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Conference call notes 20230830

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Kenneth Hoste edited this page Sep 12, 2023 · 5 revisions

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Notes on the 228th EasyBuild conference call, Wednesday 30 Aug 2023 (15:00 UTC)

Attendees

List of attendees (11):

  • Kenneth Hoste (HPC-UGent, Belgium)
  • Simon Branford (Univ. of Birmingham, UK)
  • Alexander Grund (TU Dresden, Germany)
  • Thomas Hayward-Schneider (Max Planck Institute for Plasma Physics, Germany)
  • Thomas Hoffman (EMBL, Heidelberg, Germany)
  • Adam Huffman (Adam Huffman (Big Data Institute, Oxford, UK)
  • Sam Moors (Vrije Universiteit Brussel, Belgium)
  • Sebastien Moretti (SIB, Switzerland)
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Bart Oldeman (Digital Research Alliance of Canada)
  • Jure Pečar (EMBL, Germany)

Agenda

  • overview of recent developments
  • Q&A

Recent developments

  • latest EasyBuild release: 4.8.0 (7 July 2023)
    • ETA for next EasyBuild release: ASAP
  • recent changes
    • docs (merged PRs)
      • ...
    • framework (merged PRs)
      • bug fixes
        • don't use FileExistsError in mkdir function (doesn't exist in Python 2.7) (PR #4328)
      • enhancements
        • add end-to-end test for running EasyBuild in different Linux distros using containers (PR #3968)
        • add --silence-hook-trigger configuration option to supress printing of debug message every time a hook is triggered (PR #4329)
        • add definitions for ifbf and iofbf toolchain (PR #4337)
        • add support for using fine grained Github tokens (PR #4332)
        • add support for submodule filtering and specifying extra Git configuration in git_config (PR #4338)
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • implement support in run function for running command in different working directory + switch to run function in filetools (PR #4327)
        • sync 5.0.x branch with develop after introduction of run_shell_cmd hook in run_cmd (cfr. PR #4323)
        • trigger run_shell_cmd hook in run function (PR #4334)
        • rename run function to run_shell_cmd (PR #4335 + PR #4336)
    • easyblocks (merged PRs)
      • bug fixes
        • fix typo in TensorFlow easyblock when finding libdir of OpenSSL (PR #2989)
      • enhancements
        • improve cpu-arch optimization settings for OpenCV (PR #2954)
        • enhance PythonPackage easyblock to deal with posix_local installation scheme used by Python in recent Debian/Ubuntu versions (PR #2977 + PR #2978)
          • fixes issue #2976: Python packages are being installed to local/lib/python*/dist-packages due to tweaks to sysconfig.py in OS (Ubuntu 22.04)
        • enhance PyTorch easyblock to print individual failed tests (PR #2983)
      • updates
        • update MXNet easyblock + don't try to install R extension by default for MXNet >= 1.0 (PR #2955)
      • changes
        • ...
      • new easyblocks
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • ...
    • easyconfigs (merged PRs)
      • ~100 easyconfig PRs were merged since last conf call
      • bug fixes
        • remove superflous dependencies from Horovod easyconfig on top of PyTorch (PR #18262)
        • add patches to fix PyTorch 1.12 (CPU-only) w/ foss/2022a on POWER (PR #18490)
        • add alternative checksum for Extrae v4.0.4 (PR #18564)
        • add patches to fix PyTorch-1.12.1 w/ foss/2021a + CUDA v11.3.1 on POWER (PR #18492)
        • add patches to fix PyTorch-1.12.1 w/ foss/2021b + CUDA v11.5.2 on POWER (PR #18493)
        • add patches to fix PyTorch-1.12.1 w/ foss/2022a + CUDA v11.7.0 on POWER (PR #18494)
        • switch to CargoPythonPackage in maturin easyconfig (PR #18596)
        • fix sanity check for ccache by setting LC_ALL=C (PR #18677)
        • make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (PR #18680)
      • enhancements
        • add RnBeads extensions to R-bundle-Bioconductor v3.16 (PR #18682)
      • (noteworthy) new software
      • noteworthy software updates
      • changes
        • use Perl instead of Perl minimal as build dependency for libcerf and remove EasyConfig for Perl minimal with GCCcore/12.3.0 (PR #18565)
        • use GCCcore/12.2.0 toolchain for gnuplot 5.4.6 + disable wx support (PR #18648)
    • docs (open PRs + issues)
    • framework (open PRs + issues)
      • reported bugs / bug fixes
        • improve error when checksum dict has no entry for a file (PR #4150)
        • fix error message when checksums is set to [None] (PR #4261)
        • only add extensions in module file if there are extensions (PR #4331)
      • enhancements
        • add CI workflow to run unit tests with Python 2 (again) (PR #4333)
          • needs more work due to handful of tests failing in a weird way (incl. due to genuine bugs in Python 2.7), should maybe use Ubuntu 20.04 rather than CentOS 7.9 which is dead and buried...
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • improved error reporting by run_shell_cmd function (now just raises subprocess.CalledProcessError)
        • should shell option for run_shell_cmd function be renamed to use_bash?
    • easyblocks (open PRs + issues)
      • bug reports/fixes
        • RPackage easyblock is not compatible with --sanity-check-only (issue #2986)
      • enhancements
        • add options to MesonNinja easyblock to customize build_cmd, install_cmd, builddir (PR #2963)
        • append EGL vendor dirs directly in Mesa easyblock (PR #2985)
        • enhance PETSc easyblock to support using custom $PETSC_ARCH (PR #2987)
      • updates
        • update CP2K easyblock to use do_regtest.py script for recent versions (WIP PR #2984)
        • update TensorFlow easyblock for v2.13 since LMDB is no longer a dependency (PR #2982)
      • new easyblocks
        • add generic CargoPythonBundle easyblock (PR #2964)
        • new custom easyblock for tensorflow-compression (PR #2990)
      • changes
        • ...
      • EasyBuild 5.0 (to 5.0.x branch)
        • ...
    • easyconfigs (open PRs + issues)
      • bug fixes/reports
        • set $MUJOCO_PY_FORCE_CPU to avoid that mujoco-py checks for nvidia-smi and aborts installation because /usr/lib/nvidia is not in $LD_LIBRARY_PATH (PR #18641)
        • remove executable flag from easyconfigs (PR #18646)
      • enhancements
        • Paraview 5.11.1 fat build compatible with hardware rendering, software rendering, headless server mode, as well as interactive mode (PR #18631)
        • add test for easyconfig file permissions (PR #18647)
      • new software
      • noteworthy software updates
      • changes
        • ...

Q&A

  • 2023b update of common toolchains
    • most likely using GCC 13.2 as a base
    • need to check whether classic Intel Fortran compiler 2023.2.1 is compatible with GCC 13.2 (relevant for libstdc++, etc.)
  • start archiving easyconfigs using oldest toolchain before EasyBuild 5.0?
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