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{2023.06}[system,a64fx] circumvent fusemount issue, improve module use, and add some packages #1025

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Merged
merged 4 commits into from
Apr 14, 2025
Merged

{2023.06}[system,a64fx] circumvent fusemount issue, improve module use, and add some packages #1025

merged 4 commits into from
Apr 14, 2025

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trz42
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@trz42 trz42 commented Apr 12, 2025 •
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This PR provides three things:

  1. Solves the issue that the build container could not fusemount software.eessi.io
  2. Solves the issue that $EASYBUILD_INSTALLPATH got reset by some module use ... statement (just before creating/updating Lmod configuration files)
  3. Adds a few basic packages installed with the toolchain system.

Fusemount issue

Hit a strange issue on Deucalion. The CernVM-FS repository for software.eessi.io could not be mounted. It resulted in the error

CernVM-FS: loading Fuse module... Failed to initialize root file catalog (16 - file catalog failure)

When the mounting of cvmfs-config.cern.ch was disabled, it worked again. Also multiple eessi.io repositories could be mounted.

This PR opens the possibility to not mount cvmfs-config.cern.ch when the environment variable $EESSI_DO_NOT_MOUNT_CVMFS_CONFIG_CERN_CH is set. Setting this variable can be done in a site script (see app.cfg setting site_config_script).

Empty $EASYBUILD_INSTALLPATH issue

For details see comments #1025 (comment) and #1025 (comment)

Adds the following packages

EasyBuild/4.8.2
EasyBuild/4.9.0
EasyBuild/4.9.1
EasyBuild/5.0.0
EESSI-extend/2023.06-easybuild
Nextflow/23.10.0
Pandoc/3.6.2
ReFrame/4.3.3
ReFrame/4.6.2

@trz42 trz42 added bug Something isn't working enhancement New feature or request labels Apr 12, 2025
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Instance eessi-bot-mc-aws is configured to build for:

  • architectures: x86_64/generic, x86_64/intel/haswell, x86_64/intel/sapphirerapids, 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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Instance eessi-bot-mc-azure is configured to build for:

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

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

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

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Instance eessi-bot-surf is configured to build for:

  • architectures: x86_64/amd/zen4, x86_64/amd/zen2
  • repositories: eessi-hpc.org-2023.06-software, eessi.io-2023.06-software, eessi.io-2023.06-compat, eessi-hpc.org-2023.06-compat

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Instance rt-Grace-jr is configured to build for:

  • architectures: aarch64/nvidia/grace
  • repositories: eessi.io-2023.06-software

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Instance trz42-GH200-jr is configured to build for:

  • architectures: aarch64/nvidia/grace
  • repositories: eessi.io-2023.06-software

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trz42 commented Apr 12, 2025

Try building on Deucalion...
bot: build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx

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    • expanded format: build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx

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    • expanded format: build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx

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eessi-bot-deucalion bot commented Apr 12, 2025 •
edited by trz42
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New job on instance eessi-bot-deucalion for CPU micro-architecture aarch64-a64fx for repository eessi.io-2023.06-software in job dir /home/eessibot/new-bot/jobs/2025.04/pr_1025/401954

  • failed with 
    >> Creating/updating Lmod RC file (/.lmod/lmodrc.lua)...
ERROR: Usage: /projects/I20240007/new-bot/jobs/2025.04/pr_1025/event_898fed30-17f6-11f0-97d0-728236bf62d2/run_000/linux_aarch64_a64fx/eessi.io-2023.06-software/create_lmodrc.py <software prefix>
ESC[31mERROR: Failed to create /.lmod/lmodrc.luaESC[0m
    it looks like some prefix is missing, possibly an environment variable is not set
  • it should use $EASYBUILD_INSTALLPATH as prefix. this is set correctly earlier in the build job, but later it seems empty.
  • will add some print/echo statements to debug the issue
date job status comment
Apr 12 23:33:35 UTC 2025 submitted job id 401954 awaits release by job manager
Apr 12 23:34:12 UTC 2025 released job awaits launch by Slurm scheduler
Apr 12 23:35:15 UTC 2025 running job 401954 is running
Apr 13 00:38:49 UTC 2025 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-401954.out
✅ no message matching FATAL:
❌ found 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-a64fx-1744504620.tar.gzsize: 35 MiB (37651014 bytes)
entries: 17121
modules under 2023.06/software/linux/aarch64/a64fx/modules/all
EasyBuild/5.0.0.lua
EESSI-extend/2023.06-easybuild.lua
software under 2023.06/software/linux/aarch64/a64fx/software
EasyBuild/5.0.0
EESSI-extend/2023.06-easybuild
other under 2023.06/software/linux/aarch64/a64fx
no other files in tarball
Apr 13 00:38:49 UTC 2025 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-401954.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@trz42 trz42 added the a64fx label Apr 12, 2025
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trz42 commented Apr 13, 2025

Repeat building with more information about environment variable values...
bot: build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx

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  • received bot command build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx from trz42

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New job on instance eessi-bot-deucalion for CPU micro-architecture aarch64-a64fx for repository eessi.io-2023.06-software in job dir /home/eessibot/new-bot/jobs/2025.04/pr_1025/402047

