Conference call notes 20220817

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Notes on the 204th EasyBuild conference call, Wednesday 17 August 2022 (8:00 UTC)

Attendees

List of attendees (8):

• Jorg Sassmannshausen
• Kurt Lust
• Mikael Ohman
• Thomas Hayward-Schneider
• Alexander Grund
• Jasper Grimm
• Simon Branford
• Caspar van Leeuwen

Agenda

• overview of recent developments
• Q&A

Recent developments

• AMD toolchains contribution
  • PR #4058 (framework), PR #2774 (easyblocks, bugfix OMPI sanity check) and PR #16037 (easyconfigs)
  • Any thoughts on the proposed toolchain composition:
    • AOCC on top of GCCcore
    • aompi (AOCC + OpenMPI)
    • amd (aompi + AOCL math libs: BLIS, libFLAME, FFTW, ScaLAPACK)
  • Does anyone (a maintainer?) in the call have experience with AMD toolchain? Maybe review this PR...
• release timeline
  • latest release: EasyBuild v4.6.0 (8 July 2022)
  • ETA next release (EasyBuild v4.6.1?): end of Aug'22
• recent changes
  • framework
    • bug fixes
      • Autopep8 1.7.0 + Python 2.7 caused failures in CI. Fixed to autopep8 < 1.7.0 in PR 4055
    • enhancements
      • Add AI module class PR 4053
    • changes
      • ...
  • easyblocks
    • bug fixes
      • update PyTorch easyblock to capture regex for tests failing with signals (PR #2768)
      • Change to PythonPackage to make sure output from the test step always ends up in EB logs, even for return_output_ec = True (only used in PyTorch EasyBlock) (PR #2770)
    • enhancements
      • ...
    • updates
      • ...
    • changes
      • ...
    • new software
      • ...
  • easyconfigs
    • ~50 easyconfig PRs were merged since last conf call
    • bug fixes
      • add patch for GROMACS 2020 and 2021 versions for missing sync in LINCS and SETTLE CUDA kernels (PR #16027 and PR #16026)
      • Alternative checksum for plot3Drgl in R v4.1.X + v4.2.0 (PR #16011)
      • Restore ploteig in EIGENSOFT 7.2.1 (PR #15996)
      • Get correct source tarball for wannier90 in QuantumESPRESSO 7.1 (PR #15993)
      • Add missing SciPy-bundle dep for rMATS-turbo (PR #15988)
      • Add correct FOX Toolkit dependency for SUMO (PR #15986)
    • enhancements
      • Add sanity check for OpenFAST (PR #15983)
    • (noteworthy) new software
      • see also overview at https://github.com/easybuilders/easybuild-easyconfigs/issues?q=is%3Amerged+label%3Anew
      • ...
    • noteworthy software updates
      • UCC-CUDA, adds CUDA support to UCC (PR #15956)
      • Update to Java, it now picks up the Eclipse version, "Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions" (PR #16001)
    • changes
      • ...
  • framework
    • reported bugs / bug fixes
      • How to support the use of ifx in intel toolchains, specifically with mpiifort (issue #4056)
      • EasyBuild seems to rebuild dependency when --wait-on-lock-limit and --wait-on-lock-interval is used, even though dependency has been build when lock is released (PR #4059)
        • Probably, the main of the 2nd process (waiting on the dep) has passed the point where the decision to skip a dep is made. Maybe we can do the wait-on-lock earlier? Order should probably be: build dependency list, check if it's there, or if there is a lock, then wait. Might not be easy to fix.
      • EasyBuild 4.6.0 not building on beegfs due to hard-link usage. Furthermore, source here seems to contain the hardlinks, but this does not.
    • enhancements
      • add support for easystack file that contains easyconfig filenames + implement parsing of configuration options (PR #4021)
      • adding support for the use of --from-pr _and other options) in EasyStack files. Changed from previous PR, as we now reconfigure at higher level (in main.py) in between items in the EasyStack file. Very much WIP (issue #4057)
    • changes
      • ...
  • easyblocks
    • bug reports/fixes
      • Some issue with detecting C++11 support when building CMake. Seems quite specific to this user though. (issue # 2769)
      • Issue with cleanup in post install step of fftw.mpi on certain distros (PR #2771)
    • enhancements
      • New (dedicated) EasyBlock for RELION, WIP (PR #2773)
      • Better detection of CMake version (PR 2772)
      • Avoid superfluous warning for NVHPC (PR #2767)
    • updates
      • ...
    • new software
      • ...
    • changes
      • ...
  • easyconfigs
    • close to 700 open easyconfig PRs...
    • bug fixes
      • ...
    • new software
      • see https://github.com/easybuilders/easybuild-easyconfigs/labels/new
      • ...
    • noteworthy software updates
      • CP2K v9.1 & v2022.1 for foss 2022a (PR #16007)
      • TensorFlow 2.9.1 (PR #16008)
    • changes
      • ...

Q&A

• Should we use Java suffix? issue #16038

  • Maybe for System toolchains, yes, and for others no? We can discuss in the issue
  • Which versions should we use? Java 13-16, don't use it for anything, support is dropped upstream. Java 17 seems to work with the Eclipse version. Let's see if we can go for this in the next toolchain.
  • What about using e.g. multideps for Java, for software where the version of Java is not critical? (e.g. in PR #16034)
    • Might be good if we just add sanity check, then people can easily duplicate the EC and change Java version

• yaff has problems with HDF5 1.12, Jorg contacted the devs, but hasn't heard back from them. (PR #15854)

  • There's a compatibility option that might help.
  • It might also be that the issue is actually in h5py?

• netCDF test suite, there are tests that are failing on Generoso with Intel, other user has seen it fail with foss. It's running some parallel I/O tests.

  • What filesystem does Generoso mount?
  • Maybe we should comment out the parallel tests, which are actually more like benchmarks. Michael wil make a PR for this. ...