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Conference call notes 20210818

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Kenneth Hoste edited this page Aug 18, 2021 · 6 revisions

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Notes on the 179th EasyBuild conference call, Wednesday Aug 18th 2021 (15:00 UTC)

Attendees

Alphabetical list of attendees (XXXX):

  • Kenneth Hoste (HPC-UGent, Belgium)

  • Sebastian Achilles (Jülich Supercomputing Centre, Germany)

  • Simon Branford (Univ. of Birmingham, UK)

  • Alexander Grund (TU Dresden, Germany)

  • Victor Holanda Rusu (CSCS, Switzerland)

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

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

  • Mikael Öhman (Chalmers University of Technology, Sweden)

  • Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)

Agenda

  • overview of recent developments
  • update on support for installing 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
        • add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX) (PR #13628)
      • enhancements
        • (none)
      • changes
        • create libtinfo symlinks in easyconfigs for ncurses 6.2 (PR #13660 + #13661)
    • easyblocks
      • bug fixes
        • set $I_MPI_ROOT correctly for 2021.x in impi easyblock (PR #2537)
          • only requires eb --module-only to fix installed impi/2021.* modules
      • enhancements
      • new easyblocks
      • changes
        • (none)
    • easyconfigs
      • ~150 easyconfig PRs merged since last conf call!
      • bug fixes
        • enable EGL in recent libepoxy easyconfigs (PR #13684)
      • enhancements
        • (nothing major)
      • new software
        • easyconfigs for over 20 new software tools, incl. jax, DistributedStream, CellRank, GOATOOLS, ...
      • noteworthy software updates
        • ~100 PRs with software updates...
        • lots of easyconfigs with updated software versions using GCCcore/11.2.0 toolchain (prep for 2021b generation of easyconfigs)
  • to merge/fix/tackle soon
    • framework
      • reported bugs / bug fixes
        • make logdir writable also when --stop/--fetch is given (PR #3771)
        • don't parse patch files as EasyConfigs when searching for patch usage (PR #3786)
        • include easyblocks from multiple PRs at the same time (PR #3792)
        • no static libraries available for FlexiBLAS (PR #3783)
          • problem with GROMACS, see issue #2521
          • see issue in FlexiBLAS repo w.r.t. static linking
          • we should let framework define a list of shared libs, and then update easyblocks to use them
          • should we check whether libraries exist before including them in $BLAS_STATIC_LIBS
        • find_software_name_for_patch can fail when non UTF8 files exist (PR #3781)
        • add optimal optimization flags for Intel compilers on AMD CPUs (PR #3793)
          • -xHost results in only using SSE2 on AMD systems...
        • broken download for PyTorch 1.9.0 because of v1.9.0 branch that was shadowing v1.9.0 tag (see upstream issue)
          • does this point out a bug in the way we download sources from a Git repo?
      • enhancements
        • 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)
          • needs more test + a dedicated unit test
          • should be marked experimental at first?
        • finding modules with multiple modulepaths and HMNS (issue #3703)
        • check for recursive symlinks by default before copying a folder (PR #3784)
        • add easybuild.tools.LooseVersion (PR #3794)
          • required because distutils which provides LooseVersion will be removed in Python 3.10+ ...
      • changes
        • fully drop support code for Python < 2.7 (PR #3788)
        • test suite improvements (PR #3790)
    • easyblocks
      • reported bugs / bug fixes
        • explicitly use only OpenBLAS for PyTorch if MKL is not used (PR #2448)
        • clean up installation of Tkinter (PR #2509)
        • reset runtest in CMakePythonPackage PR #2536
        • fix motorBike test in sanity check for OpenFOAM 9 (PR 2544#)
      • enhancements
        • enhance test and install step of CMakePythonPackage easyblock (PR #2318)
        • add support for installing R extensions in parallel (WIP) (PR #2408)
        • enable make check and sanity check exec for OpenMPI (PR #2444)
        • OpenSSL-1.1.eb does not install corresponding pkg-config file (PR #2525)
      • changes
        • (nothing major)
      • new software
    • easyconfigs

Common toolchains

2021b (WIP!)

  • base: GCCcore/11.2.0
    • what about compatibility with Intel compilers?
  • merged easyconfigs PRs with GCCcore/11.2.0:
  • easyconfig for OpenMPI 4.1.1 with GCCcore/11.2.0: https://github.com/easybuilders/easybuild-easyconfigs/pull/13668
    • same OpenMPI as in foss/2021a
    • should we wait until OpenMPI 4.1.2 is released?
    • is OpenMPI 4.1.1 actually compatible with PMIx 4.x?
  • PR for intel/2021.07 (candidate for intel/2021b): #13639

AlphaFold

Q&A

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