Conference call notes 20211208

(back to Conference calls)

Notes on the 187th EasyBuild conference call, Wednesday Dec 8th 2021 (16:00 UTC)

Attendees

Alphabetical list of attendees (11):

• Simon Branford (Univ. of Birmingham, UK)
• John Dey (Fred Hutch, Seattle, US)
• Em Dragowsky (Case Western Reserve University, Ohio, US)
• Bob Dröge (Univ. of Groningen, Netherlands)
• Fotis Georgatos (EPFL, Switzerland)
• Kenneth Hoste (HPC-UGent, Belgium)
• Mikael Öhman (Chalmers University of Technology, Sweden)
• Bart Oldeman (ComputeCanada)
• Jurij Pečar (EMBL, Germany)
• Åke Sandgren (Umeå University, Sweden)
• Alexandre Strube (Jülich Supercomputer Centre, Germany)

Agenda

• overview of recent developments
• outlook to EasyBuild v4.5.1 release
• EasyBuild User Meeting 2022
• Q&A

Recent developments

• release timeline
  • latest release: EasyBuild v4.5.0 (Oct 29th 2021)
  • ETA next release: ASAP...
• recent changes
  • framework
    • bug fixes
      • introduce EasyBlock.post_init method to correctly define builddir variable when build-in-installdir mode is enabled in easyconfig or easyblock (PR #3900)
      • also show download progress bar when using --inject-checksums (PR #3905)
      • pick up custom extract_cmd specified for extension (PR #3907)
    • enhancements
      • fall back to sequential installation for extensions with unknown dependencies when using --parallel-extensions-install (PR #3906)
    • changes
      • ...
  • easyblocks
    • bug fixes
      • avoid patching binary files + other enhancements for MUMmer easyblock (PR #2630)
      • set OpenMPI configuration for ORCA sanity check (PR #2596)
      • enable build-in-installdir mode in constructor of PETSc and SLEPc easyblocks (PR #2631)
    • enhancements
      • enhance Rpm generic easyblock to support installing tarball of RPMs (by unpacking it first) + take into account (pre)installopts (PR #2580)
      • add option to ignore PLUMED version check for GROMACS (PR #2621)
      • enhance tbb easyblock by adding option to build Python bindings (PR #2626)
    • changes
      • ...
  • easyconfigs
    • over 100 easyconfig PRs merged since last conf call!
    • bug fixes
      • add patch for PyTorch 1.10.0 to fix RPATH-related issues (PR #14382)
      • add patch for GCCcore 9.1-9.3 + 10.1-11.1 to fix compatibility with recent kernel headers (PR #14453 + PR #14454)
      • add patch to fix CVE-2021-43527 in NSS (PR #14497)
      • add patch to fix broken (hanging) Mash binaries (PR #14511)
    • enhancements
      • ...
    • (noteworthy) new software
      • see also overview at https://github.com/easybuilders/easybuild-easyconfigs/issues?q=is%3Amerged+label%3Anew
      • BabelStream (PR #14503)
      • pkgconf (PR #14423)
        • drop-in replacement for pkg-config (see also issue #14390)
    • noteworthy software updates
      • OpenMPI v4.1.2 (PR #14425)
      • OpenCV v4.5.3 (PR #14115)
      • PyTorch v1.10.1 with foss/2021a (CPU-only) (PR #14460)
      • pangolin with more recent pangoLEARN (PR #14310)
        • used in context of COVID-19 Omicron variant
    • changes
      • comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0 (PR #14335)
        • doesn't belong in foss toolchain, also requires accepting accepting the Intel oneAPI EULA
        • Bart: a "wrapper" library can be added to the imkl installation so it can be used easily as a FlexiBLAS backend (via $FLEXIBLAS_DEFAULT)
• to merge/fix/tackle soon
  • framework
    • reported bugs / bug fixes
      • git_config confuses branches and tags (issue #3902)
        • using a branch name as value for tag in git_config in sources used to work, but is broken since EasyBuild v4.4.2
    • enhancements
      • allow oversubscription in sanity check for OpenMPI-based toolchains (PR #3909)
        • see also easyblocks PR #2615 (allow oversubscription in OpenFOAM sanity check)
  • easyblocks
    • bug fixes
      • set wm_* class variable in OpenFOAM easyblock when using --sanity-check-only (PR #2616)
    • enhancements
      • add option to control MKL-DNN in jaxlib (PR #2619)
      • add CUDA support in SuiteSparse easyblock (PR #2627)
    • changes
      • allow oversubscription in OpenMPI sanity check (PR #2611)
    • new software
      • add custom easyblock for Clang-AOMP (PR #2617)
        • required for dependencies of HIP/ROCm 4.5.0 (see PR #14339 and PR #14355)
  • easyconfigs
    • bug fixes
      • pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 (PR #14502)
      • don't add bin subdir to $PATH in ReFrame easyconfigs (PR #14415)
    • new software
      • see https://github.com/easybuilders/easybuild-easyconfigs/labels/new
      • HIP (PR #14339)
      • ROCm (PR #14355
    • noteworthy software updates
      • AlphaFold v2.1.1 with foss/2021a (PR #14500)
    • changes
      • consolidate easyconfigs for grace/Grace (PR #14493)

EasyBuild User Meeting

• week 24-28 Jan 2022, fully virtual
• preliminary program available at https://easybuild.io/eum22/#program

Q&A

• Mikael: apps to test UCX-CUDA with?
  • some microbenchmarks assume CUDA support and segfault if it is not there...
  • (Åke) PyTorch checks for smcuda in ompi_info output
    • added a patch to also check for ucx_info output
  • LAMMPS: see recent Slack thread
    • should probably ask OpenMPI community
  • 2 mechanisms to check whether OpenMPI supports CUDA
    • in header file (used by LAMMPS) => doesn't work with UCX-CUDA approach (but it's patchable)
    • function call to check at runtime, but only checks OPAL things (not UCX)...
      • does OPAL basically mean BTL? UCX does not fall under this...
  • Bart: on Omnipath cluster, using PSM2 library with CUDA support (since UCX doesn't work well there)
  • see also https://github.com/easybuilders/easybuild-easyconfigs/issues/14517