Conference call notes 20220105

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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
      • see also overview at https://github.com/easybuilders/easybuild-easyconfigs/issues?q=is%3Amerged+label%3Anew
      • Clang-AOMP (PR #14327)
      • HIP (PR #14339)
      • ROCm (PR #14355)
      • mold (PR #14595)
    • noteworthy software updates
      • intel/2022.00 (PR #14620)
      • CUDAcore 11.4.0 (PR #13301)
      • jax 0.2.24 with foss/2021a + CUDA 11.3.1 (PR #14334)
      • numba 0.54.1 with foss/2021b (on top of LLVM 12.0.1) (PR #14575)
      • OpenFOAM v2112 (PR #14636)
      • Qt5 v5.15.2 (PR #14017)
      • SuiteSparse v5.10.1 w/ foss/2021a + CUDA 11.3.1 (PR #14637)
    • 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
      • see https://github.com/easybuilders/easybuild-easyconfigs/labels/new
    • noteworthy software updates
      • AlphaFold v2.1.1 with foss/2021a (PR #14500)
      • Bazel 3.7.2 w/ GCCcore/11.2.0 (PR #14654)
    • 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