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Conference call notes 20220105

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Kenneth Hoste edited this page Jan 5, 2022 · 5 revisions

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Notes on the 188th EasyBuild conference call, Wednesday 5 Jan 2022 (09:00 UTC)

Attendees

Alphabetical list of attendees (8):

  • Simon Branford (Univ. of Birmingham, UK)
  • Miguel Dias Costa (Univ. of Singapore)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Terje Kvernes (University of Oslo, Norway)
  • Kurt Lust (Univ. of Antwerp, Belgium + LUMI User Support Team)
  • Lars Viklund (Umeå University, Sweden)
  • Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)
  • Alexandre Strube (Jülich Supercomputer Centre, Germany)

Agenda

  • overview of recent developments
  • Q&A

Recent developments

  • release timeline
    • latest release: EasyBuild v4.5.1 (Dec 13th 2021)
    • ETA next release: mid Jan'21 ?
  • recent changes
    • framework
      • bug fixes
        • ...
      • enhancements
        • allow oversubscription in sanity check for OpenMPI-based toolchains (PR #3909)
        • automatically prepend env-for-shebang value with sysroot (PR #3919)
      • changes
        • ...
    • easyblocks
      • bug fixes
        • set wm_* class variables in OpenFOAM easyblock constructor (to fix --sanity-check-only) (PR #2616)
        • fix patching of CMakeLists.txt in for Eigen v3.4 (PR #2633)
        • skip netcdf4-python tests that require network connectivity (PR #2634)
        • fix shebang of scripts in Perl installation if installation prefix is too long (PR #2640)
        • enhance IntelBase easyblock to avoid crash when $USER is not set (PR #2642)
      • enhancements
        • update AOCC easyblock to support version 3.2.0 (PR #2643)
        • remove necessity for license for oneAPI versions (>= 2021.x) in itac easyblock (PR #2492)
        • add option to control MKL-DNN in jaxlib (PR #2619)
        • add CUDA support in SuiteSparse easyblock (PR #2627)
        • add option to not copy the license file for Gurobi (PR #2639 + PR #2641)
        • use all available cores for running Perl test suite (PR #2637)
        • don't grep for specific version in --version output of Intel compiler commands for versions 2022.x (PR #2644)
      • changes
        • allow oversubscription in OpenMPI sanity check (PR #2611)
      • new software
        • add custom easyblock for Clang-AOMP (PR #2617)
    • easyconfigs
      • ~150 easyconfig PRs merged since last conf call!
      • bug fixes
        • fix homepage and source_urls for GLIMMER 3.02b (PR #7945)
        • don't add bin subdir to $PATH in ReFrame easyconfigs (PR #14415)
        • pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 (PR #14502)
        • seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs (PR #14537)
        • add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (PR #14584)
        • specify compiler to use in WildMagic easyconfig (PR #14594)
        • fix broken patch file for recent GPAW versions (PR #14619)
        • add alternative checksum for Siesta-4.1-MaX-1.0 (PR #14643)
        • add missing PCRE dependency for pullseq + add sanity check commands (PR #14650)
      • enhancements
        • include output of failing code style check in message produced by failing easyconfigs style test (PR #14578)
      • (noteworthy) new software
      • noteworthy software updates
      • changes
        • consistently use 'Grace' software name + sync homepage/source_urls + fix easyconfig for Grace v5.1.25 with foss/2021a (PR #14493)
        • update Java 1.8 wrapper to 1.8.0_311 for x86_64 (PR #14644)
  • to merge/fix/tackle soon
    • framework
      • reported bugs / bug fixes
        • change copy_file to ignore failing copy of file metadata by using shutil.copyfile + shutil.copystat rather than shutil.copy2 (PR #3912)
          • motivated by problems that occur when copying files from filesystem with extra attributes (like CernVM-FS), see issue #3910
      • enhancements
        • extend framework to enable modules to ship RPATH wrappers (issue #3918)
      • changes
        • deprecate use of patch files that don't have a filename ending with .patch (PR #3920)
    • easyblocks
      • bug fixes
        • (nothing major)
      • enhancements
        • convert version numbers to stricly numerical in Siesta easyblock (PR #2553)
        • install and load RPATH wrappers in GCCcore module (WIP) (PR #2638)
      • changes
        • (nothing major)
    • easyconfigs
      • bug fixes
        • fix checksum and versions of annovar v20191024 (PR #14579)
        • use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs (PR #14655)
        • Rust-1.54.0-GCCcore-11.2.0.eb does not use OpenSSL from deps and fails (issue #14647)
      • new software
      • noteworthy software updates
      • changes
        • bundle LAPACKE with FlexiBLAS (PR #14591)
          • required for EIGENSOFT
          • Jörg also hit a missing LAPACKE somewhere
          • should LAPACKE just be a separate easyconfig file?

Q&A

  • Jörg: PyTorch with CUDA support is failing in test step, unclear why
    • using foss/2021a toolchain
    • follow-up via Slack to try and figure out what's wrong...
    • Alexandre has been trying to get PyTorch to build with GCC 11.x
  • Jörg: open PR for BGEN (PR #14150)
    • library isn't being installed when using Waf easyblock, that's why CmdCp is used
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