{2023.06}[2023a] Rebuild LAMMPS 2Aug2023_update2 with proper Sapphire Rapids support #906

bedroge · 2025-02-03T12:59:52Z

The existing version was built for Icelake, as the version of archspec (build dependency of LAMMPS) was too old to detect Sapphire Rapids CPUs. This rebuild uses a newer archspec version and an updated easyblock that contains a mapping for Sapphire Rapids.

I don't think we have to rebuild it for any other architectures, because archspec itself is just a build dependency (it has been added to the stack for all CPU targets in #905), and the easyblock does not seem to contain relevant fixes for other architectures (except for generic builds, but that's already handled in #788).

Note: a build should only be triggered after #905 has been ingested.

eessi-bot · 2025-02-03T12:59:56Z

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

eessi-bot · 2025-02-03T12:59:57Z

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

bedroge · 2025-02-03T18:14:32Z

Archspec 0.2.5 should be available now.

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

eessi-bot · 2025-02-03T18:14:35Z

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/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:
- submitted job 44405, for details & status see {2023.06}[2023a] Rebuild LAMMPS 2Aug2023_update2 with proper Sapphire Rapids support #906 (comment)

eessi-bot · 2025-02-03T18:14:36Z

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

gpu-bot-ugent · 2025-02-03T18:14:36Z

Updates by the bot instance eessi-bot-vsc-ugent (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

eessi-bot · 2025-02-03T18:14:40Z

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/2025.02/pr_906/44405

date	job status	comment
Feb 03 18:14:39 UTC 2025	submitted	job id `44405` awaits release by job manager
Feb 03 18:14:54 UTC 2025	released	job awaits launch by Slurm scheduler
Feb 03 18:20:56 UTC 2025	running	job `44405` is running
Feb 03 19:01:39 UTC 2025	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-44405.out` ✅ no message matching `FATAL:` ❌ 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-x86_64-intel-sapphire_rapids-1738608471.tar.gz` size: 0 MiB (45 bytes) entries: 0 modules under 2023.06/software/linux/x86_64/intel/sapphire_rapids/modules/all no module files in tarball software under 2023.06/software/linux/x86_64/intel/sapphire_rapids/software no software packages in tarball other under 2023.06/software/linux/x86_64/intel/sapphire_rapids no other files in tarball
Feb 03 19:01:39 UTC 2025	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] (1/9) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos %scale=1_node /aeb2d9df @BotBuildTests:x86_64_intel_sapphire_rapids+default P: perf: 567.371 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_sapphire_rapids+default P: latency: 2.03 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_sapphire_rapids+default P: latency: 1.79 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_sapphire_rapids+default P: latency: 4.14 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_sapphire_rapids+default P: latency: 3.96 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_sapphire_rapids+default P: latency: 0.43 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_sapphire_rapids+default P: latency: 0.31 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_sapphire_rapids+default P: bandwidth: 13150.19 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_sapphire_rapids+default P: bandwidth: 12849.92 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-44405.out` ❌ found message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

bedroge · 2025-02-03T19:21:20Z

== Determined cpu arch: SPR
== Using Kokkos package with arch: CPU - SPR, GPU - None

The build went fine, but this failed due to the issue solved by #907.

bedroge · 2025-02-03T20:22:28Z

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

eessi-bot · 2025-02-03T20:22:30Z

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/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:
- submitted job 44406, for details & status see {2023.06}[2023a] Rebuild LAMMPS 2Aug2023_update2 with proper Sapphire Rapids support #906 (comment)

eessi-bot · 2025-02-03T20:22:31Z

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

gpu-bot-ugent · 2025-02-03T20:22:31Z

Updates by the bot instance eessi-bot-vsc-ugent (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