  • considering the log output 
    >> Using /home/eessibot/new-bot/shared/easybuild/sources as shared EasyBuild source path
DEBUG: adding path '/cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/a64fx/modules/all' to MODULEPATH='/cvmfs/software.eessi.io/host_injections/2023.06/software/linux/aarch64/a64fx/modules/all:/cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/a64fx/modules/all:/projects/I20240007/new-bot/jobs/2025.04/pr_1025/event_bf471780-186b-11f0-9f5c-55b2242e7e7d/run_000/linux_aarch64_a64fx/eessi.io-2023.06-software/init/modules'

Inactive Modules:
  1) EESSI-extend/2023.06-easybuild     2) EasyBuild/5.0.0

DEBUG: after adding module path // MODULEPATH='/cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/a64fx/modules/all:/cvmfs/software.eessi.io/host_injections/2023.06/software/linux/aarch64/a64fx/modules/all:/projects/I20240007/new-bot/jobs/2025.04/pr_1025/event_bf471780-186b-11f0-9f5c-55b2242e7e7d/run_000/linux_aarch64_a64fx/eessi.io-2023.06-software/init/modules'
>> MODULEPATH set up: /cvmfs/software.eessi.io/versions/2023.06/software/linux/aarch64/a64fx/modules/all:/cvmfs/software.eessi.io/host_injectios/2023.06/software/linux/aarch64/a64fx/modules/all:/projects/I20240007/new-bot/jobs/2025.04/pr_1025/event_bf471780-186b-11f0-9f5c-55b2242e7e7d/run_000/linux_aarch64_a64fx/eessi.io-2023.06-software/init/modules
No missing installations, party time!
DEBUG: before creating/updating lmod config files // EASYBUILD_INSTALLPATH=''
DEBUG: lmod_rc_file='/.lmod/lmodrc.lua'
    it looks like the problem is caused by the statement 
    module use $EASYBUILD_INSTALLPATH/modules/all
    possibly because that directory is already in $MODULEPATH or because the modules EESSI-extend/2023.06-easybuild and EasyBuild/5.0.0 are provided through this directory and then deactivated which leads to environment variables such as $EASYBUILD_INSTALLPATH being unset
  • we should check if the directory $EASYBUILD_INSTALLPATH/modules/all is already in $MODULEPATH, and only add it if it isn't
date job status comment
Apr 13 13:32:36 UTC 2025 submitted job id 402047 awaits release by job manager
Apr 13 13:33:25 UTC 2025 released job awaits launch by Slurm scheduler
Apr 13 13:34:28 UTC 2025 running job 402047 is running
Apr 13 13:46:45 UTC 2025 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-402047.out
✅ no message matching FATAL:
❌ found 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-a64fx-1744551878.tar.gzsize: 35 MiB (37648275 bytes)
entries: 17121
modules under 2023.06/software/linux/aarch64/a64fx/modules/all
EasyBuild/5.0.0.lua
EESSI-extend/2023.06-easybuild.lua
software under 2023.06/software/linux/aarch64/a64fx/software
EasyBuild/5.0.0
EESSI-extend/2023.06-easybuild
other under 2023.06/software/linux/aarch64/a64fx
no other files in tarball
Apr 13 13:46:45 UTC 2025 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-402047.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

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bot: build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx

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New job on instance eessi-bot-deucalion for CPU micro-architecture aarch64-a64fx for repository eessi.io-2023.06-software in job dir /home/eessibot/new-bot/jobs/2025.04/pr_1025/402102

  • still not happy (although the config file was there; not fully clear what the problem could be) 
    ESC[31mERROR: Please put a ReFrame configuration file in /home/eessibot/new-bot/shared/reframe_config.py or set RFM_CONFIG_FILES in the environment of this bot instance to point to a valid ReFrame configuration file that matches the bot config. For more information, see https://gitlab.com/eessi/support/-/issues/114#note_2293660921ESC[0m
  • maybe we cannot use a symlink? 
        export RFM_CONFIG_FILES="${shared_fs_path}/reframe_config.py"
    if [ ! -f "${RFM_CONFIG_FILES}" ]; then
date job status comment
Apr 13 16:01:30 UTC 2025 submitted job id 402102 awaits release by job manager
Apr 13 16:02:06 UTC 2025 released job awaits launch by Slurm scheduler
Apr 13 16:03:09 UTC 2025 running job 402102 is running
Apr 13 16:44:30 UTC 2025 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-402102.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-aarch64-a64fx-1744562395.tar.gzsize: 381 MiB (399560517 bytes)
entries: 130356
modules under 2023.06/software/linux/aarch64/a64fx/modules/all
EasyBuild/4.8.2.lua
EasyBuild/4.9.0.lua
EasyBuild/4.9.1.lua
EasyBuild/5.0.0.lua
EESSI-extend/2023.06-easybuild.lua
Nextflow/23.10.0.lua
Pandoc/3.6.2.lua
ReFrame/4.3.3.lua
ReFrame/4.6.2.lua
software under 2023.06/software/linux/aarch64/a64fx/software
EasyBuild/4.8.2
EasyBuild/4.9.0
EasyBuild/4.9.1
EasyBuild/5.0.0
EESSI-extend/2023.06-easybuild
Nextflow/23.10.0
Pandoc/3.6.2
ReFrame/4.3.3
ReFrame/4.6.2
other under 2023.06/software/linux/aarch64/a64fx
no other files in tarball
Apr 13 16:44:30 UTC 2025 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-402102.out
❌ found message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case

