Conference call notes 20190123 - easybuilders/easybuild GitHub Wiki

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Notes on the 118th EasyBuild conference call, Wednesday Jan 23rd 2019 (17:00 - 18:00 CET)

Attendees

Alphabetical list of attendees (9):

  • Damian Alvarez (JSC, Germany)
  • Fotis Georgatos (SDSC, Switzerland)
  • Victor Holanda (CSCS, Switzerland)
  • Kenneth Hoste (HPC-UGent, Belgium)
  • Adam Huffman (Big Data Institute, UK)
  • Alan O'Cais (JSC, Germany)
  • Mikael Öhman (Chalmers University of Technology, Sweden)
  • Bart Oldeman (ComputeCanada)
  • Davide Vanzo (Vanderbilt University, US)

Agenda

  • updates on upcoming EasyBuild v3.8.1
  • test report for proposed 2019a common toolchains
  • follow-up on moving Python to GCCcore
  • update on porting EasyBuild to Python 3
  • Q&A

Outlook to EasyBuild v3.8.1

Test report for proposed 2019a common toolchains

  • see https://gist.github.com/boegel/68b542fa564fd370e8b0e7710a320f6f

  • not having a CUDA compatible with GCC 8.x is not considered a blocker for using GCC 8.x in fosscuda/2019a

  • Damian: some of the failures may have already been fixed in JSC repo

    • ELPA: some codes depend on old ELPA versions
      • 2016.5 & 2018.x worked with Intel 2019

  • Victor: why is ELPA needed as dependency for QuantumESPRESSO?

    • Alan: extra capabilities/performance improvements?

  • no objections were raised to go forward with current foss/2019a and intel/2019a proposals based on test report

  • unclear which Python 3.x to go with for 2019a generation of easyconfigs (3.6 vs 3.7)?

Follow-up on moving Python to GCCcore

  • cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7463

  • motivation: one single easyconfig for pkgs like ...

  • preferred option is suggestion 1

  • main disadvantage is that numpy will not actually use libimf even when linked to it

    • libm get precedence because it's used by the Python interpreter
    • results in performance hit
      • one IntelPython benchmark showed significant slowdown
      • in theory could be 3-4x slowdown, but unclear whether it's actually relevant in real world applications
    • only workaround is to enforce use of libimf via $LD_PRELOAD (not tried yet by Mikael)
    • Bart: statically linking libimf in numpy?
      • was tried by Mikael, but didn't seem to work
    • Alan: another option could be to use RPATH
    • problem will get less severe over time since glibc is catching up on libimf
      • but getting a new glibc in the OS takes a long time

  • bundle vs separate easyconfigs

  • module alias: Python/3.6.6-intel-2019a -> SciPy/2019-intel-2019a-Python-3.6.6

  • Bart: working on support for installing a single easyconfig for multiple Python versions

    • iterate over builddependencies
    • not rely on $PYTHONPATH but on a self-defined one (e.g. $EBPYTHONPREFIX) together with a site.py script
    • opens the door to renaming Python/2.x to Python2 and allowing to load it together with Python 3.x

  • to be discussed also during EasyBuild User Meeting next week

Update on porting EasyBuild to Python 3

Other

  • Åke: UCX and PMIx for OpenMPI: include in OpenMPI easyconfigs in the future?

    • additional deps for OpenMPI?
    • Damian: UCX usually comes with OFED stack, low-level lib, not well suited for inclusion as dep
      • Bart: UCX is more like a low-level lib (on top of ibverbs)
        • similar to
        • installed as a module at Umeå
        • decision whether to include as a dependency or not is site-specific
        • Davide: UCX is needed to make OpenMPI versions work with MOFED 4.4.x...
          • only OpenMPI 3.1.x supports (Mellanox) OFED 4.4.x, be aware of this before you upgrade!
        • Bart: also better w.r.t. performance
      • Bart: PMIx is even worse (used for job startup & communication with job scheduler)
        • OpenMPI already includes a specific version of PMIx, which have to be compatible with Slurm you're using
    • Bart: not a good idea to include it by default, since UCX + Omnipath does not work
    • Damian: UCX gets half the bandwidth compared to OpenIB (related to not being able to use multiports?)
      • Victor: similar at CSCS
    • Kenneth: could be best handled via login in an OpenMPI easyblock...
      • dedicated docs on how to configure OpenMPI would be great

  • Victor (CSCS) expressed interest in helping out with porting of EasyBuild to Python 3

  • all talks at EasyBuild User Meeting will be streamed & recorded

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