Conference call notes 20201209

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Notes on the 162nd EasyBuild conference call, Wednesday December 9th 2020 (16:00 UTC - 17:00 CET)

Attendees

Alphabetical list of attendees (XXX):

• Kenneth Hoste (HPC-UGent, Belgium)

• Sebatian Achilles (Jülich Supercomputing Centre, Germany)

• Simon Branford (University of Birmingham, UK)

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

• Jörg Saßmannshausen (NIHR Biomedical Research Centre, UK)

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

Agenda

• update on recent developments + upcoming EasyBuild release (v4.3.2)
• considering switch to BLIS for foss common toolchains
• agenda for (virtual) EasyBuild User Meeting
• Q&A

Recent developments

• recent changes
  • framework
    • bug fixes
      • fix combination of --copy-ec and --from-pr (PR #3482)
      • fix regression in apply_regex_substitutions: also accept list of paths to patch (PR #3507)
    • enhancements
      • add (experimental) support for specifying easyconfig files via "easystack" file (PR #3479)
        • see also https://easybuild.readthedocs.io/en/develop/Easystack-files.html
      • add Support for BLIS+libFLAME toolchain (gobff) (PR #3505)
      • add support for skiping unit tests (test step) via --skip-test-step (PR #3524)
  • easyblocks
    • bug fixes
      • don't set $PYTHONNOUSERSITE in Python extension filter, it breaks some installations (PR #2267)
        • rolls back change made in PR #2224
        • follow-up for better approach in issue #2269
      • fix setting of $RUNPARALLEL in h5py easyblock (PR #2250)
        • required for running HDF5 tests, see issue #11825
      • set $UCX_TLS to 'all' for impi installed on top of UCX (PR #2253)
      • enhance PyTorch easyblock to ensure it finds MKL (via $MKLROOT) (PR #2257)
      • fix hardcoded path in NVHPC easyblock to support multiple architectures (PR #2233)
    • enhancements
      • add support for building Clang with OpenMP offload support (PR #2229)
      • add support for withnvptx easyconfig parameter, to enable GPU offloading, in GCC easyblock (PR #2235)
      • allow wxPython to be installed as an extension (PR #2227)
        • • follow-up to add (back) symbolic links for libwx_*so.0 files in wxPython installation (PR #2275)
      • also add 'bin' subdir to $PATH when installing a Python package (PR #2244)
    • new software
      • new custom easyblocks for code-server (PR #2255) and Metagenome-Atlas (PR #2219)
  • easyconfigs
    • bug fixes
      • patch to fix possible memory leak in OpenBLAS (PR #11745)
      • don't add include/node to $CPATH in nodejs easyconfigs + tweak V8 easyconfigs accordingly (PR #11845)
        • this broke the installation of R v4.0.3 (see PR #11663) on CentOS 7
        • follow-up in issue #11846 w.r.t. making nodejs use system OpenSSL
      • add mising gnuplot dependency for OpenFOAM (PR #11770 + PR #11800)
        • see also enhanced sanity check in OpenFOAM easyblock at PR #2256
    • enhancements
      • enable NVPTX offload support in GCCcore 10.2.0 easyconfig (PR #11720)
    • new software
      • (nothing special)
    • software updates
      • (nothing special)
    • easyconfigs for 2020b generation
      • HDF5 (PR #11828), h5py (PR #11829), intelcuda/2020b (PR #11730), matplotlib (PR #11835), PyQt5 (PR #11563), Qt5 (PR #11555), scikit-learn (PR #11833), SciPy-bundle 2020.11 (PR #11629 + PR #11818)
      • disable broken numpy test in SciPy-bundle 2020.11 easyconfig using intel/2020b (PR #11792)
    • changes
      • renaming (for consistency/correctness)
        • Ray to Ray-assembler + Ray-project (PR #11727)
        • Sumo to SUMO (PR #11791)
• to merge soon
  • framework (v4.4.0 milestone)
    • support additional features in easystack files (see issues #3468, #3512, #3513, #3516)
    • directories that don't contain any library files shouldn't be added to $LD_LIBRARY_PATH (issue #3504)
  • easyblocks (v4.4.0 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)
      • check 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)
      • run motorBike tutorial case for recent (community) OpenFOAM versions (PR #2201)
        • needs testing...
      • add support for statically linking Bazel (PR #2272)
      • add options to run unit tests to TensorFlow easyblock (PR #2263)
    • new software
      • custom easyblock for ADIOS (PR #2070), JAX (PR #2262), RELION (PR #2274)
  • easyconfigs (v4.4.0 milestone)
    • bug fixes
      • added missing space in configopts in ParaView 5.8.0 easyconfigs using 2020a toolchain (PR #10989)
        • (cfr. discussion last conf call)
    • enhancements
    • new software
      • gobff toolchains (PR #11761)
    • 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)

BLIS for foss common toolchains?

• follow-up on discussion with Sebastian Achilles (JSC)
• see notes
• PR #11761 for gobff toolchains

Easyconfigs merge sprint

• Fri Dec 11th 2020!

Agenda for (virtual) EasyBuild User Meeting

• see https://github.com/easybuilders/easybuild/wiki/6th-EasyBuild-User-Meeting
• TO PLAN:
  • talk on EESSI project
  • talk on Gentoo Prefix
  • talk on PRACE Best Practice Guide
  • talk on OpenHPC?
  • talk on Cluster-in-the-Cloud?
  • Singularity demo or workshop by Jörg
    • talk to introduce Singularity (Mon)
    • multiple short workshops
  • site presentations (~15min + Q&A)
  • JSC
  • CSCS?
  • AstraZeneca (to be confirmed)
  • other?

Q&A