024-10-13T08:31:16Z

Failure are for jax-0.4.25-gfbf-2023a.eb due to:

Failed to determine installation prefix for binutils (at easybuild/easyblocks/j/jaxlib.py:73 in configure_step)

It seems like we'll need to make that easyblock sysroot-aware...

boegel · 2024-10-14T15:46:26Z

The issue with jaxlib is actually related to the combination of using RPATH + binutils in filter-deps, should be fixed via easybuilders/easybuild-easyblocks#3486...

boegel · 2024-10-14T15:46:39Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2024-10-14T15:46:42Z

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

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- 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/amd/zen4 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 23210, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)

eessi-build-deploy-bot-deucalion · 2024-10-14T15:46:42Z

Updates by the bot instance boegel-bot-deucalion (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- 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/amd/zen4 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 · 2024-10-14T15:46:42Z

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/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- 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/amd/zen4 resulted in:
- submitted job 1493, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted

eessi-bot · 2024-10-14T15:46:47Z

New job on instance eessi-bot-mc-azure for CPU micro-architecture x86_64-amd-zen4 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/1493

date	job status	comment
Oct 14 15:46:45 UTC 2024	submitted	job id `1493` awaits release by job manager
Oct 14 15:46:58 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 14 15:52:02 UTC 2024	running	job `1493` is running
Oct 14 16:01:19 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-1493.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-x86_64-amd-zen4-1728921149.tar.gz` size: 0 MiB (742 bytes) entries: 1 modules under 2023.06/software/linux/x86_64/amd/zen4/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/amd/zen4/software no software packages in tarball other under 2023.06/software/linux/x86_64/amd/zen4 `2023.06/init/minimal_eessi_env`
Oct 14 16:01:19 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos /aeb2d9df @BotBuildTests:x86-64-amd-zen4-node+default P: perf: 1795.515 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos /04ff9ece @BotBuildTests:x86-64-amd-zen4-node+default P: perf: 1786.482 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /31ac6ab9 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 3.52 us (r:0, l:None, u:None) [ OK ] ( 4/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /f3be40a2 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 3.51 us (r:0, l:None, u:None) [ OK ] ( 5/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /10e66fba @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 10.12 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /5be57ae7 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 12.13 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /c8c9aff5 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 0.3 us (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /9795e491 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 0.3 us (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /48da21c5 @BotBuildTests:x86-64-amd-zen4-node+default P: bandwidth: 48800.08 MB/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /1b8c1ca2 @BotBuildTests:x86-64-amd-zen4-node+default P: bandwidth: 49451.34 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-1493.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-10-14T15:46:47Z

New job on instance eessi-bot-mc-aws for CPU micro-architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/23210

date	job status	comment
Oct 14 15:46:46 UTC 2024	submitted	job id `23210` awaits release by job manager
Oct 14 15:47:08 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 14 15:54:11 UTC 2024	running	job `23210` is running
Oct 14 16:02:23 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-23210.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-neoverse_v1-1728921328.tar.gz` size: 0 MiB (742 bytes) entries: 1 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all no module files in tarball software under 2023.06/software/linux/aarch64/neoverse_v1/software no software packages in tarball other under 2023.06/software/linux/aarch64/neoverse_v1 `2023.06/init/minimal_eessi_env`
Oct 14 16:02:23 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos /aeb2d9df @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 985.721 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos /04ff9ece @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 944.461 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /31ac6ab9 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.4 us (r:0, l:None, u:None) [ OK ] ( 4/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /f3be40a2 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.09 us (r:0, l:None, u:None) [ OK ] ( 5/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /10e66fba @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 4.24 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /5be57ae7 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 5.13 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /c8c9aff5 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.38 us (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /9795e491 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.36 us (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /48da21c5 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 28409.44 MB/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /1b8c1ca2 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 27898.98 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-23210.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2024-10-15T08:12:11Z

ERROR: Failed to import easyblock easybuild.easyblocks.generic.easyblock_specific from /tmp/eb-8jhgh9v7/eb-9n3khefk/included-easyblocks-hrubc4ot/easybuild/easyblocks/generic: No module named 'test.easyblocks'

