Conference call notes 20240410 - easybuilders/easybuild GitHub Wiki

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Notes on the 244rd EasyBuild conference call, Wednesday 10 Apr 2024 (15:00 UTC)

Attendees

List of attendees (XXX):

  • Alex Domingo (Vrije Universiteit Brussel, Belgium)
  • Adam
  • Bart Oldeman
  • Chia-Jung Hsu
  • Em Dragowsky
  • Jasper Grimm
  • Jörg Saßmannshausen
  • Mikael
  • Thomas Hayward-Schneider
  • Yunqi Shao

Agenda

  • overview of recent developments
  • Q&A

Recent developments

  • latest EasyBuild release: 4.9.1 (3 Apr 2024)
  • next EasyBuild release: EasyBuild v5.0.0
    • ETA: in the coming weeks...
    • started doing short sprint meetings, each Monday at 15:00 CE(S)T to set next 5 goals to tackle that week
    • monthly sync meetings every 1st Wed of the month at 14:00 CE(S)T: next today Wed 7 Feb'24 at 14:00 CET
    • see also https://hackmd.io/tZtz6vMmRfGL6N9Rf__OEA
    • to test development version of EasyBuild 5.0: 
      # set up Python virtual environment, and jump into it
python3 -m venv eb5
source eb5/bin/activate

# install EasyBuild 5.0 development version into it
pip install https://github.com/easybuilders/easybuild-framework/archive/5.0.x.tar.gz
pip install https://github.com/easybuilders/easybuild-easyblocks/archive/5.0.x.tar.gz
pip install https://github.com/easybuilders/easybuild-easyconfigs/archive/5.0.x.tar.gz

