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Conference call notes 20230201

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Kenneth Hoste edited this page Feb 15, 2023 · 9 revisions

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Notes on the 215th EasyBuild conference call, Wednesday 1 February 2023 (09:00 UTC)

Attendees

List of attendees (11):

  • Simon Branford (Univ. of Birmingham, UK)
  • Alex Domingo (Vrije Universiteit Brussel, Belgium)
  • Jasper Grimm (University of York, UK)
  • Kenneth Hoste (HPC-UGent)
  • Adam Huffman (Big Data Institute, Oxford, UK)
  • Kurt Lust (UAntwerpen & LUST)
  • Sebastien Moretti (SIB, Switzerland)
  • Jakub Kropáček (IT4Innovations, Czech Republic)
  • Jurij Pečar (EMBL, Germany)
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Åke Sandgren (Umeå University, Sweden)

Agenda

Recent developments

  • release timeline
    • latest release: EasyBuild v4.7.0 (9 Jan 2023)
    • ETA next release (EasyBuild v4.7.1): mid Feb'23
  • recent changes
    • framework
      • bug fixes
        • fix use of locate in check_os_dependency (PR #4166)
        • use better test assertions by replacing use of assertFalse/assertTrue (PR #4170)
        • avoid GC3Pie deprecation warning (PR #4185)
        • correctly restore sys.path in tests (PR #4186)
        • suppress output of --skip-test-step test (PR #4187)
        • fix flaky test_search_file due to accidental matches for .*C++ search pattern (PR #4190)
        • print warning when non-existing start_dir is specified for extension (PR #4201)
      • enhancements
        • add testinstall custom easyconfig parameter to PythonPackage easyblock (PR #2872)
        • enforce absolute paths as start dir of extensions (PR #4196)
      • changes
        • ...
      • docs
        • ...
    • easyblocks
      • bug fixes
        • check that sanity_check_module_loaded attribute exists before querying it in PythonPackage easyblock (PR #2865)
        • fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets (PR #2873)
      • enhancements
        • make NAMD easyblock aware of (pre)testopts (PR #2856)
      • updates
        • ...
      • changes
      • new software
        • ...
    • easyconfigs
      • ~75 easyconfig PRs were merged since last conf call
      • bug fixes
        • add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (PR #17165)
        • add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (PR #17140)
        • add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (PR #17165)
        • fix typo in PMIx-4.1.0 for EBROOTLIBFABRIC (PR #17204)
        • remove dependency on Pillow from scikit-bio v0.5.7 (PR #17178)
      • enhancements
        • add sanity check command to OpenMolcas v22.10 (PR #17128)
        • add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (PR #17151)
        • add additional extensions to Python 3.10.8 (required for scipy test suite) (PR #17159)
        • add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (PR #17213)
        • enhance OpenFold 1.0.1 for standalone usage (PR #17206)
      • (noteworthy) new software
      • noteworthy software updates
      • changes
        • use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (PR #17167)
        • stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes (PR #16703)
        • HDF5 has a FORTRAN api so must be at compiler level (PR #17221)
          • should we add a check in EasyBuild framework that produces a warning (or opt-in installation failure) if .mod files are being found in the installation directory and GCCcore;
  • work in progress
    • framework
      • reported bugs / bug fixes
        • Python packages are being installed to local/lib/python*/dist-packages due to tweaks to sysconfig.py in OS (issue #4128)
        • check type of versionsuffix value in det_full_ec_version, and raise useful error message if it's not a string (PR #4184)
        • use skip markers and skipTest in tests (PR #4188)
        • reduce number of CI jobs by testing for Lua and Tcl module syntax in a single CI job (PR #4192)
        • dependencies of first build are still loaded for all next builds with an easystack file (issue #4194)
        • using multiple PRs in --from-pr gives symlink error when combined with --copy-ec (issue #4197)
      • enhancements
        • fixes/enhancements w.r.t. checksums (PR #4159, PR #4150, PR #4164)
        • allow to directly import EasyConfig constants from the module (PR #4144)
        • providing OS_LIBCUDA_FOUND and GPU_AVAILABLE type constants to easyconfigs for convenient checking (issue #4183)
        • make --search aware of extensions (issue #4189)
        • add pre/post extension hook (triggered before/after individual extension installations) (PR #4193, fixes issue #4191)
          • adding pre_extension_hook is confusing w.r.t. existing pre_extensions_hook
          • better naming?
            • pre_install_extension_hook?
            • pre_single_extension_hook?
            • other suggestions?
        • enhance documentation of checksums easyconfig parameter (docs PR #853)
      • changes
        • ...
    • easyblocks
      • bug reports/fixes
        • fix finding of failed tests in output of PyTorch test step (PR #2859)
        • fix JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions (PR #2869)
      • enhancements
        • allow use of test_cmd without runtest for ConfigureMake (PR #2837)
        • enhance CMakeMake easyblock to run ctest command if runtest is True (PR #2838)
        • modified the logic to find the PyQt5 sipdir in more places (PR #2868)
      • updates
        • update scipy easyblock for scipy >= 1.9 to correctly configure BLAS/LAPACK library to use via Meson (PR #2862)
        • fix TensorFlow easyblock for new versions of Bazel & TensorFlow (PR #2854)
        • update IPP easyblock to support versions >= 2021.2 (PR #2672)
      • new software
        • ...
      • changes
        • ...
    • easyconfigs

Update on porting of EasyBuild docs to MarkDown

  • revamped EasyBuild documentation now available at https://docs.easybuild.io
  • automatic redirects are in place, there should be no broken links (docs.easybuild.io/en/latest/... and easybuild.readthedocs.io/...)

Source tarballs provided by GitHub will change

Q&A

  • Mikael: UCC 1.1.0 (used as dep for OpenMPI in 4.1.4 in foss/2022b) is not compatible with CUDA 12
    • can we patch UCC 1.1.0 in UCC-CUDA to make it compatible with CUDA 12?
    • maybe with https://github.com/openucx/ucc/pull/700 ?
    • other option is in-place update of UCC in OpenMPI 4.1.4
    • but there's no new UCC release yet (expected April 2023)
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