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9th EasyBuild hackathon

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Kenneth Hoste edited this page Sep 4, 2017 · 19 revisions

EasyBuild hackathon @ Basel

Basic Information

  • date: Monday May 4th - Tuesday May 5th 2015
  • venue: Multifunction room Debatti, 1st floor at Life Science Center, Keilaranta 14, CSC, Espoo, Finland (see https://www.csc.fi/contact-info)
  • in conjunction with the Nordic e-Infrastructure Conference (NeIC) see http://neic2015.nordforsk.org/
  • organisers: Kenneth Hoste (HPC-UGent), Olli-Pekka Lehto (CSC.fi)

Attendees

For practical reasons, the number of participants is limited.

Please contact Kenneth Hoste ([email protected]) or Olli-Pekka Lehto ([email protected]) to register.

list of confirmed attendees:

  • Luis Alves (CSC, Finland)
  • Jani Heikkinen (CSC, Finland)
  • Petar Forai (IMP/IMBA, Austria; EasyBuild user and contributor)
  • Johan Guldmyr (CSC, Finland)
  • Kenneth Hoste (HPC-UGent, Belgium; EasyBuild developer and release manager)
  • Dan Jonsson Johan (University of Tromsø, Norway)
  • Olli-Pekka Lehto (CSC, Finland) excused
  • Marco Passerini (CSC, Finland)
  • Jarmo Pirhonen (CSC, Finland)
  • Ari-Matti Saren (CSC, Finland)
  • Atte Sillanpää (CSC, Finland)

Topics

Attendees are free to work on what they want, but a couple of topics of interest are typically attached to each hackathon. The intention is to have discussions on these topics, and that some attendees work on these issues:

  • Introduction to EasyBuild
  • EasyBuild on Cray

Agenda

(initial agenda, subject to change)

The hackathon slots are intended to work on what attendees are most interested in, with support from the experts.

Monday May 4th 2015

  • 9am - 10am: setup, coffee, introductions
  • 10am - 12pm: Introduction to EasyBuild (and Lmod) (Kenneth Hoste) (slides)
    • incl. demos, Q&A
  • 12pm - 1pm: lunch
  • 1pm - 2pm: EasyBuild on Cray: current status & open problems (Petar Forai) (slides)
  • 2pm - 3pm: Getting started with EasyBuild and Lmod: installation and configuration, basic usage (hands-on)
  • 3pm - 5pm: hackathon

Tuesday May 5th 2015

  • 9am - 12pm: hackathon (continued)
  • 12pm - 1pm: lunch
  • 1pm - 5pm: hackathon (continued)

Notes

Monday

  • Luis: use EasyBuild to install software in CVMFS

    • via Stratum server to have write access to filesystem

  • build and install without having modules at all?

    • EasyBuild relies heavily on modules, for resolving dependencies and checking what's already there
    • use --installpath-modules to locate modules somewhere else, without exposing them to users
    • both, then you're on your own w.r.t. providing runtime libraries, etc. (which may not be a big problem when linking statically or using rpath)

  • (Jarmo) 'module purge' should never be used on a Cray, default set of loaded modules is too fragile

    • use 'module swap' instead (sidenote: also in generated modules?)
    • this issue came up when running into problems when (re)loading the slurm module after loading PrgEnv (after using purge)

  • problem with system-installed Lmod (which is too old) still being picked on Taito, via $LMOD_CMD which gets redefined via /etc/profile.d

  • support for eb --show-current-config would be really useful, since it's not always clear which configuration has been done on the various levels, and how these interact (e.g. --prefix with $EASYBUILD_INSTALLPATH, etc, etc)

  • (Jarmo) support for directly specifying compiler flags (i.e. $CFLAGS value, etc); useful to have full control if needed (e.g., when benchmarking)

  • using system tcsh avoids hanging WRF build on Sisu => don't include EasyBuild-built tcsh as a build dep?

  • how to avoid stepping on each others toes when having multiple instances running?

    • problem is not really unique to EasyBuild
    • support for using --job with GC3Pie may help?

  • (Kenneth) source_urls for netCDF are broken, old sources have been moved to /old

  • (Johan) --search should only take basename into account when matching with provided pattern, not whole path

Tuesday

  • (Atte) parallel build can be reenabled for recent CP2K versions (works fine for 2.6.1)

    • drop parallel = 1 in recent CP2K easyconfig files

  • (Atte) GROMACS requires that a script is sourced before it is used, how can that be handled in module file?

    • similar for OpenFOAM
    • module file can not source a script (why not? Kenneth will ask Robert)
    • msgonload to remind user to source the script
    • use env2 tool (see Lmod's contrib dir) to generate module file for script to-be-sourced
      • supports both Tcl and Lua module files
      • just evaluates, doesn't retain login in script, so far from perfect

  • performance testing of CP2K

    • benchmarks included in CP2K sources (see tests/QS/benchmark*)
    • benchmarks rely on fact that ../../../data is around
    • simple H2O benchmarks, different sizes
    • benchmark_HFX: test for psmp, 10x faster with hybrid functionals
    • how to build a static build of CP2K (doesn't work in 1-2-3 on Cray)

  • (Jarmo) support for using external modules as toolchain in EB

    • e.g. existing intel modules on Taito
    • provide compilers + MPI + MKL + IPP + TBB
    • FFT is enabled in MKL for some of them (automagically available in recent versions, according to Ake?)
    • should be possible via (very simple) Python module for custom toolchain, e.g. intel-taito, cfr. approach for Cray modules
    • support for --custom-toolchains configure option should be added (next to --custom-easyblocks, --custom-module-naming-schemes)
    • see https://github.com/hpcugent/easybuild-framework/issues/1010

  • missing documentation on use of --try @ easybuild.readthedocs.org

  • (Jarmo) modules for Intel tools do not set $MIC_* environment variables yet

    • Taito provides a bunch of nodes with MIC cards

  • --try-amend=runtest=False doesn't work as expected: False vs 'False'

    • can only be resolved by properly handling types for easyconfig parameters

  • --try-software-version --try-toolchain --dry-run => recursion is disabled entirely when --try-software-version is used, which is wrong; only changing version should not be applied recursively, rest should!

  • missing cmdline option: eb --list-software

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