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Conference call notes 20230927

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Kenneth Hoste edited this page Sep 27, 2023 · 2 revisions

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Notes on the 230th EasyBuild conference call, Wednesday 27 Sep 2023 (15:00 UTC)

Attendees

List of attendees (13):

  • Em Dragowsky (Case Western Reserve University, Ohio, US)
  • Jasper Grimm (University of York, UK)
  • Thomas Hayward-Schneider (Max Planck Institute for Plasma Physics, Germany)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Chia-Jung Hsu (colleague of Mikael)
  • Adam Huffman (Big Data Institute, Oxford, UK)
  • Kurt Lust (UAntwerpen, Belgium + LUMI User Support Team)
  • Sam Moors (Vrije Universiteit Brussel, Belgium)
  • Sebastien Moretti (SIB, Switzerland)
  • Alan O'Cais (CECAM, Univ. of Barcelona)
  • Bart Oldeman (Digital Research Alliance of Canada
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Jörg Saßmannshausen (Imperial College London, UK)

Agenda

  • overview of recent developments
  • Q&A

Recent developments

  • latest EasyBuild release: 4.8.1 (11 Sept 2023)
    • ETA for next EasyBuild release: end of Oct'23
    • ETA for EasyBuild 5.0 release: by the end of 2023 (?)
  • recent changes
    • docs (merged PRs)
      • ...
    • framework (merged PRs)
      • bug fixes
        • include major version (*majver) templates in auto-generated documentation (PR #4347)
        • reset tempfile.tempdir to None to avoid that tmpdir path gets progressively deeper with each easystack item (PR #4350)
          • fix for nested temporary directories for easystack items (issue #4291)
      • enhancements
        • add CI workflow to run unit tests with Python 2 (again) (PR #4333)
          • 4 failing tests (out of 854) on top Python 2.7 are skipped
          • running test suite on top of Python 2.7 takes over 1h...
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • ...
    • easyblocks (merged PRs)
      • bug fixes
        • fix creation of symlink for libraries in TBB easyblock (PR #2927)
        • add error regexp for PyTorch tests run in subprocess and enhance error message (PR #3003)
        • replace umlaut in docstring of PerlBundle easyblock (to fix Non-ASCII character error when using Python 2.7) (PR #3008)
      • 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)
        • enhance Conda easyblock: add support for using custom conda command (like mamba), and clean up after installation (PR #2996)
        • update numpy easyblock to be able to use FlexiBLAS with MKL as dependency (PR #2999)
      • updates
        • ...
      • changes
        • ...
      • new easyblocks
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • ...
    • easyconfigs (merged PRs)
      • ~60 easyconfig PRs were merged since last conf call
      • bug fixes
        • backport lchown patch to PMIx 3.1.x + 3.2.x (PR #18759)
        • add patch for OpenBLAS 0.3.23 to fix hanging tests (PR #18790)
        • rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (PR #18785)
        • add patch to fix build of util-linux 2.39 on CentOS 7 (PR #18855)
        • add patch to fix finding of tk.tcl for Tk 8.6.13 (PR #18864)
        • also copy scripts directory for Clair3 (PR #18783)
        • add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (PR #18833)
        • fix permission issues when copying xvfb-run script in Xvfb easyconfigs (PR #18834)
        • add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (PR #18870)
      • enhancements
        • ...
      • (noteworthy) new software
        • ...
      • noteworthy software updates
        • PyTorch v1.13.1 w/ foss/2022a + CUDA 11.7.0 (PR #18424)
        • PyTorch v1.13.1 w/ foss/2022b (PR #18421)
        • Qt6 v6.5.2 (PR #18683)
          • PyQt6 would be next step
          • gnuplot not compatible yet with Qt6
      • changes
        • ...
  • work-in-progress
    • docs (open PRs + issues)
    • framework (open PRs + issues)
      • reported bugs / bug fixes
        • ...
      • enhancements
        • ...
      • changes
        • reduce number of CI jobs by testing for Lua and Tcl module syntax in a single CI job (PR #4192)
      • EasyBuild 5.0 (to 5.0.x branch)
        • TODO:
