Conference call notes 20230719

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Notes on the 225th EasyBuild conference call, Wednesday 19 July 2023 (08:00 UTC)

Attendees

List of attendees (15):

• Adam Huffman (Big Data Institute, Oxford, UK)
• Alex Domingo (Vrije Universiteit Brussel, Belgium)
• Alexander Grund (ZIH, Dresden, Germany)
• Jasper Grimm (University of York, UK)
• Jure Peĉar (EMBL, Heidelberg, Germany)
• Jörg Saßmannshausen (Imperial College London, UK)
• Jorge Guerra (???)
• Kurt Lust (UAntwerpen, Belgium + LUMI User Support Team)
• Mikael
• Sam Moors (Vrije Universiteit Brussel, Belgium)
• Sebastien Moretti (SIB, Switzerland)
• Simon Branford (Univ. of Birmingham, UK)
• Thomas Hoffman (EMBL, Heidelberg, Germany)

Agenda

• overview of recent developments
• Q&A

Recent developments

• EasyBuild v4.8.0 is released!
  • 2023a toolchains are here
  • new PerlBundle and Cargo easyblocks
  • many fixes
• progress on EasyBuild 5.0
  • see updates in https://github.com/easybuilders/easybuild/wiki/EasyBuild-5.0-working-group
• recent changes
  • docs (merged PRs)
    • ...
  • framework (merged PRs)
    • bug fixes
      • ...
    • enhancements
      • ...
    • changes
      • ...
    • EasyBuild 5.0 (to 5.0.x branch)
      • remove support for 32-bit targets (PR #4272)
  • easyblocks (merged PRs)
    • bug fixes
      • use checkMCR.sh to determine if we have the correct MCR for FreeSurfer (PR #2962)
    • enhancements
      • ...
    • updates
      • ...
    • changes
      • ...
    • new easyblocks
      • ...
    • EasyBuild 5.0 (to 5.0.x branch)
      • ...
  • easyconfigs (merged PRs)
    • over 30 easyconfig PRs were merged since last conf call
    • bug fixes
      • ...
    • (noteworthy) new software
      • see also https://github.com/easybuilders/easybuild-easyconfigs/pulls?q=is%3Apr+is%3Amerged+label%3Anew
      • HOOMD-blue v4.0.1 (PR #18218)
      • segment-anything v1.0 (PR #18290)
      • HDF-EOS2 v3.0 ([PR #18297] https://github.com/easybuilders/easybuild-easyconfigs/pull/18297))
    • noteworthy software updates
      • see also https://github.com/easybuilders/easybuild-easyconfigs/pulls?q=is%3Apr+is%3Amerged+label%3Aupdate+
      • Horovod w/ TensorFlow (PR #18265)
      • Horovod w/ PyTorch (PR #18266)
      • Z3 w/ Python bindings (PR #18284)
    • changes
      • set JULIA_DEPOT_PATH in Julia easyconfigs with default value (PR #17976)
  • docs (open PRs + issues)
    • project board to perform yearly review cycle of all documentation pages: https://github.com/orgs/easybuilders/projects/17/views/1
    • ...
  • framework (open PRs + issues)
    • reported bugs / bug fixes
      • ...
    • enhancements
      • ...
    • changes
      • ...
    • EasyBuild 5.0 (to 5.0.x branch)
      • ...
  • easyblocks (open PRs + issues)
    • bug reports/fixes
      • ...
    • enhancements
      • ...
    • updates
      • ...
    • new easyblocks
      • new easyblock for cargopythonbundle (PR #2964)
        • inherits both PythonBundle and Cargo, but inheritance is not trivial (see linked issue in PR)
        • useful to have bundles with some extensions depending on setuptools-rust
    • changes
      • ...
  • easyconfigs (open PRs + issues)
    • bug fixes/reports
      • ...
    • enhancements
      • ...
    • new software
      • ...
    • noteworthy software updates
      • Python-bundle-PyPI v2023.06, hatchling v1.18.0, virtualenv v20.23.1, cryptography, bcrypt (PR #18208)
        • 
        • merge cffi and pycparser in a single PythonBundle
        • in the future, once CArgoPythonBundle is ready, cryptography could bundle cffi and pycparser
        • useful to have virtualenv in one of the main Python bundles (i.e. Python-bundle-PyPI)
    • changes
      • ...

Q&A

• Jorg: installation of ColabFold in empty cluster failed because SWIG was not found. But SWIG is in the list of packages to be built by EasyBuild. Building SWIG manually works and the re-installing ColabFold afterwards works. Might it be that the logic constructing the dependency graph fails for big dependency lists?
  • Miket: if its a second order dependency, it might be that EB does not know about it.
  • Jorg: EB lists SWIG as one of the packages to be installed. I'll open an issue about this.
  • Miket: not clear where the dependency of SWIG comes from
  • Alexander: OpenMM might been already been installed and then EB will not check its dependencies (which might include SWIG). Easyconfig of OpenMM could also been updated between installations
  • Miket: seems like SWIG was installed at some point, but then disappeared
• Thomas: it is confusing that ColabFold depends on a version of AlphaFold that is not the standard DeepMind version. I merged them in a single easyconfig Bundle
  • Alex: alternatively the module of AlphaFold fork from Colab can be hidden in Lmod
  • Miket: it is useful to have all AlphaFolds with the same name to make them conflict and not be loadable at the same time