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Conference call notes 20220928

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Mikael Öhman edited this page Sep 28, 2022 · 17 revisions

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Notes on the 206th EasyBuild conference call, Wednesday 28 September 2022 (15:00 UTC)

Attendees

List of attendees (15):

  • Mikael Öhman (Chalmers University of Technology, Sweden)

  • Bart Oldeman (Digital Research Alliance of Canada)

  • Jörg Saßmannshausen (Imperial College London, UK)

  • Kurt

  • Thomas Hayward-Schneider (Max Planck Institute for Plasma Physics, Germany)

  • Sam Moors (Vrije Universiteit Brussel, Belgium

  • Sebastien Moretti (SIB, Switzerland)

  • Jasper Grimm (University of York, UK)

  • Adam

  • Alan

  • Sebastian Achilles

  • Casper

  • Simon Branford (Univ. of Birmingham, UK)

  • Em Dragowsky (Case Western Reserve University, Ohio, US)

  • Kenneth Hoste (HPC-UGent, Belgium)

  • Abhishek Mukherjee (New Jersey Institute of Technology, US)

  • Åke Sandgren (Umeå University, Sweden)

  • Alexandre Strube (JSC, Germany)

  • Davide Vanzo (Microsoft Azure)

  • Matthew West (University of Exeter, UK)

Agenda

  • overview of recent developments + outlook to next EasyBuild release
  • how to communicate that some software packages have been replaced going forward (pkg-config, GTK+, ...)
  • NVHPC toolchains
  • FFmpeg and GLEW dep conflicts
  • backwards-incompatible changes being considered for EasyBuild v5.0
  • Q&A

Recent developments

  • release timeline
    • latest release: EasyBuild v4.6.0 (8 July 2022)
    • ETA next release (EasyBuild v4.6.1): ASAP
  • progress on problems with older Intel MPI versions on RHEL 8.6 (see issue #15651)
    • Should be fixed with updating to kernel-4.18.0-372.26.1.el8_6.x86_64.rpm
  • recent changes
    • framework
      • bug fixes
        • Checksum checking PR #4076
        • Various fixes to scripts
        • ensure we call EasyBlock.patch_step for postinstallpatches (PR #4063)
        • fix leaked stty handle (PR #4066)
        • fix type-checking of patches to allow dict values (PR #4070)
        • fix top level Makefile for AmberTools 20/21 (PR #16150, PR #16151, PR #16152)
      • enhancements
        • run python in the same process as eb wrapper script by using exec (PR #4048
        • update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (PR #4064)
          • breaks container tests because yum can no longer be installed easily in Ubuntu 20.04 via apt...
      • changes
        • ...
    • easyblocks
      • bug fixes
        • Fix non-cuda builds of suitesparse PR #2790
        • don't enable building of ld.gold when installing binutils on a RISC-V system + don't configure GCC to use gold as default linker on a RISC-V system (PR #2780)
        • add and fix patches for PyTorch 1.9.0 on POWER (PR #15919)
        • use versioned syms in system level ncurses (PR #16064)
        • fix checksum for Stacks v2.62 (due to silent re-release without version bump) (PR #16134)
        • fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (PR #16145)
        • ...
      • updates
      • changes
        • ...
      • new software
        • ...
    • easyconfigs
      • Probably a whole bunch of merge easyconfigs since last conf call
      • bug fixes
        • add libffi and elfutils as dependency for Clang v11.0.1 + v12.0.1 (PR #15935)
          • should also be fixed for other Clang easyconfigs
        • remove modextrapaths to add top-level install directory to $PATH for InterProScan v5.55-88.0 (now done by default by Binary easyblock) (PR #16167)
        • ...
      • enhancements
        • use det_cmake_version function to determine CMake version in CMakeMake generic easyblock (PR 2772)
      • (noteworthy) new software
      • noteworthy software updates
        • ...
      • changes
        • simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (PR #15981)
        • use OpenJDK for Java 8 (PR #16062)
        • drop HDF5 from 1.13.1 to 1.12.2 (PR #16153)
        • ...
  • work in progress
    • framework
      • reported bugs / bug fixes
      • 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 (WIP PR #4057)
      • changes
        • print potential errors after running a command only once (PR #4065)
        • fix run_cmd error handling (PR #4067)
    • easyblocks
      • bug reports/fixes
        • ...
      • enhancements
        • ...
      • updates
        • ...
      • new software
        • ...
      • changes
        • ...
    • easyconfigs

Should we start requiring use of SYSTEM instead of "True" in system level deps?

  • SYSTEM variable has been usable for some time, just the CI tests that were not happy with it. Should we now start enforcing it?

How to communicate that some software packages have been replaced going forward (pkg-config, GTK+, ...)

  • make easyconfigs test suite complain in PRs
  • also add comment in easyconfigs?
  • README in easyconfigs directory for that software
  • also in documentation? (and refer to that from everywhere)
  • other cases: util-linux, texinfo (makeinfo), numpy/scipy/pandas now in SciPy-bundle, ...

NVHPC toolchains

  • cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/16066
  • Add CUDA as versionsuffix to NVHPC easyconfigs, to make it clear which CUDA is being used
  • drop nvompic in favor of nvompi + CUDA (similar to recent foss + CUDA)
  • should current NVHPC be renamed (to nv-compilers) so we can use nvhpc as toolchain name for a full toolchain?
  • or use nvoff as full toolchain name?
    • nv for NVHPC, o for OpenMPI, ff for FlexiBLAS + FFTW
  • should NVHPC that is used in a toolchain be named nv-compilers, while also keeping NVHPC modules stand-alone?

Backwards-incompatible changes being considered for EasyBuild v5.0

Q&A

  • ...
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