Conference call notes 20170315

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Notes on the 72nd EasyBuild conference call, Wednesday March 15th 2017 (5pm - 6pm CET)

Attendees

Alphabetical list of attendees (6):

• Damian Alvarez (JSC, Germany)
• Markus Geimer (JSC, Germany)
• Kenneth Hoste (HPC-UGent, Belgium)
• Bart Oldeman (McGill University, Canada)
• Shahzeb Siddiqui (Pfizer)
• Davide Vanzo (Vanderbilt University)

Agenda

• outlook to EasyBuild v3.1.2 (bugfix/update release)
• update on automatic style checking for easyconfig PRs
• IRC vs Slack for #easybuild chat channel
• Python on GCCcore
• Q&A

Notes

EasyBuild v3.1.2

• ETA: no later than end of this week

• bug fixes in framework, cfr. https://github.com/hpcugent/easybuild-framework/milestone/45?closed=1

  • really fix problem of superfluous load statements with hierarchical module naming scheme
    • see https://github.com/hpcugent/easybuild-framework/pull/2152
  • fix broken packaging support, changes made in EasyBuild v3.1.1 broke the way in which fpm was being called
    • see https://github.com/hpcugent/easybuild-framework/pull/2153
  • fix broken --try-software-version (for some easyconfigs), cfr. https://github.com/hpcugent/easybuild-framework/pull/2166
  • fixes for framework test suite (cfr. https://github.com/hpcugent/easybuild-framework/issues/2154)

• easyblocks: https://github.com/hpcugent/easybuild-easyblocks/milestone/37?closed=1

  • easyblock for QScintilla (https://github.com/hpcugent/easybuild-easyblocks/pull/1127)

• minor bug fixes, style fixes, enhancements in existing + a bunch of new easyconfigs, cfr. https://github.com/hpcugent/easybuild-easyconfigs/milestone/40?closed=1

  • add patch to FFTW 3.3.6 to fix broken MPI Fortran03 interface
  • lots of style fixes to make easyconfigs pass eb --check-style
  • don't use $root since it is not compatible with module files in Lua syntax
  • fix $PYTHONPATH in ROOT easyconfigs
  • new supported software (11): DBG2OLC, disambiguate, fqtrim, GFOLD, LSMS, L_RNA_scaffolder, PileOMeth, psycopg2, QGIS, QJson, QScintilla

• Is there something that people would like to add to 3.1.2?

  • Bart is waiting for https://github.com/hpcugent/easybuild-framework/pull/2104
  • Markus: no hard requirements but would be nice to see https://github.com/hpcugent/easybuild-easyblocks/pull/1102 merged.

Automatic style checking for easyconfig PRs

• goal is to soon require that all easyconfigs in repository pass eb --check-style
  • enable checking of easyconfigs style in Travis
  • NO strict requirement in eb itself
• WIP update to documentation @ https://github.com/hpcugent/easybuild/pull/311
  • see preview @ http://boegel-eb.readthedocs.io/en/easyconfigs_style/Code_style.html#easyconfigs-style-guide
• first need to make sure that all easyconfigs in easybuild-easyconfigs repository pass
  • now >90% done
• --check-style should also check order/grouping of easyconfig parameters
  • cfr. https://github.com/hpcugent/easybuild-framework/pull/2165
• Thoughts?
  • Davide: make checksum mandatory (don't make it retroactive, just for new PRs)
    • Damian: use md5 as default or something else?
    • Markus: for sanity checking md5 should be fine
    • Damian: to protect ourselves against corrupted files md5 is enough for security sha* should be more robust
    • Markus, Davide: happy with md5 for the moment
    • Shahzeb: might be useful to specify the checksum from the command line. Making checksum mandatory might break some packages with "dynamic" tarballs (matlab requires that in some cases)

IRC vs Slack for #easybuild

• obligatory XKCD: https://xkcd.com/1810
• switch away from IRC to Slack?
• support both channels?
  • OK for Kenneth, who is already using both IRC and Slack anyway
• Kenneth: possible to interface both with bot
• Davide: small issue with slack, it needs invitation, would have to figure out a way to make it work

Python in GCCcore with numpy, pandas, etc at top level

• Needs to redefine LDSHARE(https://github.com/hpcugent/easybuild-easyblocks/issues/1136)

Q&A

• Shahzeb: Is there a reason for the particular order in the python easyconfig? Why not using pip for python packages?
• Kenneth: We want to keep control of which versions are installed
• Shahzeb: Is there a way to start in a specific package (for packages with extensions)?
• Kenneth, Damian: Yes, use --skip --force. But the module has to be there. Tricks: use --module-only or have a successful bare installation to add packages on top.
• Markus: With PGI installation as an example: there are some files/directories that don't get proper permissions.
• Kenneth: EB changes read permissions, not write permissions, so if the package is "broken" that way you'll have to fix it to manually remove it
• Markus: The PGI easyblock creates an empty directory in the modules directory