@trz42 trz42 changed the title allow to not always mount cvmfs-config.cern.ch {2023.06}[system,a64fx] allow to not always mount cvmfs-config.cern.ch, add some packages too Apr 13, 2025
@trz42 trz42 changed the title {2023.06}[system,a64fx] allow to not always mount cvmfs-config.cern.ch, add some packages too {2023.06}[system,a64fx] circumvent fusemount issue, improve module use, and add some packages Apr 13, 2025
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trz42 commented Apr 13, 2025

Retry after creating a physical copy of reframe_config.py in the correct directory...
bot: build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx

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  • received bot command build instance:eessi-bot-deucalion repository:eessi.io-2023.06-software architecture:aarch64/a64fx from trz42

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eessi-bot-deucalion bot commented Apr 13, 2025 •
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New job on instance eessi-bot-deucalion for CPU micro-architecture aarch64-a64fx for repository eessi.io-2023.06-software in job dir /home/eessibot/new-bot/jobs/2025.04/pr_1025/402140

date job status comment
Apr 13 17:33:58 UTC 2025 submitted job id 402140 awaits release by job manager
Apr 13 17:34:47 UTC 2025 released job awaits launch by Slurm scheduler
Apr 13 17:35:50 UTC 2025 running job 402140 is running
Apr 13 18:20:17 UTC 2025 finished
😁 SUCCESS (click triangle for details)
Details
✅ job output file slurm-402140.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-aarch64-a64fx-1744567920.tar.gzsize: 381 MiB (399574884 bytes)
entries: 130356
modules under 2023.06/software/linux/aarch64/a64fx/modules/all
EasyBuild/4.8.2.lua
EasyBuild/4.9.0.lua
EasyBuild/4.9.1.lua
EasyBuild/5.0.0.lua
EESSI-extend/2023.06-easybuild.lua
Nextflow/23.10.0.lua
Pandoc/3.6.2.lua
ReFrame/4.3.3.lua
ReFrame/4.6.2.lua
software under 2023.06/software/linux/aarch64/a64fx/software
EasyBuild/4.8.2
EasyBuild/4.9.0
EasyBuild/4.9.1
EasyBuild/5.0.0
EESSI-extend/2023.06-easybuild
Nextflow/23.10.0
Pandoc/3.6.2
ReFrame/4.3.3
ReFrame/4.6.2
other under 2023.06/software/linux/aarch64/a64fx
no other files in tarball
Apr 13 18:20:17 UTC 2025 test result
😁 SUCCESS (click triangle for details)
ReFrame Summary
[ OK ] (1/1) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:aarch64_a64fx+default
P: perf: 581.44 timesteps/s (r:0, l:None, u:None)
[ PASSED ] Ran 1/1 test case(s) from 1 check(s) (0 failure(s), 0 skipped, 0 aborted)
Details
✅ job output file slurm-402140.out
✅ no message matching ERROR:
✅ no message matching [\s*FAILED\s*].*Ran .* test case
Apr 14 08:49:37 UTC 2025 uploaded transfer of eessi-2023.06-software-linux-aarch64-a64fx-1744567920.tar.gz to S3 bucket succeeded

@trz42 trz42 added ready-to-deploy Mark a PR as ready to deploy ready-to-review labels Apr 13, 2025
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lgtm, the changes have been validated on an alternative system and fulfill the intended purpose.

@trz42 trz42 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 Apr 14, 2025
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trz42 commented Apr 14, 2025

Tarball ingested and available via /cvmfs

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trz42 commented Apr 14, 2025

Waiting for rerun of CI.

@trz42 trz42 merged commit 772149b into EESSI:2023.06-software.eessi.io Apr 14, 2025
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eessi-bot bot commented Apr 14, 2025

PR merged! Moved [] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.04.14

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PR merged! Moved ['/home/eessibot/new-bot/jobs/2025.04/pr_1025/402073', '/home/eessibot/new-bot/jobs/2025.04/pr_1025/402102', '/home/eessibot/new-bot/jobs/2025.04/pr_1025/402068', '/home/eessibot/new-bot/jobs/2025.04/pr_1025/401954', '/home/eessibot/new-bot/jobs/2025.04/pr_1025/402047', '/home/eessibot/new-bot/jobs/2025.04/pr_1025/402140'] to /home/eessibot/new-bot/trash-bin/EESSI/software-layer/2025.04.14

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eessi-bot bot commented Apr 14, 2025

PR merged! Moved [] to /project/def-users/SHARED/trash_bin/EESSI/software-layer/2025.04.14

Neves-P added a commit to Neves-P/software-layer that referenced this pull request Apr 14, 2025
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Squashed commit of the following:
47831da 
commit 772149b
Merge: f8d73f1 f5f4595
Author: Thomas Röblitz <[email protected]>
Date:   Mon Apr 14 12:18:03 2025 +0200

    Merge pull request EESSI#1025 from trz42/allow_to_not_mount_cvmfs-config.cern.ch

    {2023.06}[system,a64fx] circumvent fusemount issue, improve module use, and add some packages

commit f8d73f1
Merge: e421525 e64207f
Author: Thomas Röblitz <[email protected]>
Date:   Mon Apr 14 09:56:02 2025 +0200

    Merge pull request EESSI#1013 from trz42/2023.06-grace-2022b-eb490-apps

    {2023.06}[2022b,grace] apps originally built with EB 4.9.0

commit e64207f
Merge: 4151b6b e421525
Author: Thomas Roeblitz <[email protected]>
Date:   Sun Apr 13 20:56:39 2025 +0200

