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Conference call notes 20230510

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Kenneth Hoste edited this page May 23, 2023 · 3 revisions

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Notes on the 221st EasyBuild conference call, Wednesday 10 May 2023 (15:00 UTC)

Attendees

List of attendees (14):

  • Matvey Debolskiy (NORCE Norwegian Research Centre)
  • Alex Domingo (Vrije Universiteit Brussel, Belgium)
  • Craig Gross (Michigan State University, US)
  • Thomas Hayward-Schneider (Max Planck Institute for Plasma Physics, Germany)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Emily Loomeijer (TU Eindhoven, Netherlands)
  • Kurt Lust (UAntwerpen, Belgium + LUMI User Support Team)
  • Sebastien Moretti (SIB, Switzerland)
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Bart Oldeman (Digital Research Alliance of Canada)
  • Jurij Pečar (EMBL, Germany)
  • Jörg Saßmannshausen (Imperial College London, UK)
  • Alexandre Strube (JSC, Germany)
  • Alain van Hoof (TU Eindhoven, Netherlands)

Agenda

  • overview of recent developments + outlook to next release
  • 2023a update of common toolchains
  • Q&A

Recent developments

  • release timeline
    • latest release: EasyBuild v4.7.1 (20 Mar 2023)
    • ETA next release (EasyBuild v4.7.2?): ASAP
  • EasyBuild User Survey
  • recent changes
    • docs
    • framework
      • bug fixes
        • fix typo in condition guarding installation of GitHub token in CI workflow to run unit tests + fix broken tests related to GitHub integration features (PR #4216)
          • fixes tests that require GitHub token are always skipped in CI due to silly typo in GitHub Actions workflow (issue #4214)
      • use "/usr/bin/env python" in test_run_cmd_script (PR #4241)
      • enhancements
        • ...
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • remove support for Python 2 and 3.5 (PR #4229)
          • EasyBuild 5.0 will require Python >= 3.6
          • use of easybuild.tools.py2vs3 is deprecated
        • remove (deprecated) EasyBuild bootstrap script (PR #4233)
        • remove deprecated dummy toolchain (PR #4240)
        • remove experimental support for YAML-based easyconfig format (.yeb) (PR #4237)
        • remove deprecated --wait-on-lock option (PR #4239)
        • remove deprecated --accept-eula option (PR #4242)
        • remove deprecated is_generic_easyblock from easyconfig.py (PR #4243)
        • remove deprecated use_git_am option to apply_patch (PR #4244)
        • remove deprecated fetch_extension_sources (PR #4245)
        • change default for change_into_dir to False for extract_file (PR #4246)
        • enforce correct .patch(.*) extension for patch files (PR #4247)
        • bump version to 5.0.0.dev0 (PR #4236)
    • easyblocks
      • bug fixes
        • add output log to MATLAB installs, actually parse for common errors (PR #2924)
      • enhancements
        • let MATLAB easyblock raise an error if the MATLAB installation key is not provided (PR #2905)
        • enhance Gurobi easyblock to allow using $EB_GUROBI_LICENSE_FILE environment variable (PR #2926)
      • updates
        • ...
      • changes
        • ...
      • new software
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • stop importing from deprecated easybuild.tools.py2vs3 module + stop testing with Python 2.7 and 3.5 (PR #2916)
      • > 100 easyconfig PRs were merged since last conf call
      • bug fixes
        • fix configure step for ELSI 2.5.0+ (and add missing foss versions) (PR #17288)
        • fix homepage in ELPA easyconfigs (due to switch to new domain) (PR #17697)
        • add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (PR #17713)
        • use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (PR #17717)
        • install shared libraries for tesseract (PR #17721)
        • make excluded tests for PyTorch 1.12.1 consistent + also exclude flaky test_optim rather than adding patch to try and fix it (PR #17737)
        • add missing PCRE dependency for InterProScan 5.55-88.0 (PR #17762)
        • correct the python building of DGL, requires static libs (PR #17764)
        • only use QEF gitlab source url for QuantumESPRESSO itself (PR #17766)
        • specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (PR #17830)
        • fix broken source URL for AOCC 4.0.0 (PR #17794)
        • FLINT needs BLAS so move it up from GCC level (PR #17868)
        • fix broken tarball links for ispc 1.6, 1.10 and 1.12 easyconfigs (PR #17875)
      • enhancements
        • add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (PR #17887)
      • (noteworthy) new software
      • noteworthy software updates
      • changes
        • bump versions in Java wrappers to latest builds that include ppc: Java/8.362, Java/11.0.8, Java/17.0.6 (PR #17775)
        • move Arb and polymake to gfbf/foss (PR #17869)
  • work in progress
    • docs
    • 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)
        • new checksum listing with dictionaries leads to confusing errors if you forget to update them (issue #4254)
      • enhancements
        • make the RPATH section check with readelf -d in sanity check optional (PR #4249)
        • change tar command used in get_source_tarball_from_git to get reproducible tarballs (PR #4248)
      • changes
        • change github_* template descriptions to be somewhat clearer (PR #4251)
        • Use version suffixes in PR title instead of Python versions when using --new-pr (PR #4253)
      • EasyBuild 5.0 (to 5.0.x branch)
        • enable --trace by default (PR #4250)
        • implement new run function with cleaner API to replace run_cmd + run_cmd_qa (issue #4252)
    • easyblocks
      • bug reports/fixes
        • avoid warnings being treated as errors when installing imkl-FFTW with Intel OneAPI compilers and RPATH linking (PR #2912, see also issue #2910)
        • custom RPATH sanity check for Go packages that doesn't actually check for an RPATH section in the binary (PR #2913)
        • update GCC easyblock to ensure that --sysroot is passed to linker (PR #2921)
        • fix creation of symlink for libraries in TBB easyblock (PR #2927)
      • enhancements
        • use proxy in sanity check of EB_OpenSSL_wrapper (PR #2922)
        • add external pio option for ESMF versions greater than 8.4.0 (PR #2923)
      • updates
        • update CP2K easyblock for compatibility wiht CP2K v2023.1 release (GCC only) + fix GPU support (PR #2918)
      • new software
        • add 2 generic easyblocks for installing Rust crates with cargo: Cargo and CargoPythonPackage (PR#2902)
      • changes
        • ...
    • easyconfigs
      • still over 800 open easyconfig PRs...
      • bug fixes/reports
        • add missing dependencies for funannotate (PR #17690)
        • Add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (PR #17779)
        • OpenMPI's smcuda btl selected on non-GPU nodes? (issue #17854)
          • unclear whether this problem is specific to Miguel or not, so others should check if they can reproduce it
          • could be a side effect of building OpenMPI with --with-cuda=internal, so we should also check with fosscuda/2020b where we don't do this
          • could be a bug in OpenMPI itself
          • it's certainly possible to disable smcuda btl at runtime, using an environment variable => we should document in the issue how to do that
      • enhancements
        • switch bamtofastq to Cargo easyblock (PR #17595)
        • extend sanity check paths for Raven (PR #17617)
        • update easyconfig for Longshot 0.4.5 to use Cargo easyblock (PR #17666)
      • new software
      • noteworthy software updates
      • changes
        • ...

2023a update of common toolchains

Q&A

  • old texlive easyconfigs are broken because default mirror of repository is too old (based on year)
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