Looks like it cannot use the files from easybuilders/easybuild-easyblocks#3486. I suspect it's because of the test/easyblocks subdirectory/module, which doesn't have an __init__.py when it's downloaded from the PR to a temporary dir?

boegel · 2024-10-16T21:36:57Z

ERROR: Failed to import easyblock easybuild.easyblocks.generic.easyblock_specific from /tmp/eb-8jhgh9v7/eb-9n3khefk/included-easyblocks-hrubc4ot/easybuild/easyblocks/generic: No module named 'test.easyblocks'
Looks like it cannot use the files from easybuilders/easybuild-easyblocks#3486. I suspect it's because of the test/easyblocks subdirectory/module, which doesn't have an __init__.py when it's downloaded from the PR to a temporary dir?

That's essentially a bug in framework, --include-easyblocks-from-* should only pick up actual easyblocks under easybuild/easyblocks, or at the very least ignore stuff under test/easyblocks.

I'll split up easybuilders/easybuild-easyblocks#3486 in two commits, by creating a separate commit for the tests included in there...

boegel · 2024-10-16T21:41:20Z

bot: build repo:eessi.io-2023.06-software arch:aarch64/a64fx
bot: build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2024-10-16T21:41:22Z

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

received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 23627, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)

eessi-build-deploy-bot-deucalion · 2024-10-16T21:41:22Z

Updates by the bot instance boegel-bot-deucalion (click for details)

received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- submitted job 171320, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 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 · 2024-10-16T21:41:23Z

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

received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
received bot command build repo:eessi.io-2023.06-software arch:x86_64/amd/zen4 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:x86_64/amd/zen4 resulted in:
- submitted job 1528, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted

eessi-build-deploy-bot-deucalion · 2024-10-16T21:41:28Z

New job on instance boegel-bot-deucalion for CPU micro-architecture aarch64-a64fx for repository eessi.io-2023.06-software in job dir /home/kehoste/project_dir/bot/jobs/2024.10/pr_785/171320

date	job status	comment
Oct 16 21:41:27 UTC 2024	submitted	job id `171320` awaits release by job manager
Oct 16 21:41:32 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 16 21:42:34 UTC 2024	running	job `171320` is running
Oct 17 02:55:18 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-171320.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-a64fx-1729128722.tar.gz` size: 51 MiB (54215772 bytes) entries: 1284 modules under 2023.06/software/linux/aarch64/a64fx/modules/all `absl-py/2.1.0-GCCcore-12.3.0.lua` `Bazel/6.3.1-GCCcore-12.3.0.lua` `flatbuffers-python/23.5.26-GCCcore-12.3.0.lua` `ml_dtypes/0.3.2-gfbf-2023a.lua` `pytest/7.4.2-GCCcore-12.3.0.lua` `pytest-xdist/3.3.1-GCCcore-12.3.0.lua` `Zip/3.0-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/a64fx/software `absl-py/2.1.0-GCCcore-12.3.0` `Bazel/6.3.1-GCCcore-12.3.0` `flatbuffers-python/23.5.26-GCCcore-12.3.0` `ml_dtypes/0.3.2-gfbf-2023a` `pytest/7.4.2-GCCcore-12.3.0` `pytest-xdist/3.3.1-GCCcore-12.3.0` `Zip/3.0-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/a64fx no other files in tarball
Oct 17 02:55:18 UTC 2024	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite was not run, test step itself failed to execute. Details ✅ job output file `slurm-171320.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-10-16T21:41:28Z