    Merge branch '2023.06-software.eessi.io' of github-trz:EESSI/software-layer into 2023.06-grace-2022b-eb490-apps

commit f5f4595
Author: Thomas Roeblitz <[email protected]>
Date:   Sun Apr 13 17:05:55 2025 +0200

    add EB versions, ReFrame, NextFlow and Pandoc

commit fd62084
Author: Thomas Roeblitz <[email protected]>
Date:   Sun Apr 13 16:43:30 2025 +0200

    only add directory to MODULEPATH if it is not yet included

commit c1ab568
Author: Thomas Roeblitz <[email protected]>
Date:   Sun Apr 13 15:29:40 2025 +0200

    add a few echo statements to debug missing prefix

commit afebf4c
Author: Thomas Roeblitz <[email protected]>
Date:   Sun Apr 13 01:23:08 2025 +0200

    allow to not always mount cvmfs-config.cern.ch

commit e421525
Merge: a96d759 63c27f8
Author: Thomas Röblitz <[email protected]>
Date:   Sun Apr 13 00:21:25 2025 +0200

    Merge pull request EESSI#1022 from trz42/add_lmod_hook_for_scipy_bundle_grace

    add Lmod hook that prints warning for SciPy-bundle on NVIDIA Grace

commit 63c27f8
Author: Thomas Roeblitz <[email protected]>
Date:   Sat Apr 12 18:30:46 2025 +0200

    use --contain when launching container for test step

commit 2cb94cb
Author: Thomas Roeblitz <[email protected]>
Date:   Sat Apr 12 16:26:57 2025 +0200

    need to escape line returns

commit 38a74b9
Author: Thomas Roeblitz <[email protected]>
Date:   Sat Apr 12 15:45:26 2025 +0200

    add Lmod hook that prints warning for SciPy-bundle on Grace/Hopper

commit a96d759
Merge: be88499 8b2c7c3
Author: Bob Dröge <[email protected]>
Date:   Fri Apr 11 14:32:04 2025 +0200

    Merge pull request EESSI#1021 from TopRichard/eessi-2023.06-grace--add-known-issues-for-2023a

    {2023.06}[2023a,grace] Register known issues for 2023a on NVIDIA/Grace

commit be88499
Merge: cebb355 6de46da
Author: Bob Dröge <[email protected]>
Date:   Fri Apr 11 12:30:16 2025 +0200

    Merge pull request EESSI#1020 from TopRichard/eessi-2023.06-grace-apps-rebuild-Siesta-5.2.2-foss-2023a

    {2023.06}[2023a,grace] Rebuild Siesta/5.2.2 in 2023a easystack

commit cebb355
Merge: 56f930b 080b226
Author: Bob Dröge <[email protected]>
Date:   Fri Apr 11 11:17:04 2025 +0200

    Merge pull request EESSI#1019 from ocaisa/rebuild_siesta

    {2023.06}[foss/2023a] Rebuild Siesta 5.2.2, EasyBuild 5.0.0

commit 8b2c7c3
Author: Richard Top <[email protected]>
Date:   Fri Apr 11 08:45:49 2025 +0000

    {2023.06}[2023a,grace] Register known issues for 2023a on NVIDIA/Grace

commit 6de46da
Merge: d8aa15b 56f930b
Author: Richard Top <[email protected]>
Date:   Fri Apr 11 05:38:14 2025 +0000

    Merge branch '2023.06-software.eessi.io' of ssh://github.com/EESSI/software-layer into eessi-2023.06-grace-apps-rebuild-Siesta-5.2.2-foss-2023a

commit 56f930b
Merge: 409f54e 30bb3c6
Author: TopRichard <[email protected]>
Date:   Fri Apr 11 07:38:00 2025 +0200

    Merge pull request EESSI#1018 from TopRichard/eessi-2023.06-grace-apps-EB-4.9.4-sync-with-EESSI-stack

    {2023.06}[2023a,grace] sync with EESSI EB 4.9.4 easystack

commit 409f54e
Merge: 6b87519 95dd24a
Author: Thomas Röblitz <[email protected]>
Date:   Fri Apr 11 06:42:07 2025 +0200

    Merge pull request EESSI#999 from trz42/2023.06-grace-hopper-eb494-2023b-GROMACS-CUDA

    {2023.06}[2023b,grace,CUDA] GROMACS 2024.4 with CUDA 12.4.0

commit 080b226
Author: Alan O'Cais <[email protected]>
Date:   Thu Apr 10 21:25:49 2025 +0200

    Be more careful with the filename

commit 66e616d
Author: ocaisa <[email protected]>
Date:   Thu Apr 10 18:51:49 2025 +0200

    Update 20250410-eb-5.0.0-siesta-rebuild-eb-controlled-optimisations.yml

commit d8aa15b
Author: Richard Top <[email protected]>
Date:   Thu Apr 10 14:43:53 2025 +0000

    {2023.06}[2023a,grace] rebuild Siesta/5.2.2 in 2023a easystack

commit c6f11cd
Author: Alan O'Cais <[email protected]>
Date:   Thu Apr 10 14:58:07 2025 +0200