eessi-bot · 2025-02-03T20:22:34Z

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/2025.02/pr_906/44406

date	job status	comment
Feb 03 20:22:33 UTC 2025	submitted	job id `44406` awaits release by job manager
Feb 03 20:22:48 UTC 2025	released	job awaits launch by Slurm scheduler
Feb 03 20:28:50 UTC 2025	running	job `44406` is running
Feb 03 21:10:33 UTC 2025	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-44406.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-1738616267.tar.gz` size: 154 MiB (162484499 bytes) entries: 4461 modules under 2023.06/software/linux/x86_64/intel/sapphire_rapids/modules/all `LAMMPS/2Aug2023_update2-foss-2023a-kokkos.lua` software under 2023.06/software/linux/x86_64/intel/sapphire_rapids/software `LAMMPS/2Aug2023_update2-foss-2023a-kokkos` other under 2023.06/software/linux/x86_64/intel/sapphire_rapids no other files in tarball
Feb 03 21:10:33 UTC 2025	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ OK ] ( 1/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos %scale=1_node /aeb2d9df @BotBuildTests:x86_64_intel_sapphire_rapids+default P: perf: 605.648 timesteps/s (r:0, l:None, u:None) [ OK ] ( 2/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:x86_64_intel_sapphire_rapids+default P: perf: 650.17 timesteps/s (r:0, l:None, u:None) [ OK ] ( 3/10) 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_sapphire_rapids+default P: latency: 1.99 us (r:0, l:None, u:None) [ OK ] ( 4/10) 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_sapphire_rapids+default P: latency: 1.86 us (r:0, l:None, u:None) [ OK ] ( 5/10) 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_sapphire_rapids+default P: latency: 3.83 us (r:0, l:None, u:None) [ OK ] ( 6/10) 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_sapphire_rapids+default P: latency: 3.92 us (r:0, l:None, u:None) [ OK ] ( 7/10) 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_sapphire_rapids+default P: latency: 0.38 us (r:0, l:None, u:None) [ OK ] ( 8/10) 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_sapphire_rapids+default P: latency: 0.36 us (r:0, l:None, u:None) [ OK ] ( 9/10) 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_sapphire_rapids+default P: bandwidth: 13403.23 MB/s (r:0, l:None, u:None) [ OK ] (10/10) 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_sapphire_rapids+default P: bandwidth: 13201.82 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-44406.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`
Feb 04 15:19:32 UTC 2025	uploaded	transfer of `eessi-2023.06-software-linux-x86_64-intel-sapphire_rapids-1738616267.tar.gz` to S3 bucket succeeded

casparvl · 2025-02-04T15:19:01Z

== Using Kokkos package with arch: CPU - SPR, GPU - None

from the build logs of 44406. LGTM!

bedroge · 2025-02-04T15:51:25Z

In order to clean up leftovers from the old installations (for both this PR and #788), I've run the following:

#!/bin/bash
cvmfs_server transaction software.eessi.io

rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/generic/software/LAMMPS/29Aug2024-foss-2023b-kokkos
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/generic/software/LAMMPS/2Aug2023_update2-foss-2023a-kokkos
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/LAMMPS/29Aug2024-foss-2023b-kokkos
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/generic/software/LAMMPS/2Aug2023_update2-foss-2023a-kokkos
rm -rf /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/sapphire_rapids/software/LAMMPS/2Aug2023_update2-foss-2023a-kokkos

cd /cvmfs/software.eessi.io/versions

tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-aarch64-generic-1738597602.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-generic-1738597887.tar.gz
tar -xzf /srv/tmp/tarballs/eessi-2023.06-software-linux-x86_64-intel-sapphire_rapids-1738616267.tar.gz

cd

cvmfs_server diff --worktree software.eessi.io > PR788and906-diff.txt
cvmfs_server publish -m "rebuilds of LAMMPS for */generic and sapphirerapids, PR 788 and 906" software.eessi.io

eessi-bot · 2025-02-04T16:46:08Z

PR merged! Moved ['/project/def-users/SHARED/jobs/2025.02/pr_906/44405', '/project/def-users/SHARED/jobs/2025.02/pr_906/44406'] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.02.04

eessi-bot · 2025-02-04T16:46:09Z

PR merged! Moved [] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.02.04

gpu-bot-ugent · 2025-02-04T16:46:09Z

PR merged! Moved [] to /scratch/gent/vo/002/gvo00211/SHARED/trash_bin/EESSI/software-layer/2025.02.04

easystack for rebuilding LAMMPS 2Aug2023 (for Sapphire Rapids)

5be1e03

bedroge added 2023.06-software.eessi.io 2023.06 version of software.eessi.io sapphirerapids labels Feb 3, 2025

bedroge added the ready-to-deploy Mark a PR as ready to deploy label Feb 3, 2025

casparvl 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 Feb 4, 2025

bedroge mentioned this pull request Feb 4, 2025

Rebuild LAMMPS for */generic targets to make sure that CPU-specific optimizations are disabled #788

Merged

casparvl approved these changes Feb 4, 2025

View reviewed changes

casparvl merged commit 224e170 into EESSI:2023.06-software.eessi.io Feb 4, 2025
49 checks passed

bedroge deleted the lammps_2Aug2023_sapphire_rapids_rebuild branch February 4, 2025 17:00

trz42 mentioned this pull request Mar 31, 2025

{2023.06}[2023a,grace] Apps from EB 4.9.0 2023a easystack #990

Merged

{2023.06}[2023a] Rebuild LAMMPS 2Aug2023_update2 with proper Sapphire Rapids support #906

{2023.06}[2023a] Rebuild LAMMPS 2Aug2023_update2 with proper Sapphire Rapids support #906

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