New job on instance eessi-bot-mc-azure for CPU micro-architecture x86_64-amd-zen4 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/1528

date	job status	comment
Oct 16 21:41:27 UTC 2024	submitted	job id `1528` awaits release by job manager
Oct 16 21:42:14 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 16 21:46:18 UTC 2024	running	job `1528` is running
Oct 16 22:51:18 UTC 2024	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-1528.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-zen4-1729118200.tar.gz` size: 169 MiB (178050905 bytes) entries: 5116 modules under 2023.06/software/linux/x86_64/amd/zen4/modules/all `AlphaFold/2.3.2-foss-2023a.lua` `Blosc/1.21.5-GCCcore-12.3.0.lua` `HH-suite/3.3.0-gompi-2023a.lua` `Kalign/3.4.0-GCCcore-12.3.0.lua` `OpenMM/8.0.0-foss-2023a.lua` `Optax/0.2.2-gfbf-2023a.lua` `absl-py/2.1.0-GCCcore-12.3.0.lua` `dm-haiku/0.0.12-foss-2023a.lua` `dm-tree/0.1.8-GCCcore-12.3.0.lua` `jax/0.4.25-gfbf-2023a.lua` `ml_dtypes/0.3.2-gfbf-2023a.lua` `pytest-xdist/3.3.1-GCCcore-12.3.0.lua` `pytest/7.4.2-GCCcore-12.3.0.lua` `tensorstore/0.1.65-foss-2023a.lua` software under 2023.06/software/linux/x86_64/amd/zen4/software `AlphaFold/2.3.2-foss-2023a` `Blosc/1.21.5-GCCcore-12.3.0` `HH-suite/3.3.0-gompi-2023a` `Kalign/3.4.0-GCCcore-12.3.0` `OpenMM/8.0.0-foss-2023a` `Optax/0.2.2-gfbf-2023a` `absl-py/2.1.0-GCCcore-12.3.0` `dm-haiku/0.0.12-foss-2023a` `dm-tree/0.1.8-GCCcore-12.3.0` `jax/0.4.25-gfbf-2023a` `ml_dtypes/0.3.2-gfbf-2023a` `pytest-xdist/3.3.1-GCCcore-12.3.0` `pytest/7.4.2-GCCcore-12.3.0` `tensorstore/0.1.65-foss-2023a` other under 2023.06/software/linux/x86_64/amd/zen4 no other files in tarball
Oct 16 22:51:18 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos /aeb2d9df @BotBuildTests:x86-64-amd-zen4-node+default P: perf: 1805.836 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos /04ff9ece @BotBuildTests:x86-64-amd-zen4-node+default P: perf: 460.877 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /31ac6ab9 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 3.84 us (r:0, l:None, u:None) [ OK ] ( 4/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /f3be40a2 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 3.38 us (r:0, l:None, u:None) [ OK ] ( 5/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /10e66fba @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 10.58 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /5be57ae7 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 10.74 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /c8c9aff5 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 0.29 us (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /9795e491 @BotBuildTests:x86-64-amd-zen4-node+default P: latency: 0.3 us (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /48da21c5 @BotBuildTests:x86-64-amd-zen4-node+default P: bandwidth: 48242.0 MB/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /1b8c1ca2 @BotBuildTests:x86-64-amd-zen4-node+default P: bandwidth: 47207.43 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-1528.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-10-16T21:41:28Z

New job on instance eessi-bot-mc-aws for CPU micro-architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/23627

date	job status	comment
Oct 16 21:41:28 UTC 2024	submitted	job id `23627` awaits release by job manager
Oct 16 21:41:49 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 16 21:46:52 UTC 2024	running	job `23627` is running
Oct 16 22:34:02 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-23627.out` ❌ found message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts No artefacts were created or found.
Oct 16 22:34:02 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos /aeb2d9df @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 983.455 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos /04ff9ece @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 957.016 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /31ac6ab9 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.01 us (r:0, l:None, u:None) [ OK ] ( 4/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /f3be40a2 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 2.91 us (r:0, l:None, u:None) [ OK ] ( 5/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /10e66fba @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 4.5 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /5be57ae7 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 4.52 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /c8c9aff5 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.39 us (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /9795e491 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.39 us (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /48da21c5 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 36473.29 MB/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /1b8c1ca2 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 35894.33 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-23627.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

boegel · 2024-10-17T06:30:26Z

On neoverse_v1, the build failed due to a crash of CernVM-FS:

cvmfs2: /root/deb/wd_src/cvmfs/util/smalloc.h:108: void* smmap(size_t): Assertion `(mem != MAP_FAILED) && "Out Of Memory"' failed.
terminate called after throwing an instance of 'ECvmfsException'
  what():  PANIC: /root/deb/wd_src/cvmfs/monitor.cc : 587
watchdog disappeared, aborting

I think this happened during the build of jax, but it's not immediately obvious from the build log.