          • improved error reporting by run_shell_cmd function (now just raises subprocess.CalledProcessError)
          • should shell option for run_shell_cmd function be renamed to use_bash?
          • see also EasyBuild 5.0 sync meeting notes
    • easyblocks (open PRs + issues)
      • bug reports/fixes
        • fix extension filter for Perl packages (PR #2699)
          • some recent progress on this by Åke, see easyconfigs PR #18789
          • PerlBundle also runs tests for all extension
            • fixing that for all existing Perl easyconfigs would be very painful (whole bunch of Test::* extensions to add + fix order)
        • update WRF easyblock to avoid running tests directly in installation directory (PR #3006)
          • needs more work since test installations with existing WRF easyconfigs failed
        • fix --sanity-check-only and --module-only for UCX plugins (PR #3007)
          • nice example of how to make easyblocks compatible with --sanity-check-only and --module-only
      • enhancements
        • ...
      • updates
        • update CP2K easyblock for compatibility with CP2K v2023.1 release (GCC only) + fix GPU support (PR #2918)
        • update CP2K easyblock to use do_regtest.py script for recent versions (WIP PR #2984)
        • update Clang-AOMP easyblock for ROCm 5.6 (PR #2958)
        • update WRF easyblock to correctly determine wrf_subdir for version >= 4.5.1 (PR #2997)
      • new easyblocks
        • new custom easyblocks for Spparks and Stitch (PR #2948)
        • add generic CargoPythonBundle easyblock (PR #2964)
      • changes
        • Install only SuiteSparse libraries with make install (PR #3004)
      • EasyBuild 5.0 (to 5.0.x branch)
        • ...
    • easyconfigs (open PRs + issues)
      • bug fixes/reports
        • installation of Transformers-4.29.2-foss-2022a.eb is broken, requires newer Rust (issue #18611)
        • prepend $EBROOTFREESURFER/lib/qt/lib to $LD_LIBRARY_PATH in order to override the qt libraries from $EBROOTMCR (PR #18795)
        • add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (PR #18847)
      • enhancements
        • also run easyconfigs test suite with Python 3.11 (PR #18009)
          • we will probably need to rename CVS to something else to dance around recent setuptools filtering out directories named CVS...
        • Paraview 5.11.1 fat build compatible with hardware rendering, software rendering, headless server mode, as well as interactive mode (PR #18631)
        • improve CUDA 11 compatibility of GCC 12.2 (PR #18854)
      • new software
        • ...
      • noteworthy software updates
        • AlphaPulldown v0.30.7 w/ foss/2022a (WIP PR #18506)
        • intel/2023.07 (PR #18439)
          • awaiting bump to GCCcore/13.2.0 as dependency for intel-compilers...
        • PETSc 3.19.4 w/ foss/2023a (PR #18608)
        • rocm-smi v5.6.0 (PR #18278)
        • HIP v5.6.0 (amd) (PR #18277)
        • hipBLAS v1.0.0, rocBLAS v3.0.0, rocSOLVER v3.22.0, ... w/ ROCm 5.6.0 (PR #18772)
        • PyTorch v1.13.1 w/ foss/2022b + CUDA 11.7.0 (PR #18853)
        • PyTorch v1.13.1 w/ foss/2022b + CUDA 12.0.0 (PR #18806)
        • SciPy-bundle v2023.07 w/ iimkl/2023a (PR #18875)
          • if installation works, we'll probably still have some trouble with the tests (cfr. PR #17539)
          • we could check if f2py part is optional? may be used internally by numpy/scipy? should we ask the developers?
      • changes
        • ...

Q&A

  • time to plan another easyconfigs merge sprint?
  • Jörg's PR for GAMESS-US easyblock
    • needs a bit of work to get it ready to merge
    • creates install.info file rather than doing Q&A dance
    • we don't care too much about the existing GAMESS-US easyconfigs, which are ancient
    • uses ILP64 for BLAS
      • Bart has been looking into this recently
      • ILP64 variants of OpenBLAS/FlexiBLAS can be included in existing installation, no need for separate easyconfigs/installations
      • Jasper has looked into this a while ago too (see PR #15748)
    • Kurt also mentioned that GAMESS-US is a mess to get installed
    • there's one optional module in GAMESS-US that claims it needs MKL
    • there seems to be a Python script as well that just accepts options rather than using Q&A
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