Conference call notes 20160608

(back to Conference calls)

Notes on the 53rd EasyBuild conference call, Wednesday June 8th 2016 (5pm - 5.30pm CEST)

Attendees

Alphabetical list of attendees (4):

• Fotis Georgatos (Illumina, UK)
• Kenneth Hoste (HPC-UGent)
• Alan O'Cais (JSC, Germany)
• Robert Schmidt (OHRI, Canada)

Agenda

• discuss candidates for foss/2016b & intel/2016b common toolchains

  • my proposals (currently being tested thoroughly):
    • foss/2016b: foss/2016.06` (WIP), w/ GCC 5.4 & binutils 2.26 + OpenMPI 1.10.3
      • https://github.com/hpcugent/easybuild-easyconfigs/pull/3184
    • intel/2016b: intel/2016.03-GCC-5.4 (latest Intel tools on top of GCC 5.4 & binutils 2.26)
      • https://github.com/hpcugent/easybuild-easyconfigs/pull/3185
  • testing intel/2016a --try-toolchain-version=2016.03-GCC-5.4 --robot
  • Damian ported lots of stuff to a GCC v5 based toolchain @ JSC
  • things that may be a problem with GCC 5.x probably already require GCC 4.8.x already (so doesn't work with 2016a already...)

• ideas & suggestions for improvements to --new-pr & --update-pr

  • cfr. http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html & https://github.com/hpcugent/easybuild-framework/issues/1674

• Q&A

Notes

2016b update of common toolchains

• Kenneth's proposals (currently being tested thoroughly):
  • foss/2016b: foss/2016.06` (WIP), w/ GCC 5.4 & binutils 2.26 + OpenMPI 1.10.3
    • https://github.com/hpcugent/easybuild-easyconfigs/pull/3184
  • intel/2016b: intel/2016.03-GCC-5.4 (latest Intel tools on top of GCC 5.4 & binutils 2.26)
    • https://github.com/hpcugent/easybuild-easyconfigs/pull/3185
  • these are being tested with all existing foss/2016a and intel/2016a easyconfigs (resp.), via --robot --try-toolchain-version
  • Kenneth will report back results via EasyBuild mailing list
  • idea is to fix definition of 2016b by the end of the month
  • Damian ported lots of stuff to a GCC v5 based toolchain @ JSC
  • Rob: software that may be a problem with GCC 5.x probably already requires GCC 4.8.x (so doesn't work with 2016a toolchains anyway...)
    • 2nd/3rd point release should make compiler eligible for inclusion in common toolchains
  • first GCC 4.9 release was April 2014... (cfr. https://gcc.gnu.org/develop.html#timeline)

Ideas --new-pr & --update-pr

• documentation for experimental implementation of --new-pr & --update-pr is now updated @ http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html
• central issue to track ideas for improvements: https://github.com/hpcugent/easybuild-framework/issues/1674
• currently include:
  • synergy with --robot: make --new-pr pick up easyconfigs for dependencies
  • add support for also including patch files
  • also support PRs to easyblocks/framework repos

Other topics

• two separate repos for bioinfo easyconfigs

  • https://github.com/hpcbios/hpcbios-easybuild-easyconfigs
  • https://github.com/hpcbios/HPCBIOS-easyconfigs
  • unclear where this is going, time is a b*tch...
  • overhead
  • would something like "eb --new-pr --from-repo https://github.com/hpcbios/HPCBIOS-easyconfigs blast.eb" help?
    • 80/20 rule is the real problem: "good enough for me"
  • add support in EB for other (remote) easyconfig collections
  • add support for 'atomic' installs, don't blast away working installs
    • could also means jails (e.g. integreation wit Guix)...
    • install in jail, push to production once validated

• better structured log files, e.g. in YAML syntax: https://github.com/hpcugent/easybuild-framework/issues/1796

  • example: http://bazaar.launchpad.net/~luigi-genovese/+junk/1.8/view/head:/bigdft/tests/DFT/cubic/C/C.out.ref.yaml
  • allows to support replaying of EB sessions
    • very useful for debugging!
  • makes it easier to make sense from logs

• JHBuild as an easier way to install X11 stack

  • cfr. https://developer.gnome.org/jhbuild/stable/ & https://wiki.gnome.org/HowDoI/Jhbuild
  • may help a lot https://github.com/hpcugent/easybuild-easyblocks/pull/843

• use case for 'special' module/Lmod configs

  • cfr. https://github.com/plabrop/bic: repository for Bright-Illumina collaboration (Fotis & co) with lots of goodies related to Lmod
  • exchange info between Fotis & Alan on this
  • good resource for scripts/.specs for Lmod packages
    • Kenneth will share HPC-UGent efforts w/ Fotis (mostly housed in private repositories)