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Conference call notes 20220119

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Kenneth Hoste edited this page Jan 19, 2022 · 7 revisions

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Notes on the 189th EasyBuild conference call, Wednesday 19 Jan 2022 (16:00 UTC)

Attendees

Alphabetical list of attendees (12):

  • Simon Branford (University of Birmingham, UK)
  • Jasper Grimm (University of York, UK)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Kurt Lust (Univ. of Antwerp, Belgium + LUMI User Support Team)
  • Sam Moors (Vrije Universiteit Brussel, Belgium)
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Bart Oldeman (ComputeCanada)
  • Jurij Pečar (EMBL, Germany)
  • Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)
  • Åke Sandgren (Umeå University, Sweden)
  • Alexandre Strube (JSC, Germany)
  • Adam Huffman (Big Data Institute, Oxford, UK)

Agenda

  • overview of recent developments
  • Q&A

Recent developments

  • release timeline
    • latest release: EasyBuild v4.5.1 (13 Dec 2021)
    • ETA next release: in the coming days (most likely 24 Jan 2022)
  • recent changes
    • framework
      • bug fixes
        • ...
      • enhancements
        • add support for update_build_options + enhance update_build_options to return original value (PR #3923)
        • fix compatibility with Python 3.10 (PR #3926)
          • a significant effort will be needed to stop relying on distutils modules (LooseVersion, ...), which is deprecated in Python 3.10 and will be removed in Python 3.12; see https://www.python.org/dev/peps/pep-0632/
        • enhance get_cpu_architecture and get_cpu_family to be aware of RISC-V (PR #3931)
        • make intelfftw toolchain component aware of GCCcore (PR #3929)
        • also take /etc/os-release into account in get_os_name and get_os_version (PR #3930)
          • fixes OS name/version in output of eb --show-system-info for Gentoo, openSUSE Leap, etc.
      • changes
        • deprecate use of patch files that don't have a filename ending with .patch (PR #3920)
    • easyblocks
      • bug fixes
        • fix quotes in definition of default platform macro and enhance sanity check in GATE easyblock (PR #2645)
        • avoid excessively long shebang line in compile script for WRF (PR #2648)
        • fix checking of Intel Fortran compiler version in CP2K easyblock for recent toolchains (PR #2651)
      • enhancements
        • convert version numbers to stricly numerical in Siesta easyblock (PR #2553)
        • update Libint easyblock for LibInt v2.7.0 which requires configuring via CMake (PR #2650)
        • update Mathematica easyblock for version 13 (PR #2652)
        • add sanity check command for Bazel (PR #2653)
        • add support for enabling sanity checks for specific components in the Bundle easyblock (PR #2649)
        • update NAMD easyblock to allow non-system csh (PR #2654)
        • add util subdirectory to $PATH for WPS (PR #2658)
      • changes
        • ...
      • new software
        • ...
    • easyconfigs
      • >75 easyconfig PRs merged since last conf call!
      • bug fixes
        • fix checksum and versions of annovar v20191024 (PR #14579)
        • add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ... (PR #14726)
        • set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension in Ray-project + TensorFlow easyconfigs (PR #14728, PR #14729, PR #14730)
        • enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (PR #14741)
        • do not use external libgcrypt or python for libxslt with recent toolchains (PR #14756)
        • fix CVE-2021-23437 in Pillow v7 and v8 + update to Pillow v8.3.2 in easyconfigs using a 2021b toolchain (PR #14765)
          • should we also patch Pillow-SIMD for this CVE? => check with Alex?
        • also install libaio.so.1 symlink in easyconfigs for libaio v0.3.112 (PR #14745)
      • enhancements
      • (noteworthy) new software
      • noteworthy software updates
      • changes
        • update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (PR #14731 + PR #14755)
          • to work around problems with M4 1.4.18 on recent systems, cfr. issue #14727
        • bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (PR #14738)
    • framework
      • reported bugs / bug fixes
        • enhance RPATH wrappers to avoid duplicate/useless entries (issue #3534)
        • CI test 'test_toy_lock_cleanup_signals' occassionally fails (issue #3924)
      • enhancements
        • extend option --hidden to keep correct module name (not prefixing with dot) (issue #3922)
        • extend framework to enable modules to ship RPATH wrappers (issue #3918)
        • support for searching for extensions (--search-ext?) (issue #3901)
      • changes
        • ...
    • easyblocks
      • bug fixes
        • (nothing major)
      • enhancements
        • install and load RPATH wrappers in GCCcore module (WIP) (PR #2638)
          • current implementation is a proof-of-concept, several changes in framework required to be implemented cleanly (see issue #3918)
        • set CUDA target architecture(s) for GROMACS based on cuda_cc_semicolon_sep template value (PR #2655)
        • enhance CUDA easyblock to create version independent pkgconfig files (PR #2656)
      • changes
        • set cairo as default bitmaptype for R in etc/Rprofile.site (PR #2647)
    • easyconfigs
      • over 530 open pull requests...
        • large backlog (>300) of PRs that were opened longer than 6 months ago
        • plus an additional ~100 PRs that were opened longer than 2 months ago
        • time for another hackathon with a strong focus on cleaning up old/stale PRs?
        • some software is a big time sink (TensorFlow, PyTorch, AlphaFold)
        • a lot of time is spent on waiting rebuilding stuff
          • can we add support for setting a "breakpoint" after which checkpoint of build/install directory is taken + environment
        • add support for starting an interactive shell with correct environment/working directory + command in dumped script
      • bug fixes
        • add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (PR #14743)
      • new software
      • noteworthy software updates
        • AlphaFold v2.1.1 with foss/2021a (PR #14500)
          • tests are failing on A100 GPU cluster @ HPC-UGent?
      • changes
        • ...

Q&A

  • Jörg: problems with OpenMPI on system with multiple different networks supported
    • how to set $UCX_* environment variables that influence OpenMPI test environment
    • Mikael: could be done via a custom hook (by tweaking preconfigopts + modextravars)
      • Åke: look at contrib subdirectory in easybuild-framework repository
    • just for testing: UCX_TLS=tcp eb ... works too (only for the installation, won't be added to the module file)
    • see also Lua script that is included in OpenMPI module files by ComputeCanada via modluafooter
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