    {2023.06}[foss/2023a] Rebuild Siesta 5.2.2, EasyBuild 5.0.0

commit 30bb3c6
Author: Richard Top <[email protected]>
Date:   Thu Apr 10 10:03:13 2025 +0000

    {2023.06}[2023a,grace] sync with EESSI easystack EB 4.9.4

commit 6b87519
Merge: 4623765 a4fd2a8
Author: TopRichard <[email protected]>
Date:   Thu Apr 10 12:01:03 2025 +0200

    Merge pull request EESSI#1017 from TopRichard/eessi-2023.06-grace-apps-Siesta-5.2.2-foss-2023a

    {2023.06}[2023a,grace] add Siesta/5.2.2 in 2023a easystack

commit 4623765
Merge: 28cea37 1a41987
Author: Thomas Röblitz <[email protected]>
Date:   Thu Apr 10 11:54:43 2025 +0200

    Merge pull request EESSI#994 from casparvl/add_zstd_support_to_build_pipeline

    Add zstd support for faster tarball creation or extraction in eessi_container.sh

commit a4fd2a8
Author: Richard Top <[email protected]>
Date:   Thu Apr 10 07:26:59 2025 +0000

    {2023.06}[2023a,grace] add Siesta/5.2.2 in 2023a easystack

commit 28cea37
Merge: fad5fe7 101472d
Author: TopRichard <[email protected]>
Date:   Thu Apr 10 09:22:58 2025 +0200

    Merge pull request EESSI#1012 from TopRichard/eessi-2023.06-grace-2023a-cuda-apps

    {2023.06}[2023a,CUDA,grace] CUDA/12.1.1, cuDNN/8.9.2.26, CUDA-Samples/12.1 + apps with CUDA

commit 101472d
Merge: 4a32cbc fad5fe7
Author: Richard Top <[email protected]>
Date:   Wed Apr 9 08:41:09 2025 +0000

    Merge branch '2023.06-software.eessi.io' of ssh://github.com/EESSI/software-layer into eessi-2023.06-grace-2023a-cuda-apps

commit fad5fe7
Merge: c5a696a 79d0ea8
Author: TopRichard <[email protected]>
Date:   Wed Apr 9 10:40:52 2025 +0200

    Merge pull request EESSI#1016 from TopRichard/eessi-2023.06-grace-apps-Perl-bundle-CPAN-5.36.1

    {2023.06}[2023a,grace] add Perl-bundle-CPAN/5.36.1 in 2023a easystack

commit 79d0ea8
Author: Richard Top <[email protected]>
Date:   Wed Apr 9 06:11:47 2025 +0000

    added eessi-2023.06-eb-4.9.2-2023a.yml for Perl-bundle-CPAN

commit a52fdd5
Author: Richard Top <[email protected]>
Date:   Wed Apr 9 05:30:09 2025 +0000

    {2023.06}[2023a,grace] add Perl-bundle-CPAN/5.36.1 in 2023a easystack

commit c5a696a
Merge: 2d91c3e 07605ed
Author: Bob Dröge <[email protected]>
Date:   Tue Apr 8 23:10:34 2025 +0200

    Merge pull request EESSI#1015 from TopRichard/eessi-2023.06-grace-apps-GDRCopy-2.3.1-GCCcore-12.3.0

    {2023.06}[2023a,grace] add GDRCopy/2.3.1 in 2023a easystack

commit 4a32cbc
Author: Richard Top <[email protected]>
Date:   Tue Apr 8 18:00:07 2025 +0000

    added NCCL-2.18.3-GCCcore-12.3.0

commit 4151b6b
Author: Thomas Roeblitz <[email protected]>
Date:   Tue Apr 8 19:18:50 2025 +0200

    tolerate failing tests for SciPy-bundle-2023.02 on NVIDIA Grace

commit 07605ed
Author: Richard Top <[email protected]>
Date:   Tue Apr 8 17:18:27 2025 +0000

    {2023.06}[2023a,grace] add GDRCopy/2.3.1 in 2023a easystack

commit 31a0221
Author: Richard Top <[email protected]>
Date:   Tue Apr 8 17:13:13 2025 +0000

    skipping LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb for now

commit e476faf
Author: Thomas Roeblitz <[email protected]>
Date:   Tue Apr 8 17:28:52 2025 +0200

    skip some tests building Highway/1.0.3 on NVIDIA Grace

commit 926aa43
Merge: 9818b0f 2d91c3e
Author: Thomas Roeblitz <[email protected]>
Date:   Tue Apr 8 17:06:25 2025 +0200

    Merge branch '2023.06-software.eessi.io' of github-trz:EESSI/software-layer into 2023.06-grace-2022b-eb490-apps

commit e6aa008
Author: Richard Top <[email protected]>
Date:   Tue Apr 8 11:32:17 2025 +0000

    added missing UCX+UCC with CUDA

commit 95dd24a
Author: Thomas Roeblitz <[email protected]>
Date:   Tue Apr 8 13:14:04 2025 +0200

    avoid using SVE instructions for GROMACS 2024.4 on NVIDIA Grace/Hopper

commit f06d063
Merge: 4ade001 2d91c3e
Author: Thomas Roeblitz <[email protected]>
Date:   Tue Apr 8 13:09:28 2025 +0200

    Merge branch '2023.06-software.eessi.io' of github-trz:EESSI/software-layer into 2023.06-grace-hopper-eb494-2023b-GROMACS-CUDA

commit 9818b0f
Author: Thomas Roeblitz <[email protected]>
Date:   Tue Apr 8 12:36:29 2025 +0200

