Conference call notes 20221026

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Notes on the 208th EasyBuild conference call, Wednesday 26 October 2022 (15:00 UTC)

Attendees

List of attendees (XXX):

• Kenneth Hoste (HPC-UGent)

• Simon Branford (Univ. of Birmingham, UK)

• Jasper Grimm (University of York, UK)

• Adam Huffman (Big Data Institute, Oxford, UK)

• Kurt Lust (UAntwerpen & LUST)

• Sebastien Moretti (SIB, Switzerland)

• Mikael Öhman (Chalmers University of Technology, Sweden)

• Jurij Pečar (EMBL, Germany)

• Jörg Saßmannshausen (Imperial College London, UK)

• Åke Sandgren (Umeå University, Sweden)

• Caspar van Leeuwen (SURF, Netherlands)

Agenda

• overview of recent developments + outlook to next EasyBuild release
• impact of vectorizer fixes for GCC + OpenBLAS
• call for help: porting EasyBuild docs to MarkDown
• 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
      • fix trying to generate RPATH wrappers for Clang (PR #4088)
      • first look for patch in alt_location when it is specified (PR #4093)
    • enhancements
      • add support for easystack file that contains easyconfig filenames + implement parsing of configuration options (PR #4021)
    • changes
      • use SYSTEM template constant in dependencies instead of True in framework tests (PR #4094)
  • easyblocks
    • bug fixes
      • correctly count errors/failures in PyTorch test summary (PR #2803)
        • fix for incorrect regex used in PR #2794
      • use python -m pip instead of pip in PythonPackage easyblock (PR #2807)
      • enhance EasyBuildMeta easyblock: auto-enable installing with pip + fix setup.py of easyconfigs package so installation with setuptools >= 61.0 works (PR #2805)
    • enhancements
      • enhance TensorFlow easyblock to take into account provided OpenSSL dependency (PR #2575)
      • enhance OpenBLAS easyblock to support running LAPACK test suite + checking how many tests fail (PR #2801)
      • accept both None and empty value for optarch to let OpenCV detect host CPU (PR #2804)
      • make numexpr easyblock aware of toolchain with GCC + imkl (PR #2810)
      • add sanity check commands for netCDF (PR #2811)
    • updates
      • ...
    • changes
      • ...
    • new software
      • custom easyblock for CUDA compatibility libraries (PR #2764)
      • custom easyblock for mamba (PR #2808)
  • 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
      • also use EasyConfig instances cache in process_easyconfig when build_specs is empty dict (PR #4107)
      • 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)
      • update Xmipp easyblock: versions >= 3.20.07 use noAsk option to configure (PR #2809)
    • new software
      • ...
    • changes
      • ...
  • easyconfigs
    • still over 700 open easyconfig PRs...
    • bug fixes/reports
      • LAPACK tests are failing with OpenBLAS-0.3.20 and GCC-11.3.0 (issue #16380)
        • OpenBLAS easyblock should be enhanced so the test step fails if any serious problems are found
        • OpenBLAS-0.3.20-GCCcore-11.3.0.eb should be changed to disable use of -ftree-vectorize
        • are more changes required short-term?
        • should we stop trying to control the compiler options used for OpenBLAS?
          • even that would not be enough, see auto-enabling of vectorization by GCC 12 (https://www.phoronix.com/news/GCC-12-Auto-Vec-O2)
        • we should also revist the ignored scipy failing tests (cfr. issue #2237)
      • FlexiBLAS cause core dump (simple test example) (issue #16387)
    • new software
      • see https://github.com/easybuilders/easybuild-easyconfigs/labels/new
      • ...
    • noteworthy software updates
      • CP2K v9.1 & v2022.1 for foss 2022a (PR #16007)
      • TensorFlow 2.9.1 (PR #16008)
    • changes
      • ...

Impact of vectorizer fixes for GCC + OpenBLAS

• all details in issue #16380
• relevant PRs:
  • OpenBLAS easyblock: PR #2801
  • GCC 11.x + 12.x easyconfigs: PR #16411
  • OpenBLAS easyconfigs: PR #16406

Call for help: porting EasyBuild docs to MarkDown

• See https://github.com/easybuilders/easybuild-docs

Q&A

• ...