Conference call notes 20181212 - easybuilders/easybuild GitHub Wiki

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Notes on the 116th EasyBuild conference call, Wednesday Dec 11th 2018 (17:00 - 18:00 CET)

Attendees

Alphabetical list of attendees (4):

• Damian Alvarez (JSC, Germany)
• Kenneth Hoste (HPC-UGent, Belgium)
• Bart Oldeman (ComputeCanada)
• Davide Vanzo (Vanderbilt University, US)

Agenda

• updates on upcoming EasyBuild v3.8.0
• an easyblock for OpenMPI?
• Q&A

Outlook to EasyBuild v3.8.0

• ETA: (unknown, but soonish)
• framework
  • https://github.com/easybuilders/easybuild-framework/milestone/60
  • highlights:
    • fix for easyconfig files saved in reprod dir
      • cfr. https://github.com/easybuilders/easybuild-framework/pull/2664
    • deprecating of ictce, goolf and oldest intel toolchains
    • some shuffling around of code to make implementation of other features easier
  • TODO
    • fix for long-standing issue where robot always required easyconfig files when resolving dependencies via subtoolchains
      • cfr. https://github.com/easybuilders/easybuild-framework/issues/2375
      • WIP PR with fix in https://github.com/easybuilders/easybuild-framework/pull/2690
  • postponed
    • support for eb --new: postponed until future release (EB v3.9.0?)
      • cfr. https://github.com/easybuilders/easybuild-framework/pull/2665
• easyblocks
  • https://github.com/easybuilders/easybuild-easyblocks/milestone/52
  • highlights:
    • various minor bug fixes & enhancements to existing easyblocks
  • TODO:
    • Trilinos (Davide)
      • cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/1601
      • should maybe be changed to only configure for MKL with recent versions (> 12.12)?
• easyconfigs
  • https://github.com/easybuilders/easybuild-easyconfigs/milestone/55
  • highlights:
    • fix for SCOTCH 6.0.5 easyconfigs: incorrect version & source URL
      • cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/7159
      • see also enhanced SCOTCH easyblock to catch these errors: https://github.com/easybuilders/easybuild-easyblocks/pull/1580
    • fix for SKESA easyconfigs: incorrect version & source URL
      • cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/7275
    • various other small bug fixes, enhancements, updates & easyconfigs for new software
  • TODO:
    • OpenBLAS (Bart)
      • cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/7271
    • missing build deps for Qt5: flex/Bison/Python2
      • cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/7300

Easyblock for OpenMPI

• now easyconfigs only, lots of hardcoding
• recent OpenMPI versions have better support for auto-detecting what is there
  • or even for fat builds
• recent OpenMPI versions prefer UCX/libfabric
• rely on auto-detection that OpenMPI configure does?
  • with dedicated easyconfig parameters for things like ibverbs, ucx, torque/slurm, ...
• reach out to OpenMPI community about this?
• Bart: benchmarking: UCX is overall winner + hcoll for collective communication
  • also: SHARP, but that needs a dedicated server (only beneficial with largish jobs, 20 nodes/800 cores)

Other

• Damian: lots of problems with collectives on latest Intel MPI with large jobs (1000 cores)
  • Bart: 2019 versions have dropped everything but libfabric (OFI)
  • Damian: also similar problems with 2018 versions (w/ default fabric, DAPL?)
  • system isn't very special; JUWELS (Skylake + IB), JURECA (Haswell + IB)
  • in some collectives it hangs, sometimes segfaults, ...
  • Bart: reproducible with OSU microbenchmarks?
  • Bart can look into reproducing this on upcoming new system
  • relevant for upcoming intel/2019a
• Davide: frequent question at SC18
  • which module naming schemes should be used?
  • how to experiment with multiple module naming schemes?
  • currently require multiple 'eb' runs:
    • first run using one module naming scheme and using --fixed-installdir-naming-scheme
    • subsequent run(s) using other module naming scheme(s) using --module-only
      • main issue here is that --module-only is not perfect, and you may run into trouble here
  • support for configuring EasyBuild to install module files with multiple different naming schemes in one go should not be too difficult (famous last words...)
• Kenneth plans to make some (good) progress on porting EasyBuild to Python 3 during the holidays
  • plan is to ingest whatever parts of vsc-base are needed by EasyBuild into the EasyBuild framework repository
  • porting vsc-base to Python 3 is likely going to take too long
    • too much impact on system scripts in HPC-UGent, so changes to vsc-base have to be done with great care
  • there's also very little development going on in vsc-base, so ingesting it kind of makes sense
  • having a single code base to worry about when porting to Python 3 should help a lot with making actual progress