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Conference call notes 20220427

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Kenneth Hoste edited this page Apr 27, 2022 · 4 revisions

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Notes on the 196th EasyBuild conference call, Wednesday 27 April 2022 (08:00 UTC)

Attendees

Alphabetical list of attendees (11):

  • Simon Branford (Univ. of Birmingham, UK)
  • Jasper Grimm (University of York, UK)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Adam Huffman (Big Data Institute, Oxford, UK)
  • Diana Iusan (Uppsala Univ., Sweden)
  • Tjerje Kvernes (University of Oslo, Norway)
  • Kurt Lust (Univ. of Antwerpen, Belgium + LUMI User Support Team)
  • Pavlin Mitev (Uppsala Univ., Sweden)
  • Sam Moors (Vrije Universiteit Brussel, Belgium)
  • Jurij Pečar (EMBL, Germany)
  • Jörg Saßmannshausen (Imperial College London, UK)

Agenda

  • overview of recent developments
  • 2022a update of common toolchains
  • Q&A

Recent developments

  • release timeline
    • latest release: EasyBuild v4.5.4 (31 March 2022)
    • ETA next release: mid May 2022
  • recent changes
    • framework
      • bug fixes
        • ...
      • enhancements
        • ...
      • changes
        • change 'eb' command to import easybuild to check if it's working (PR #3995)
          • makes eb command significantly more responsive, because testing import of easybuild.main is quite expensive
          • just checking whether "import easybuild" works is way too generic though, using easybuild.framework would better (fixed in PR #3998)
    • easyblocks
      • bug fixes
        • ...
      • enhancements
        • ...
      • updates
        • ...
      • changes
        • ...
      • new software
        • ...
    • easyconfigs
      • ~75 easyconfig PRs merged since last overview (2022-03-30)
      • bug fixes
        • use x.py to boostrap Rust so that build options are properly passed through (PR #15211)
        • add missing dependencies for SlamDunk (PR #15301)
        • define $HHLIB as path to HH-suite installation directory, required by Perl scripts (PR #15324)
        • remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (PR #15316)
        • update source URLs for YAXT 0.9.x to fix download (PR #15323)
      • enhancements
        • ...
      • (noteworthy) new software
      • noteworthy software updates
      • changes
        • use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (PR #15227)
        • add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain (PR #15216)
        • disable building of documentation for DBus 1.13.18 (PR #15010)
  • to merge/fix/tackle soon
    • framework
      • reported bugs / bug fixes
        • ...
      • enhancements
        • allow searching for sources/patches in alternative location by specifying 'alt_location' in source/patch spec (PR #3994)
      • changes
        • change 'eb' command to import easybuild.framework to check if EasyBuild framework is available (PR #3998)
    • easyblocks
      • bug reports/fixes
        • fix extension filter for Perl packages (PR #2699)
        • imkl pkgconfig files don't work (but can be fixed!) (issue #2700)
        • PythonPackage code for make_module_extra looks suspicious (issue #2708)
        • remove system-compiled binutils dirs from $LDFLAGS in binutils easyblock (PR #2712)
      • enhancements
        • reduce the number of command line args for CMake configure (PR #2514)
        • enhance Clang easyblock to add support for building with AMDGPU offload (PR #2684)
        • update make_module_* methods in OpenMPI easyblock to handle special cases for OpenMPI-CUDA (PR #2710)
      • updates
        • update sanity check in OpenMPI easyblock to support OpenMPI v5.0.0 (PR #2709)
      • new software
        • ...
      • changes
        • don't use gold linker by default for GCC >= 11.3 (PR #2711)
          • in the future, we should also support easily using another linker (like the new mold, cfr. https://github.com/rui314/mold)
          • would make sense to support a toolchain option like 'use_linker': 'mold' for this
    • easyconfigs
      • now over 600 open easyconfig PRs, we're way overdue a significant cleanup round...
      • bug fixes
        • fix installation with setuptools>=61 by explicitly declaring there are no Python packages (PR #15206)
        • add missing BLIS backend for FlexiBLAS-3.0.4-GCC-10.3.0 (PR #15347)
        • update source URL for isl in GCCcore easyconfigs (PR #15320)
        • add hwloc dependency to recent tbb easyconfigs (PR #15294)
        • fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure step to be after installation (PR #15280)
      • enhancements
        • ...
      • new software
      • noteworthy software updates
        • RoseTTAFold v1.0.0 (PR #13795)
        • TensorFlow v2.7.1 (WIP) (PR #14990)
          • failing tests are for new features of TensorFlow
          • ignore these failing tests for now, report upstream
        • hipSYCL v0.9.2 (PR #15074)
        • Qt6 (PR #15096)
        • AlphaFold v2.2.0 (PR #15129)
          • failing jax tests on A100?
          • Sam: easy way out, just use older jax version that is still supported
        • PyTorch v1.11.0 (PR #15137)
        • CP2K v9.1 with foss/2021a (PR #15146) and intel/2021a (PR #15147)
          • call for testing by others, and keep an eye on result of test suite...
        • GCC 11.3.0 (PR #15311)
      • changes
        • ...

2022a update of common toolchains

  • GCC 11.3 as base (see PR #15311)
    • with ld.bfd as default linker (rather than ld.gold, which is no longer actively maintained)
  • foss/2022a:
    • latest OpenMPI 4.x (not 5.0.0)
    • latest FlexiBLAS/OpenBLAS(/BLIS)
    • FFTW, ScaLAPACK
  • intel/2022a:
    • latest currently is oneAPI 2022 update 1
    • unclear whether 2022 update 2 release is close or not
  • other software versions
    • Python 3.10?
  • tests
    • SciPy-bundle, CP2K, OpenFOAM, ...

Q&A

  • Jörg: problems with installing latest version of OpenMOLCAS
    • linking issues after only updating the OpenMOLCAS version
      • see discussion in Slack
    • different problem when building manually after setting up build environment
      • Intel compiler not finding its own libraries
      • can be fixed by patching CMake's link.txt
      • maybe EasyBuild does more magic in the build environment (environment variables being set)?
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