…io_AlphaFold-deps

boegel · 2024-10-17T06:32:48Z

bot: build repo:eessi.io-2023.06-software arch:x86_64/generic
bot: build repo:eessi.io-2023.06-software arch:aarch64/a64fx
bot: build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1

eessi-bot · 2024-10-17T06:32:51Z

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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- 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 23804, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/a64fx resulted in:
- no jobs were submitted
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- submitted job 23805, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)

eessi-build-deploy-bot-deucalion · 2024-10-17T06:32:51Z

Updates by the bot instance boegel-bot-deucalion (click for details)

received bot command build repo:eessi.io-2023.06-software arch:x86_64/generic from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- 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:aarch64/a64fx resulted in:
- submitted job 171973, for details & status see {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785 (comment)
handling command build repository:eessi.io-2023.06-software architecture:aarch64/neoverse_v1 resulted in:
- no jobs were submitted

eessi-bot · 2024-10-17T06:32:52Z

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 boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:x86_64/generic
received bot command build repo:eessi.io-2023.06-software arch:aarch64/a64fx from boegel
- expanded format: build repository:eessi.io-2023.06-software architecture:aarch64/a64fx
received bot command build repo:eessi.io-2023.06-software arch:aarch64/neoverse_v1 from boegel
- 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:aarch64/a64fx 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 · 2024-10-17T06:32:56Z

New job on instance eessi-bot-mc-aws for CPU micro-architecture x86_64-generic for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/23804

date	job status	comment
Oct 17 06:32:55 UTC 2024	submitted	job id `23804` awaits release by job manager
Oct 17 06:33:45 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 17 06:40:54 UTC 2024	running	job `23804` is running
Oct 17 13:22:59 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-23804.out` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts No artefacts were created or found.
Oct 17 13:22:59 UTC 2024	test result	😢 FAILURE (click triangle for details) Reason Failed for unknown reason Details ✅ job output file `slurm-23804.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-build-deploy-bot-deucalion · 2024-10-17T06:32:57Z

New job on instance boegel-bot-deucalion for CPU micro-architecture aarch64-a64fx for repository eessi.io-2023.06-software in job dir /home/kehoste/project_dir/bot/jobs/2024.10/pr_785/171973

date	job status	comment
Oct 17 06:32:56 UTC 2024	submitted	job id `171973` awaits release by job manager
Oct 17 06:33:14 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 17 06:34:17 UTC 2024	running	job `171973` is running
Oct 17 10:26:58 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-171973.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-a64fx-1729155849.tar.gz` size: 51 MiB (53788980 bytes) entries: 1285 modules under 2023.06/software/linux/aarch64/a64fx/modules/all `absl-py/2.1.0-GCCcore-12.3.0.lua` `Bazel/6.3.1-GCCcore-12.3.0.lua` `flatbuffers-python/23.5.26-GCCcore-12.3.0.lua` `ml_dtypes/0.3.2-gfbf-2023a.lua` `pytest/7.4.2-GCCcore-12.3.0.lua` `pytest-xdist/3.3.1-GCCcore-12.3.0.lua` `Zip/3.0-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/a64fx/software `absl-py/2.1.0-GCCcore-12.3.0` `Bazel/6.3.1-GCCcore-12.3.0` `flatbuffers-python/23.5.26-GCCcore-12.3.0` `ml_dtypes/0.3.2-gfbf-2023a` `pytest/7.4.2-GCCcore-12.3.0` `pytest-xdist/3.3.1-GCCcore-12.3.0` `Zip/3.0-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/a64fx `2023.06/init/easybuild/eb_hooks.py`
Oct 17 10:26:58 UTC 2024	test result	😢 FAILURE (click triangle for details) Reason EESSI test suite was not run, test step itself failed to execute. Details ✅ job output file `slurm-171973.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot · 2024-10-17T06:33:01Z

