Conference call notes 20221109

(back to Conference calls)

Notes on the 209th EasyBuild conference call, Wednesday 9 November 2022 (09:00 UTC)

Attendees

List of attendees (XXX):

• Simon Branford (Univ. of Birmingham, UK)

• Kenneth Hoste (HPC-UGent)

• Kurt Lust (UAntwerpen & LUST)

• Mikael Öhman (Chalmers University of Technology, Sweden)

• Jörg Saßmannshausen (Imperial College London, UK)

• Åke Sandgren (Umeå University, Sweden)

• Alexander Strube (JSC, Germany)

• Alex Domingo (Vrije Universiteit Brussel, Belgium)

• Bart Oldeman (Digital Research Alliance of Canada)

• Lars Viklund (Umeå University, Sweden)

• Jordi Camps (CNAG-CRG, Spain)

Agenda

• overview of recent developments + outlook to next EasyBuild release
• update on porting of EasyBuild docs to MarkDown
• 2022b common toolchain
• Q&A

Recent developments

• release timeline
  • latest release: EasyBuild v4.6.2 (21 Oct 2022)
  • ETA next release (EasyBuild v4.6.3?): by end of Nov?
• recent changes
  • framework
    • bug fixes
      • also use EasyConfig instances cache in process_easyconfig when build_specs is empty dict (PR #4107)
    • enhancements
      • ...
    • changes
      • ...
  • easyblocks
    • bug fixes
      • ...
    • enhancements
      • ...
    • updates
      • ...
    • changes
      • ...
    • new software
      • ...
  • easyconfigs
    • ~XXX easyconfig PRs were merged since last conf call
    • bug fixes
      • ...
    • enhancements
      • ...
    • (noteworthy) new software
      • see also overview at https://github.com/easybuilders/easybuild-easyconfigs/issues?q=is%3Amerged+label%3Anew
      • ...
    • noteworthy software updates
      • ...
    • changes
      • ...
• work in progress
  • framework
    • reported bugs / bug fixes
      • fix build options that should have empty list as default value (PR #4108)
      • catch easyconfig parsing failure so we can generate and post a test report (PR #4109)
      • add explicit return when no checksums match those specified in a tuple (PR #4112)
    • enhancements
      • add easybuild.tools.LooseVersion (since distutils is deprecated in Python 3.10) (PR #3794)
      • take into account custom configuration options specified in easystack file + drop support for easystack files using 'software' top-level key (PR #4057)
        • docs update (PR #832)
      • implementation of --try-dependency and --try-builddependency (PR #4097)
    • changes
      • ...
  • easyblocks
    • bug reports/fixes
      • fix installing of Clang with RPATH linking (PR #2799)
      • create $XDG_CACHE_HOME for PyTorch tests (PR #2806)
      • using SystemCompiler easyblock for wrapper around system GCC fails if an Intel license is not defined (issue #2815)
    • enhancements
      • add support for CP2K QM/MM in GROMACS easyblock (PR #2750)
    • updates
      • update PETSc easyblock for newer versions (PR #2796)
      • add generic JuliaPackage easyblock (PR #2816)
        • started from scratch by Alex, CSCS/JSC's JuliaPackage easyblock has site-specific stuff
        • can install Julia package from local tarball or Git repo
        • Julia prefers using Git repos
        • see for example https://github.com/easybuilders/easybuild-easyconfigs/pull/16494
        • we should also look again at building Julia from source (cfr. what JSC and ComputeCanada are doing)
          • see https://github.com/ComputeCanada/easybuild-easyconfigs/blob/computecanada-main/easybuild/easyconfigs/j/Julia/Julia-1.8.1-GCCcore-9.3.0.eb
          • see https://github.com/easybuilders/JSC/blob/2022/Golden_Repo/j/Julia/Julia-1.7.1-gomkl-2021b.eb
    • new software
      • ...
    • changes
      • ...
  • easyconfigs
    • still over 700 open easyconfig PRs...
    • bug fixes/reports
      • FlexiBLAS cause core dump (simple test example) (issue #16387)
      • add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility (PR #16486)
      • work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (PR #16490)
    • new software
      • see https://github.com/easybuilders/easybuild-easyconfigs/labels/new
      • CellProfiler (PR #16489)
    • noteworthy software updates
      • CP2K v9.1 & v2022.1 for foss 2022a (PR #16007)
      • TensorFlow 2.9.1 (PR #16008)
      • PyTorch v1.12.1 (PR #16453)
    • changes
      • make HDF5 thread safe (issue #16444)

Update on porting of EasyBuild docs to MarkDown

• See https://github.com/easybuilders/easybuild-docs (preview @ https://easybuilders.github.io/easybuild-docs)
• WIP framework PR #4117 to add support for MarkDown output format for auto-generated documentation

2022b common toolchains

• proposal for foss/2022b (first as foss/2022.10 - libfabric 1.16.1 was released 8 Oct'22):
  • GCC 12.2.0 + binutils 2.39 (current latest)
  • UCX 1.13.1 + libfabric 1.16.1 + OpenMPI v4.1.4 (current latest) - same as in foss/2022a
  • OpenBLAS 0.3.21 + FlexiBLAS 3.2.1 (current latest)
  • FFTW 3.3.10 (current latest) - same as in foss/2022a
  • ScaLAPACK 2.2.0 (current latest) - same as in foss/2022a
• proposal for intel/2022b:
  • see intel/2022.09
  • upstream docs: https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
  • base: GCC 12.2.0 + binutils 2.39 (current latest)
  • Intel C/C++/Fortran compilers 2022.2.0 (classic + oneAPI) (current latest)
  • Intel MPI 2021.7.0 (current latest)
  • Intel MKL 2022.2.0 (current latest)
• key software
  • Perl 5.36.0 (done, see PR #16204)
  • Python 3.10.8 (not 3.11.0)

Q&A

• ...