    {2023.06}[2022b,grace] apps originally built with EB 4.9.0

commit 3445814
Author: Richard Top <[email protected]>
Date:   Tue Apr 8 10:07:10 2025 +0000

    {2023.06}[2023a,CUDA,grace] CUDA/12.1.1, cuDNN/8.9.2.26, related apps with CUDA

commit 2d91c3e
Merge: 38a3a65 cbaeec8
Author: Bob Dröge <[email protected]>
Date:   Tue Apr 8 11:26:43 2025 +0200

    Merge pull request EESSI#1006 from TopRichard/eessi-2023.06-grace-apps-from-EB-4.9.4-easystack

    {2023.06}[2023a,grace] Apps from EB 4.9.4 2023a easystack

commit 38a3a65
Merge: 87d2ae3 df7a37d
Author: Thomas Röblitz <[email protected]>
Date:   Tue Apr 8 10:30:28 2025 +0200

    Merge pull request EESSI#1008 from trz42/2023.06-grace-2022b-eb482-remaining-apps-2

    {2023.06}[2022b,grace] QuantumESPRESSO 7.2

commit 87d2ae3
Merge: 0aa79c1 b442f44
Author: Thomas Röblitz <[email protected]>
Date:   Mon Apr 7 21:21:57 2025 +0200

    Merge pull request EESSI#966 from ocaisa/siesta

    {2023.06}[foss/2023a] Siesta 5.2.2, EasyBuild 5.0.0

commit cbaeec8
Merge: df9d86c 0aa79c1
Author: Richard Top <[email protected]>
Date:   Mon Apr 7 17:28:04 2025 +0000

    Merge branch '2023.06-software.eessi.io' of ssh://github.com/EESSI/software-layer into eessi-2023.06-grace-apps-from-EB-4.9.4-easystack

commit 0aa79c1
Merge: 3d3f302 0aea260
Author: TopRichard <[email protected]>
Date:   Mon Apr 7 19:25:26 2025 +0200

    Merge pull request EESSI#1007 from TopRichard/eessi-2023.06-grace-apps-rebuild-R-bundle-Bioconductor

    {2023.06}[2023a,grace] rebuild R-bundle-Bioconductor-3.18 in 2023a easystack

commit df7a37d
Author: Thomas Roeblitz <[email protected]>
Date:   Mon Apr 7 18:39:53 2025 +0200

    keep building QE with EB 4.8.2

commit e68af27
Author: Thomas Roeblitz <[email protected]>
Date:   Mon Apr 7 14:52:30 2025 +0200

    move building QE from EB 4.8.2 to EB 4.9.4

commit 24b6a3c
Author: Thomas Roeblitz <[email protected]>
Date:   Mon Apr 7 12:44:06 2025 +0200

    {2023.06}[2022b,grace] QuantumESPRESSO 7.2

commit 3d3f302
Merge: aa6b42d bb66a0f
Author: Thomas Röblitz <[email protected]>
Date:   Mon Apr 7 12:40:58 2025 +0200

    Merge pull request EESSI#1005 from trz42/2023.06-grace-2022b-eb482-remaining-apps

    {2023.06}[2022b,grace] Qt5 5.15.7

commit 0aea260
Author: Richard Top <[email protected]>
Date:   Mon Apr 7 07:44:26 2025 +0000

    {2023.06}[2023a,grace] rebuild R-bundle-Bioconductor-3.18 in 2023a easystack

commit bb66a0f
Author: Thomas Roeblitz <[email protected]>
Date:   Mon Apr 7 08:48:58 2025 +0200

    building QuantumESPRESSO in a separate PR

commit df9d86c
Author: Richard Top <[email protected]>
Date:   Mon Apr 7 05:16:53 2025 +0000

    {2023.06}[2023a,grace] Apps from EB 4.9.4 2023a easystack

commit aa6b42d
Merge: 0d5472f 92f2292
Author: Thomas Röblitz <[email protected]>
Date:   Sun Apr 6 22:09:10 2025 +0200

    Merge pull request EESSI#1004 from TopRichard/eessi-2023.06-grace-apps-from-EB-4.9.3-easystack

    {2023.06}[2023a,grace] Apps from EB 4.9.3 2023a easystack

commit 9ad12db
Author: Thomas Roeblitz <[email protected]>
Date:   Sun Apr 6 21:38:29 2025 +0200

    {2023.06}[2022b,grace] Qt5 5.15.7, QuantumESPRESSO 7.2

commit 0d5472f
Merge: 9380b69 738fd77
Author: Thomas Röblitz <[email protected]>
Date:   Sun Apr 6 21:30:59 2025 +0200

    Merge pull request EESSI#1003 from trz42/2023.06-grace-2022b-eb482-toolchain-and-apps

    {2023.06}[2022b,grace] foss 2022b, HarfBuzz 5.3.1

commit 92f2292
Author: Richard Top <[email protected]>
Date:   Sat Apr 5 14:03:17 2025 +0000

    {2023.06}[2023a,grace] Apps from EB 4.9.3 2023a easystack

commit 9380b69
Merge: c4d8995 0ad022c
Author: Thomas Röblitz <[email protected]>
Date:   Sat Apr 5 15:46:33 2025 +0200