# go!
eb --version
  • recent changes
    • docs (merged PRs)
      • update docs for release of EasyBuild v4.9.1 (PR #250)
      • fix toolchain graph (PR #245)
    • framework (merged PRs)
      • bug fixes
        • ...
      • enhancements
        • add generic GCC and Clang compiler flags for RISC-V (PR #4489)
        • add --short option to findUpdatedEcs (PR #4488)
      • changes
        • ...
      • code cleanup
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • bug fixes
          • switch from ls to bash in tests that are expecting this to be a binary (PR #4492)
          • fix getting all available output for interactive commands + fix logging end of output when no match was found in run_shell_cmd (PR #4504)
        • enhancements
          • implement support for running interactive commands with run_shell_cmd (PR #4453)
    • easyblocks (merged PRs)
      • bug fixes
        • set $GOPATH in configure step of GoPackage easyblock to avoid polluting $HOME/go (PR #3262)
        • ensure localrc is created in the correct subdir for NVHPC v22.9+ (PR #3240)
      • enhancements
        • easyblock for building QuantumESPRESSO with CMake (PR #3257)
      • updates
        • ...
      • changes
        • ...
      • new easyblocks
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
    • easyconfigs (merged PRs)
      • ~50 easyconfig PRs were merged since last conf call
      • bug fixes/reports
        • Drop hatchling builddep from tqdm 4.66.1 as well (PR #20200)
        • Add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency (PR #20214)
        • add patch to fix tree-optimization bug in GCC 12.3.0 and 13.1.0 for ARM architectures with SVE support (PR #20218)
        • add patch to fix for libarchive to fix error reporting in tar (PR #20254)
        • add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin (PR #20260)
        • add easyconfig test that checks if backdoored XZ versions are introduced (PR #20267)
      • enhancements
        • ...
      • (noteworthy) new software
        • ...
      • noteworthy software updates
        • {lib}[GCCcore/13.2.0] snappy v1.1.10, double-conversion v3.3.0, Qt5 v5.15.13 (PR #20201)
        • Update Java-8 wrapper to 8.402 (PR #20261)
        • {tools}[foss/2023a] Optuna v3.5.0 (PR #20264)
      • EasyBuild 5.0 (to 5.0.x branch)
        • ...
    • docs (open PRs + issues)
    • framework (open PRs + issues)
      • reported bugs / bug fixes
        • ...
      • enhancements
        • add support for data installations (PR #4474)
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • active PRs
          • rename easyconfig parameters (PR #4483)
            • see also: refactor easyconfig parameters and template constants to use a consistent naming style (issue #4464)
          • add support for disabling strict RPATH sanity check (PR #4475)
            • to deal with mixing of RPATH and non-RPATH installations
            • needs more work (incorrect regex)
          • add mechanism for easyconfig template deprecation (PR #4485)
          • Log shell cmds to temp file which allow users to revisit them (PR #4486)
          • Enable module-depends-on by default (PR #4500)
          • Make module-extensions true by default (PR #4501)
          • Prefer EBPYTHONPREFIX over PYTHONPATH (PR #4496)
          • Add custom delimiter support for update_paths, hack in special case for TCLLIBPATH (PR #4487)
        • dormant PRs/issues (for now)
          • deprecate failure to resolve a template value (PR #3285)
          • drop load storm safe guard for Environment Modules v4.2.4+ (PR #4373)
            • we should also enable depends_on by default when using Lmod as modules tool in EasyBuild 5.0
          • replace parallel easyconfig parameter by maxparallel (PR #4398)
          • bump minimum required Tmod (4.x) to 4.3.0 (PR #4425)
            • requires that PR #4415 is merged first
          • deprecate run_cmd and run_cmd_qa & co, move them to easybuild._deprecated module (WIP) (PR #4433)
          • support uninstalling software + module (issue #590)
          • clean up SLURM/Batchsystem environment before doing builds (issue #4434)
            • unset all $SLURM_* environment variables to avoid trouble with srun/MPI
            • should be done opt-in (--clean-slurm-env configuration option)
    • easyblocks (open PRs + issues)
      • bug reports/fixes
      • enhancements
        • Support GROMACS builds with SYCL (AdaptiveCpp implementation) (PR #3077)
        • Score-P easyblock: Select the oneAPI compiler suite when enabled in the Intel compiler toolchain (PR #3228)
        • enhance CMakeMake easyblock to check whether correct Python installation was picked up by cmake (PR #3233)
        • Make OpenBLAS easyblock aware to --optarch=GENERIC (issue #3230)
        • make a project environment and manage LOAD_PATH for JuliaPackage (PR #3239)
        • Explicitely mention that the PyTorch easyblock needs updating when failing for this reason (PR #3255)
      • updates
        • Update namd.py to run successfully NAMD-3.0b6-foss-2023a-mpi.eb (PR #3248)
      • new easyblocks
        • add generic Dataset easyblock (PR #3246)
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • fix extension filter for Perl packages (PR #2699)
        • update ConfigureMake easyblock to error out on unknown configure args (PR #3025 + #3026)
        • set CMake installation LIBDIR to lib by default in CMakeMake easyblock (PR #3227)
        • Always set $EBPYTHONPREFIXES instead of $PYTHONPATH (issue #2887)
    • easyconfigs (open PRs + issues)
      • bug fixes/reports
        • PyTorch v2.1.2 /w CUDA-12.1.1 still fails with too many errors (issue #20222)
        • RPATH sanity check fails for LAMMPS when (not all) dependencies are installed with RPATH (issue #20051)
        • Quantum espresso 7.2 gives segmentation faults if compiled with OpenMP (issue #20077)
        • add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (PR #20103)
        • strip Suprressor out of ResistanceGA (PR #20106)
      • enhancements
        • Correct configuration of QuantumESPRESSO for 6.7/7.2 (PR #20070)
      • new software
        • ...
      • noteworthy software updates
        • jax v0.4.24 w/ foss/2023a + CUDA 12.1.1 (PR #19841)
        • TensorFlow v2.15.1 w/ foss/2023a (PR #20191)
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • replace parallel by maxparallel (PR #19375)
      • closed PRs
        • ...

Q&A / others

  • Jorg: OpenMPI v4.1.1 with UCX v1.10.0 (GCCcore/10.2.0) does not properly support IPv6. Works with UCX v1.13.0
    • Alex: cannot update those easyconfigs anymore; solution is to customize on-site or move to newer toolchains
  • Chia-Jung: new PRs for new easyblocks for multiple software por ANSYS:
  • Jorg: Multiple open PRS for MATLAB open for quite a while.
    • Mike: try to provide test report, otherwise it might be impossible to test comercial software on our side
    • Jorg: I have test reports for MATLAB in the cluster, what is the better approach to upload them to a PR if the account cannot have GH integration
    • Mike: use token protected with SSH key
    • Jasper: use regular user account in the cluster to build and upload test