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Conference call notes 20201125

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Kenneth Hoste edited this page Nov 25, 2020 · 3 revisions

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Notes on the 161st EasyBuild conference call, Wednesday November 25th 2020 (9:00 UTC - 10:00 CET)

Attendees

Alphabetical list of attendees (6):

  • Sebatian Achilles (Jülich Supercomputing Centre, Germany)
  • Simon Branford (University of Birmingham, UK)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Alan O'Cais (Jülich Supercomputing Centre, Germany)
  • Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)
  • Adam Huffman (Big Data Institute, Oxford, UK)

Agenda

  • recent developments
  • easyconfigs for 2020b generation
  • virtual EasyBuild User Meeting
  • Q&A

Recent developments

  • recent changes
    • framework
      • bug fixes
        • don't pass username in github_api_get_request when no GitHub token is available (PR #3494)
        • graciously handle wrong PR # in fetch_pr_data (PR #3503)
      • enhancements *
      • changes *
    • easyblocks
      • bug fixes
        • fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK (PR #2212)
        • always define $FCCPP in QuantumESPRESSO easyblock (PR #2221)
        • only configure Python with --enable-optimizations when compiling Python with (recent) GCC compiler PR #2228
        • Don't try to patch newer versions of Bazel where the patches won't apply (PR #2249)
        • fix sanity check for Boost with multithreading support (PR #2231)
      • enhancements
        • enhance extension filter for Python packages to ignore user site dir when for checking Python package extensions (PR #2224)
        • add support for building Clang with OpenMP offload support (PR #2229)
        • add support for building GCC with GPU offloading support via nvptx (PR #2235)
        • evaluate numpy test results (rather than ignoring them) (PR #2238)
    • easyconfigs
      • bug fixes
        • in-place update to magma 2.5.4 for PyTorch easyconfigs using fosscuda/2019b toolchain (PR #11726
      • enhancements *
      • new software *
      • software updates
      • changes *
  • to merge soon
    • framework (v4.3.2 milestone)
      • bug fixes
        • fix combination of --copy-eb and --from-pr (PRs #3473 + #3482)
          • needs more love after other PRs that were split off have been merged...
        • crash in apply_regex_substitutions when passing list of paths to patch (issue #3493)
        • check if PR is already merged in --merge-pr (PR #3502)
      • enhancements
        • enhance apply_regex_substitutions to allow specifying action to take in case there are no matches (PR #3440)
        • add support for using customized HTTP headers in download_file (PR #3472)
        • support for specifying easyconfig files via "easystack" file (PR #3479)
    • easyblocks (v4.3.2 milestone)
      • bug fixes
        • correctly determine path to active binutils in TensorFlow easyblock (PR #2218)
        • fix taking into account --sysroot when installing/using CMake
          • two options:
            • use toolchain file in CMakeMake (PR #2247)
            • patch CMake installation (PR #2248)
        • scipy test results (PR #2241
        • some scipy tests are failing, have to tweak accuracy tolerances?
      • enhancements
        • enhance OpenBLAS easyblock to make it aware of optarch (PR #1946)
        • improve config checks for Boost.MPI and Boost.Python and fix sanity checks of MT libs (PR #2167)
        • run motorBike tutorial case for recent (community) OpenFOAM versions (PR #2201)
          • needs testing...
        • enhance OpenMPI easyblock to catch any --with-ucx* configure options (PR #2230
      • new software
        • custom easyblock for Metagenome-Atlas (PR #2219)
    • easyconfigs (v4.3.2 milestone)
      • bug fixes
        • added missing space in configopts in ParaView 5.8.0 easyconfigs using 2020a toolchain (PR #10989)
          • (cfr. discussion last conf call)
        • Add patch to fix possible memory leak in OpenBLAS (PR #11745)
      • enhancements
      • new software *
      • software updates
        • Julia 1.5.2 (PR #11522)
        • PyTorch 1.7 (WIP) (PR #11636)
        • TensorFlow 2.4.0 (WIP) (PR #11637)
        • QIIME2 2020.08 (WIP) (PR #11661)
        • see PRs for 2020b generation of easyconfigs (more below)

easyconfigs for 2020b generation

Easyconfigs merge sprint

  • next sprint (still) being planned...

Ideas for next EasyBuild User Meeting

Q&A

  • Alan: should rstudio be renamed?
    • only includes server component, shouldn't be lowercase
    • probably RStudio-Server
  • Simon: fairly recent Intel MPI on CentOS 8: segfaults...
    • at HPC-UGent the impi in intel/2019b was bumped to the one used in intel/2020a
  • Adam: should we start thinking about 2021a toolchains
  • Adam: should we promote adding of sanity check commands more?
    • require it in tests?
  • Sebastian: which math libraries do people use on AMD Rome systems?
    • magic I_MKL_DEBUG environment variable, but only works with older imkl (2019.x version)
      • also doesn't give best performance when compared to BLIS
    • toolchain with BLIS
      • ~10% faster compared to imkl
      • pure dgemm was ~40% faster
      • only double precision kernels are well optimized for AMD Rome in recent imkl
      • in latest imkl version also provides fast-ish single precision kernels (but not as good as BLIS)
    • we should follow up on this in a dedicated conf call on EasyBuild toolchains in AMD systems
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