    Merge pull request EESSI#1002 from TopRichard/eessi-2023.06-grace-apps-from-EB-4.9.2-easystack

    {2023.06}[2023a,grace] Apps from EB 4.9.2 2023a easystack

commit 738fd77
Author: Thomas Roeblitz <[email protected]>
Date:   Sat Apr 5 15:02:06 2025 +0200

    skip Qt5 & QuantumESPRESSO

commit c90ceb2
Author: Thomas Roeblitz <[email protected]>
Date:   Fri Apr 4 23:51:15 2025 +0200

    use *from-commit instead of *from-pr

commit d624a5d
Author: Thomas Roeblitz <[email protected]>
Date:   Fri Apr 4 23:00:45 2025 +0200

    {2023.06}[2022b,grace] foss 2022b, HarfBuzz 5.3.1, Qt5 5.15.7, QuantumESPRESSO 7.2

commit b442f44
Merge: 48717db c4d8995
Author: ocaisa <[email protected]>
Date:   Fri Apr 4 22:28:38 2025 +0200

    Merge branch 'EESSI:2023.06-software.eessi.io' into siesta

commit 0ad022c
Author: Richard Top <[email protected]>
Date:   Fri Apr 4 19:36:07 2025 +0000

    {2023.06}[2023a,grace] Apps from EB 4.9.2 2023a easystack

commit c4d8995
Merge: 716d979 16311d5
Author: TopRichard <[email protected]>
Date:   Fri Apr 4 21:31:45 2025 +0200

    Merge pull request EESSI#998 from TopRichard/eessi-2023.06-grace-apps-from-EB-4.9.1-easystack

    {2023.06}[2023a,grace] Apps from EB 4.9.1 2023a easystack

commit 716d979
Merge: 01b2e0f ffc1005
Author: Thomas Röblitz <[email protected]>
Date:   Fri Apr 4 20:20:16 2025 +0200

    Merge pull request EESSI#1001 from EESSI/ocaisa-patch-1

    Update install_apptainer_ubuntu.sh to fix ci

commit ffc1005
Author: ocaisa <[email protected]>
Date:   Fri Apr 4 19:11:39 2025 +0200

    Update install_apptainer_ubuntu.sh

commit 48717db
Author: ocaisa <[email protected]>
Date:   Fri Apr 4 18:11:25 2025 +0200

    Update eessi-2023.06-eb-5.0.0-2023a.yml

commit 4ade001
Author: Thomas Roeblitz <[email protected]>
Date:   Fri Apr 4 15:50:37 2025 +0200

    {2023.06}[2023b,grace,CUDA] GROMACS 2024.4 with CUDA 12.4.0

commit 269f7e9
Merge: c47eb40 01b2e0f
Author: ocaisa <[email protected]>
Date:   Fri Apr 4 15:36:47 2025 +0200

    Merge branch 'EESSI:2023.06-software.eessi.io' into siesta

commit 01b2e0f
Merge: d0346f9 bb2db14
Author: TopRichard <[email protected]>
Date:   Fri Apr 4 14:53:21 2025 +0200

    Merge pull request EESSI#997 from trz42/2023.06-grace-hopper-eb494-2023b-CUDA

    {2023.06}[2023b,CUDA,grace] CUDA/12.4, UCX-CUDA/1.15.0, UCC-CUDA/1.2.0, OSU-Micro-Benchmarks-7.5 w/ CUDA

commit 16311d5
Author: Richard Top <[email protected]>
Date:   Fri Apr 4 07:41:52 2025 +0000

    {2023.06}[2023a,grace] Apps from EB 4.9.1 2023a easystack

commit d0346f9
Merge: a2a799b 996cec6
Author: TopRichard <[email protected]>
Date:   Fri Apr 4 09:36:08 2025 +0200

    Merge pull request EESSI#995 from TopRichard/eessi-2023.06-grace-all-remaining-apps-from-EB-4.9.0-easystack

    {2023.06}[2023a,grace] Remaining apps from EB 4.9.0 2023a easystack

commit a2a799b
Merge: 29956d8 4a72b1b
Author: Bob Dröge <[email protected]>
Date:   Fri Apr 4 07:18:08 2025 +0200

    Merge pull request EESSI#996 from trz42/2023.06-grace-eb494-system-and-last-2023b-apps

commit bb2db14
Author: Thomas Roeblitz <[email protected]>
Date:   Thu Apr 3 22:35:08 2025 +0200

    need to use updated easyblock for CUDA, also use merge commit for OSU

commit 18f94c2
Author: Thomas Roeblitz <[email protected]>
Date:   Thu Apr 3 21:48:49 2025 +0200

    {2023.06}[2023b,CUDA,grace] CUDA, UCX, UCC, OSU

commit 566ead8
Author: Thomas Roeblitz <[email protected]>
Date:   Thu Apr 3 21:47:40 2025 +0200

    ensure nvidia-smi can find NVIDIA libraries

commit 4a72b1b
Author: Thomas Roeblitz <[email protected]>
Date:   Thu Apr 3 18:15:39 2025 +0200

    {2023.06}[system,2023b,grace] a few remaining apps for the system and 2023b toolchains

commit 996cec6
Author: Richard Top <[email protected]>
Date:   Thu Apr 3 15:25:52 2025 +0000

    add parmetis-4.0.3 with from-commit

commit af182e6
Merge: dfd61c5 29956d8
Author: Richard Top <[email protected]>
Date:   Thu Apr 3 12:58:23 2025 +0000

