Conference call notes 20170301 - easybuilders/easybuild GitHub Wiki

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Notes on the 71st EasyBuild conference call, Wednesday March 1st 2017 (5pm - 6pm CET)

Attendees

Alphabetical list of attendees (8):

• Damian Alvarez (JSC, Germany)
• Pablo Escobar (UniBas/sciCORE, Switzerland)
• Fotis Georgatos (Illumina)
• Kenneth Hoste (HPC-UGent, Belgium)
• Alan O'Cais (JSC, Germany)
• Bart Oldeman (McGill University, Canada)
• Åke Sandgren (Umeå University, Sweden)
• Davide Vanzo (Vanderbilt University)

Agenda

• outlook to EasyBuild v3.1.1 (bugfix/update release)
• allow running EasyBuild as root
• Python/R/Perl easyconfigs (& more) for 2017a toolchains
• Q&A

Notes

EasyBuild v3.1.1

• minor bug fixes in framework, cfr. https://github.com/hpcugent/easybuild-framework/milestone/44?closed=1
• minor bug fixes & enhancements in easyblocks, cfr. https://github.com/hpcugent/easybuild-easyblocks/milestone/36?closed=1
• minor bug fixes, style fixes, enhancements in existing + a bunch of new easyconfigs, cfr. https://github.com/hpcugent/easybuild-easyconfigs/milestone/39?closed=1

Allowing to run EasyBuild as root

• see https://github.com/hpcugent/easybuild-framework/pull/2123
• makes sense for Singularity
• doesn't allow only running part of procedure as root...
• targeted for EB v3.2.0

Easyconfigs for 2017a toolchains

• already some dependencies with GCCcore/6.3.0, but not yet for R/Python/Perl with */2017a
• partially because we want to take the opportunity to tackle a couple of enhancements, e.g.:
  • separate Python & Tkinter: https://github.com/hpcugent/easybuild-easyconfigs/pull/4225
  • plotting support in R: https://github.com/hpcugent/easybuild-easyconfigs/issues/2742
• easy_update only (supposedly) works for R & Python, not Perl
  • see https://github.com/hpcugent/easybuild-framework/pull/2061
    • Pablo/Adam: still needs manual tweaking for R (Pablo) & Python (Adam)
    • Pablo: doesn't actually pull latest version of R packages consistently
  • Pablo: generateEasyConfig.R works well for R
    • see https://github.com/fgeorgatos/easybuild.experimental/blob/master/users/pneerincx/generateEasyConfig.R
• https://github.com/hpcugent/easybuild-easyconfigs/labels/2017a

Other topics

• Fotis: preferred toolchains for bioinfo?

  • input from Pablo/Adam?
    • Pablo: quite conservative, still using goolf...
      • stuck to goolf because of user expectations, currently using goolf/1.7.20
      • could be fixed using custom module naming scheme that maps foss to goolf in module names
    • more about how toolchain is composed + versions, name isn't really important
    • Fotis: goolf/1.7.20 is convenient w.r.t. GCC 4.8.4
    • Adam: now foss/2016b
      • occasionally run into problems due to newer GCC version (5.3)
    • Pablo/Adam: to maximise the effort, a continuous integration service could be used to test with other toolchains
      • Travis can't be used for this due to time constraints for jobs
        • could be partially solved via containers, but probably not good enough to get 100% coverage
      • Pablo is working on an internal setup with GitLab for something like this, could be made public in the long term
        • GitLab seems to be up to the job
        • but, time is a bitch that takes no prisoners...
        • Fotis/Adam could try and pitch in to get this set up
        • also potential interest by Rob?

• Alan: SystemMPI easyblock: https://github.com/hpcugent/easybuild-easyblocks/pull/1106

  • works well with system OpenMPI & Intel MPI
  • Alan is processing last remarks now
  • may land in EasyBuild v3.1.1

• Davide: user request to figure location of lib/include directories for particular modules

  • user need to known which locations to specify for libraries/include files
  • current approach, via 'module show'
  • locations are not strictly needed, since $CPATH and $LIBRARY_PATH
  • or tell users to use -I$EBROOTX/include -L$EBROOTX/lib