Conference call notes 20180509

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Notes on the 101st EasyBuild conference call, Wednesday May 9th 2018 (5pm - 6pm CEST)

Attendees

Alphabetical list of attendees (7):

• Damian Alvarez (JSC, Germany)
• Fotis Georgatos (Illumina, UK)
• Kenneth Hoste (HPC-UGent, Belgium)
• Adam Huffman (Big Data Institute, University of Oxford)
• Bart Oldeman (ComputeCanada)
• Victor Cameo Ponz (CINES, France)
• Davide Vanzo (Vanderbilt University)

Agenda

• outlook to EasyBuild v3.6.1
• to AVX512 or not to AVX512?
  • discussion on trade-offs for building software using AVX-512 instructions or not on Intel Skylake
• Q&A

EasyBuild v3.6.1

• ETA: end of May (or earlier?)
• merged PRs for EB v3.6.1
  • https://github.com/easybuilders/easybuild-framework/milestone/56?closed=1
  • https://github.com/easybuilders/easybuild-easyblocks/milestone/48?closed=1
  • https://github.com/easybuilders/easybuild-easyconfigs/milestone/51?closed=1
• noteworthy open PRs to go in (hopefully) soon
  • lib64 fallback in sanity check: https://github.com/easybuilders/easybuild-framework/pull/2477
  • auto-download detection in PythonPackage: https://github.com/easybuilders/easybuild-easyblocks/pull/1377
  • Bioconductor archive URLs: https://github.com/easybuilders/easybuild-easyconfigs/pull/6311

To AVX-512 or not to AVX-512

• AVX-512 frequency scaling: https://blog.cloudflare.com/on-the-dangers-of-intels-frequency-scaling/

  • https://www.intel.com/content/www/us/en/processors/xeon/scalable/xeon-scalable-spec-update.html
  • example of frequency scaling on Intel Xeon Gold 6140:

• AVX-512 vs FFTW (with a simple benchmark)

  • https://github.com/FFTW/fftw3/issues/143
  • unclear whether this issue is relevant for actual applications
    • to benchmark with CP2K, GROMACS, ...

• discussion from GROMACS mailing list:

  • https://www.mail-archive.com/[email protected]/msg30147.html

• Fotis: we also saw this with GROMACS

  • better performance with FFTW built without AVX...

• probably early days for AVX-512?

  • only properly tuned in GCC 8.x when relying on -march=native
    • Davide: what else should be used when compiling with GCC 6.x or 7.x on Skylake?
      • Bart: depends on what you're compiling: OK for very vectorizable code
        • for other stuff, may be too heavy use of zmm registers (which may impact clock freq.)
        • recent compilers are less aggressive in that sense
    • should be careful w.r.t. performance
      • compare with installation done with --optarch=march=broadwell or --optarch=march=skylake?
        • skylake (desktop, no AVX512) vs skylake-x (server, AVX512)
  • Bart: similar on Xeon Phi, hard to get very good performance
  • orthogonal to FFTW since that uses assembly

• should start wiki page or even repository on this?

• benchmarking AVX512 performance benefits also depends a lot on:

  • which exact processor
  • the system & cooling infrastructure
  • input file used

• is it really worth to build for AVX-512 currently, or can we get away with AVX2 builds?

  • if there's no clear benefit in performance, why bother building for AVX-512?

Other

• Davide: {{fosscuda}} toolchain

  • PR for toolchain definition in framework coming up
  • easyconfigs PR for mimicing goolfc/2018a as fosscuda/2018a
  • should also become a common toolchain?

• some changes to group of EasyBuild maintainers:

  • all 8 current maintainers have been granted admin access to all 4 repositories
    • cfr. http://easybuild.readthedocs.io/en/latest/Maintainers.html
  • two additional maintainers will be invited soonish by Kenneth
  • experiment in the next couple of weeks: "EasyBuild maintainer of the week" (MotW)
    • one maintainer (other than Kenneth) who agrees to spend ~1h each (working) day looking at incoming PRs/issues/questions in GitHub repositories + EasyBuild ML
    • best effort, the '~1h' is just a guideline
    • only on voluntary basis, nobody will be forced to
    • plan is to try this in the next couple of weeks to see how it goes
    • some minor concerns were raised w.r.t. being comfortable with framework or easyconfig PRs
      • approach may be revised later to assign different MotW per EasyBuild repository
      • initial setup will be one MotW
    • wiki page will be set up with more info & guidelines