    Merge branch '2023.06-software.eessi.io' of ssh://github.com/EESSI/software-layer into eessi-2023.06-grace-all-remaining-apps-from-EB-4.9.0-easystack

commit dfd61c5
Author: Richard Top <[email protected]>
Date:   Thu Apr 3 12:57:50 2025 +0000

    fix typo

commit 589a1b4
Author: Richard Top <[email protected]>
Date:   Thu Apr 3 12:44:19 2025 +0000

    added from-commit to libxc

commit 3f34396
Author: Richard Top <[email protected]>
Date:   Thu Apr 3 07:38:54 2025 +0000

    {2023.06}[2023a,grace] Remaining apps from EB 4.9.0 2023a easystack

commit 1a41987
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 23:06:27 2025 +0200

    Remove pmt again, since that was only to demo the speedup of the build pipeline

commit cffa653
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 22:59:37 2025 +0200

    Revert "Restore original container to show original performance"

    This reverts commit 17cff91.

commit 17cff91
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 22:32:38 2025 +0200

    Restore original container to show original performance

commit 8d706de
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 22:31:47 2025 +0200

    Remove samtools, add pmt

commit fe3c227
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 22:28:49 2025 +0200

    Revert "restore original container, to show performance"

    This reverts commit 1b408d3.

commit 1b408d3
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 22:11:21 2025 +0200

    restore original container, to show performance

commit 6e7b252
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 21:56:58 2025 +0200

    Implement zstd support

commit 96bb45f
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 21:56:45 2025 +0200

    Fix typo

commit 9cad884
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 21:46:30 2025 +0200

    Restore original eessi_container.sh

commit 901dc67
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 21:40:57 2025 +0200

    Add SAMtools as a test for the build pipeline speed

commit 2d831f6
Author: Caspar van Leeuwen <[email protected]>
Date:   Wed Apr 2 21:36:53 2025 +0200

    Add zstd support for faster tarball creation or extraction when --resume and/or --save is used and zstd is avaialble

commit c47eb40
Author: ocaisa <[email protected]>
Date:   Mon Mar 24 09:43:18 2025 +0100

    Update eessi-2023.06-eb-5.0.0-2023a.yml

commit 298626f
Merge: b33c016 352e036
Author: ocaisa <[email protected]>
Date:   Fri Mar 21 17:29:02 2025 +0100

    Merge branch 'EESSI:2023.06-software.eessi.io' into siesta

commit b33c016
Merge: ad23817 b61c86a
Author: Alan O'Cais <[email protected]>
Date:   Thu Mar 20 16:14:49 2025 +0100

    Merge branch 'siesta' of github.com:ocaisa/software-layer into siesta

commit ad23817
Author: Alan O'Cais <[email protected]>
Date:   Thu Mar 20 16:12:36 2025 +0100

    Build Siesta with EasyBuild 5

commit b61c86a
Author: ocaisa <[email protected]>
Date:   Thu Mar 20 14:15:36 2025 +0100

    Update eessi-2023.06-eb-4.9.4-2023a.yml

commit 40ce5a9
Author: ocaisa <[email protected]>
Date:   Fri Mar 14 17:44:48 2025 +0100

    Update eessi-2023.06-eb-4.9.4-2023a.yml

commit f6b8f1a
Author: Alan O'Cais <[email protected]>
Date:   Mon Mar 10 11:31:55 2025 +0100

    {2023.06}[foss/2023a] Siesta 5.2.2

    ```bash
    14 out of 76 required modules missing:

    * test-drive/0.5.0-GCCcore-12.3.0 (test-drive-0.5.0-GCCcore-12.3.0.eb)
    * json-fortran/9.0.2-GCC-12.3.0 (json-fortran-9.0.2-GCC-12.3.0.eb)
    * flook/0.8.4-GCC-12.3.0 (flook-0.8.4-GCC-12.3.0.eb)
    * mctc-lib/0.3.1-GCC-12.3.0 (mctc-lib-0.3.1-GCC-12.3.0.eb)
    * mstore/0.3.0-GCC-12.3.0 (mstore-0.3.0-GCC-12.3.0.eb)
    * libfdf/0.5.1-GCC-12.3.0 (libfdf-0.5.1-GCC-12.3.0.eb)
    * TOML-Fortran/0.4.2-GCC-12.3.0 (TOML-Fortran-0.4.2-GCC-12.3.0.eb)
    * ruamel.yaml/0.17.32-GCCcore-12.3.0 (ruamel.yaml-0.17.32-GCCcore-12.3.0.eb)
    * xmlf90/1.6.3-GCC-12.3.0 (xmlf90-1.6.3-GCC-12.3.0.eb)
    * libPSML/2.1.0-GCC-12.3.0 (libPSML-2.1.0-GCC-12.3.0.eb)
    * Simple-DFTD3/1.2.1-gfbf-2023a (Simple-DFTD3-1.2.1-gfbf-2023a.eb)
    * libGridXC/2.0.2-gompi-2023a (libGridXC-2.0.2-gompi-2023a.eb)
    * PnetCDF/1.12.3-gompi-2023a (PnetCDF-1.12.3-gompi-2023a.eb)
    * Siesta/5.2.2-foss-2023a (Siesta-5.2.2-foss-2023a.eb)
    ```
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