New job on instance eessi-bot-mc-aws for CPU micro-architecture aarch64-neoverse_v1 for repository eessi.io-2023.06-software in job dir /project/def-users/SHARED/jobs/2024.10/pr_785/23805

date	job status	comment
Oct 17 06:33:00 UTC 2024	submitted	job id `23805` awaits release by job manager
Oct 17 06:33:43 UTC 2024	released	job awaits launch by Slurm scheduler
Oct 17 06:38:48 UTC 2024	running	job `23805` is running
Oct 17 07:55:28 UTC 2024	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-23805.out` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.gz created!` Artefacts `eessi-2023.06-software-linux-aarch64-neoverse_v1-1729150674.tar.gz` size: 6 MiB (6552951 bytes) entries: 1192 modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all `absl-py/2.1.0-GCCcore-12.3.0.lua` `ml_dtypes/0.3.2-gfbf-2023a.lua` `pytest/7.4.2-GCCcore-12.3.0.lua` `pytest-xdist/3.3.1-GCCcore-12.3.0.lua` software under 2023.06/software/linux/aarch64/neoverse_v1/software `absl-py/2.1.0-GCCcore-12.3.0` `ml_dtypes/0.3.2-gfbf-2023a` `pytest/7.4.2-GCCcore-12.3.0` `pytest-xdist/3.3.1-GCCcore-12.3.0` other under 2023.06/software/linux/aarch64/neoverse_v1 `2023.06/init/easybuild/eb_hooks.py`
Oct 17 07:55:28 UTC 2024	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos /aeb2d9df @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 984.37 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %scale=1_node %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos /04ff9ece @BotBuildTests:aarch64-neoverse-v1-node+default P: perf: 951.47 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /31ac6ab9 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.33 us (r:0, l:None, u:None) [ OK ] ( 4/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_allreduce %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /f3be40a2 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 3.01 us (r:0, l:None, u:None) [ OK ] ( 5/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /10e66fba @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 4.61 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_Micro_Benchmarks_coll %benchmark_info=mpi.collective.osu_alltoall %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /5be57ae7 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 8.44 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /c8c9aff5 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.39 us (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_latency %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /9795e491 @BotBuildTests:aarch64-neoverse-v1-node+default P: latency: 0.38 us (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %device_type=cpu /48da21c5 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 28769.22 MB/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_OSU_Micro_Benchmarks_pt2pt %benchmark_info=mpi.pt2pt.osu_bw %scale=1_node %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %device_type=cpu /1b8c1ca2 @BotBuildTests:aarch64-neoverse-v1-node+default P: bandwidth: 29016.92 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 10/10 test case(s) from 10 check(s) (0 failure(s), 0 skipped, 0 aborted) Details ✅ job output file `slurm-23805.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

{2023.06}[foss/2023a] Kalign 3.4.0, absl-py 2.1.0, dm-tree 0.1.8, HH-…

b1500c7

…suite 3.3.0, pytest-xdist 3.3.1, tensorstore 0.1.65 (AlphaFold dependencies)

boegel added the 2023.06-software.eessi.io 2023.06 version of software.eessi.io label Oct 12, 2024

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{2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only)

8cec803

boegel changed the title ~~{2023.06}[foss/2023a] Kalign 3.4.0, absl-py 2.1.0, dm-tree 0.1.8, HH-suite 3.3.0, pytest-xdist 3.3.1, tensorstore 0.1.65 (AlphaFold dependencies)~~ {2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) Oct 12, 2024

use enhanced jaxlib easyblock for building jax/0.4.25-gfbf-2023a

19d12fc

boegel force-pushed the 2023.06-software.eessi.io_AlphaFold-deps branch from 64af4cb to 19d12fc Compare October 16, 2024 21:39

boegel added 2 commits October 17, 2024 08:31

Merge branch '2023.06-software.eessi.io' into 2023.06-software.eessi.…

020789a

…io_AlphaFold-deps

add jax to list of memory-hungry builds

ad072bc

{2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785

Are you sure you want to change the base?

{2023.06}[foss/2023a] AlphaFold 2.3.2 (CPU-only) #785

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