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Conference call notes 20210804

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Kenneth Hoste edited this page Aug 3, 2021 · 8 revisions

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Notes on the 178th EasyBuild conference call, Wednesday Aug 4th 2021 (08:00 UTC)

Attendees

Alphabetical list of attendees (XXX):

  • Kenneth Hoste (HPC-UGent, Belgium)

  • Sebastian Achilles (Jülich Supercomputing Centre, Germany)

  • Simon Branford (Univ. of Birmingham, UK)

  • Alex Domingo (Vrije Universiteit Brussel, Belgium)

  • Alexander Grund (TU Dresden, Germany)

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

  • Kurt Lust (Univ. of Antwerp, Belgium + LUMI User Support Team)

  • Sam Moors (Vrije Universiteit Brussel, Belgium)

  • Alan O'Cais (Jülich Supercomputing Centre, Germany)

  • Mikael Öhman (Chalmers University of Technology, Sweden)

  • Bart Oldeman (Compute Canada)

  • Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)

  • Åke Sandgren (Umeå University, Sweden)

  • Davide Vanzo (Microsoft)

Agenda

  • overview of recent developments
  • AlphaFold
  • 2021b common toolchains
  • Q&A

Recent developments

  • release timeline
    • last release: EasyBuild v4.4.1 (July 6th)
    • ETA next release: by end of August (?)
  • recent changes
    • framework
      • bug fixes
        • ...
      • enhancements
        • ...
      • changes
        • ...
    • easyblocks
      • bug fixes
        • ...
      • enhancements
        • ...
      • new easyblocks
        • ...
      • changes
        • ...
    • easyconfigs
      • over 100 easyconfig PRs merged since last conf call!
      • bug fixes
        • ...
      • enhancements
        • ...
      • new software
        • ...
      • noteworthy software updates
        • ...
  • to merge/fix/tackle soon
    • framework
      • reported bugs / bug fixes
        • (nothing major?)
      • enhancements
        • support additional features in easystack files
          • support for filtering via labels (PR #3620)
        • avoid using a priority in prepend_module_path (Lmod) to avoid costly module calls (PR #3636)
        • add support for installing extensions in parallel (WIP) (PR #3667)
        • finding modules with multiple modulepaths and HMNS (issue #3703)
        • add support for NVHPC-based toolchains (PR #3736)
        • add --review-pr-max and --review-pr-filter options to limit easyconfigs shown in multi-diff (WIP) (PR #3754)
      • changes
        • also enable static analysis for Python 2.7 (PR #3725)
          • catches accidentally overwriting local variables in list comprehensions (like --from-pr --include-easyblocks-from-pr bug)
        • add per-extension timing (PR #3734)
    • easyblocks
      • bug fixes
        • treat files/directories of unpacked sources equally in PackedBinary (PR #2306)
        • --module-only doesn't always work as expected
          • we need a better way of catching this in tests
          • problem is that you typically need an actual installation to catch these problems, so can't be done in easyconfigs or easyblocks test suite run in CI
          • test installations done on generoso via boegelbot could be enhanced to catch problems with --module-only?
        • explicitly use only OpenBLAS for PyTorch if MKL is not used (PR #2448)
        • Fix CPU-only runtime for dpcpp-generated executables in custom easyblock for intel-compilers (oneAPI) (PR #2457)
        • fix detection of installed Python packages in TensorFlow (PR #2469)
        • enhance sitecustomize.py script installed by Python easyblock to fix support for virtualenv (PR #2483)
        • change Bundle easyblcok to collect altroot and altversion later so that they appear in the module when running --module-only (PR #2485)
      • enhancements
        • enhance test and install step of CMakePythonPackage easyblock (PR #2318)
        • add support for installing R extensions in parallel (WIP) (PR #2408)
        • allow for Perl modules being part of other, already installed Perl modules (PR #2386)
        • including FlexiBLAS as the default BLAS in foss will require easyblock changes (issue #2421)
        • should set BLA_VENDOR in CMakeMake easyblock if BLAS is in the toolchain (PR #2420)
        • enable make check and sanity check exec for OpenMPI (PR #2444)
        • update custom easyblock for Boost to always build single and multi threaded versions (PR #2456)
          • included CMake modules are broken (and skipped) because we install Boost libraries multiple times
        • update CMakeMake to handle old and new Boost/Boost.Python builds using custom easyblock for Boost (PR #2461)
        • enhance Java easyblock to define %(jdkarch)s template (PR #2472)
        • enhance Hypre easyblock to enable CUDA support (PR #2482)
      • changes
        • (nothing major)
      • new software
        • custom easyblocks for RepeatModeler (PR #2470), crispr-dav (PR #2487)
        • Mikael: PR coming up for UCX-CUDA
    • easyconfigs
      • bug fixes
        • improve check for multi-variant dependencies per generation of easyconfigs (PR #12687)
      • enhancements
        • (nothing major)
      • new software
        • (nothing major?)
      • software updates
        • SciPy-bundle with intel/2021a (PR #12964)
          • need to look into handful of failing tests...

Common toolchains

2021a foss+CUDA

2021b

AlphaFold

  • Status of Alpha-Fold EC file:​
  • The following EC are already around:​
    • cuDNN-8.0.5.39-CUDA-11.1.1.eb​
    • Python-3.8.6-GCCcore-10.2.0.eb
    • TensorFlow-2.5.0-foss-2020b.eb/TensorFlow-2.5.0-fosscuda-2020b.eb
    • SciPy-bundle-2020.11-foss-2020b.eb/SciPy-bundle-2020.11-fosscuda-2020b.eb ​- The following EC were created and uploaded:
    • OpenMM-7.5.1-fosscuda-2020b.eb/OpenMM-7.5.1-foss-2020b.eb (PR: 13452)
    • pdbfixer-1.7-GCCcore-10.2.0.eb (PR: 13464)
    • hhsuite-3.3.0-foss-2020b.eb (PR: 13459)
    • kalign-2.04-gcccore-10.2.0.eb/kalign-3.3.1-gcccore-10.2.0.eb (PR: 13463)
    • Biopython-1.78-foss-2020b-Python-3.8.6.eb (PR: 13574)
  • These are working EC for Python (PR: 13571)
    • opt-einsum-3.3.0-foss-2020b.eb
    • immutabledict-2.1.0-1.1.0-foss-2020b.eb
    • dm-tree-0.1.5-foss-2020b.eb
    • fastcache-1.1.0-foss-2020b.eb
    • absl-py-0.13.0-foss-2020b.eb
  • These are currently not working EC for Python (PR: 13572)
    • ml-collection--foss-2020b.eb ​ - jax-0.1.55-foss-2020b.eb
    • jaxlib-0.1.69-foss-2020b.eb
    • chex-0.0.8-foss-2020b.eb
    • dm-haiku-0.0.3-foss-2020b.eb
  • Basically, this procedure is being followed:

Q&A

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