4th EasyBuild hackathon meeting minutes day 3

Fotis Georgatos edited this page Nov 2, 2013 · 3 revisions
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(Thursday Oct 24th 2013, 9am-6pm)

The third day of the 4th EasyBuild hackathon consisted of attendees working with and on EasyBuild, trying to build software packages of interest, or adding support for them, and tackling open issues they care about. Pull requests were openend for the work that was finished during the hackathon.

These notes were taken by Kenneth, suggestions for additions and improvements are very welcome.

Attendees

  • Yossi Baruch (Isragrid, Israel)
  • Xavier Besseron (University of Luxembourg)
  • Marios Constantinou (University of Cyprus)
  • Stelios Erotokritou (The Cyprus Institute)
  • Fotis Georgatos (University of Luxembourg, HPC sysadmin and active contributor)
  • Kenneth Hoste (HPC-UGent, EasyBuild developer and release manager)
  • Thekla Loizou (Cyprus Institute, local organization)
  • Dina Mahmoud Ibrahim (Cairo University)
  • Dr. Bernd Mohr (Jülich Supercomputing Centre, UNITE)
  • Alan O'Cais (Jülich Supercomputing Centre)
  • Andreas Panteli (The Cyprus Institute)
  • George Tsouloupas (The Cyprus Institute)

(note: remote participation was not a success, no conference calls took place)

Program

(note: started with some delay due to setting up recording equipment in combination with setup for potential remote attendees)

  • [9am - 6pm] hackathon (extended due to issues with the bus in the morning)
  • [6pm - 9pm] aftermath: discussions

Hackathon notes

  • Bernd
  • default output should clearly split output for different builds
  • e.g. include a --------...------- line in between
  • working on Tau, which uses -prefix (instead of --prefix), and requires multiple configure/build/install cycles
  • very easy with EasyBuild (after support for tweaking --prefix was added to ConfigureMake easyblock, see easyblocks#287)
  • this is quite convincing since a somewhat complex/non-standard build is so easy to get working
  • Vampir is a single-command binary installation, but Binary easyblock doesn't allow this easily?
  • Binary easyblock should accept an easyconfig parameter like install_cmd (TODO: fix this)
  • Paraver software package requires list preconfigopts to be supported (is it?)
  • Xavier
  • toolchains/mpich.py and toolchains/mpich2.py are almost identical, lots of code duplication! (TODO: open issue)
  • we need an easyblock for software 'bundles' (e.g. Bundle) (TODO: fix this)
  • currently, Toolchain is used for that, but a toolchain is more than just a collection of dependencies
  • especially when we start setting environment variables for compiler toolchain in the module
  • bug in HDF5 easyblock when trying to build a serial version (see easyblocks#286)
  • discuss setup for making only a part of the modules available to users, via a separate $MODULEPATH and symlinking the modules
  • recursive use of --try-toolchain isn't working yet, would be really useful if this gets fixed (see framework#450)
  • enable building of shared libraries for MPICH (see easyconfigs#482)
  • facilitate contribuing to EasyBuild wiki by making a dedicated repository for it (TODO: fix this, document it, announce on mailing list)
  • simply define an additional remote, keeping things in sync should be fairly easy
  • git pull origin master for edits directly on wiki
  • git pull github_hpcugent master for edits via PRs
  • merge conflicts and push back to origin to update wiki pages
  • iomkl toolchain module loads both OpenMPI (element of toolchain) and impi (dependency for imkl)? (TODO: open issue)
  • Kenneth
  • enhance ConfigureMake easyblock such that --prefix can be overruled
  • planning for future EasyBuild conf. calls
  • fixed time slot, max. 30m, bi-weekly
  • tick-tock between CET timeslot and US West Coast timeslot (late evening CET)
  • for now, fixed to every 1st/3rd Tuesday of the month, 3pm CET
  • TODO:
  • set up Google calendar
  • create a wiki page per conf call
  • send reminder day before via EasyBuild mailing list
  • Andreas
  • still looking into UNITE/ExtraE issues with -fPIC
  • seems like rebuilding both binutils and GCC with -fPIC would be required
  • should try and see whether removing -fPIC from ExtraE flags helps
  • Marios
  • AMBER: working on a (hackish) easyconfig file
  • also requires an easyblock to resolve things properly in the end
  • Thekla
  • looking into ncdf and ncdf4 R packages
  • as a separate module, since they have netCDF as dependency
  • ran into a zlib version clash between R module and netCDF
  • resolved by creating new easyconfig for R/3.0.2, and using same zlib as for netCDF
  • add easyconfig for Silo and ParFlow (easyconfigs#483)
  • add easyconfig for CDO (easyconfigs#484)
  • Fotis
  • goolfc update (see easyconfigs#477)
  • new GCC, OpenMPI and other bits; also employed most recent CUDA contributed by @ajdecon; in short, latest and greatest
  • -malign-double should be enabled by default, which is required by CUDA for getting good performance and/or ABI compatibility (see framework#627)
  • help people out with questions/problems
  • Dina
  • try and get VMD plugins installation working, as a first step towards VMD support
  • results pushed to easybuild.experimental
  • Alan
  • manually create modules for system Intel compiler, MPI libraries, and Intel MKL
  • should set $EBROOT... and $EBVERSION...
  • version for icc, ifort and imkl modules is important to get exactly right
  • version of MPICH2 module is less important, should include versionsuffix that indicates it's a custom version (ParaStation)
  • need separate modules that each set the correct value for conflict (same as module name)
  • EasyBuild relies on this when checking toolchain definition against elements of toolchain module
  • create impmkl easyconfig file to obtain toolchain module
  • add impmkl toolchain definition to EasyBuild (Kenneth`, see framework#736)
  • Yossi
  • add easyconfig for new version of scipy (easyconfigs#480)
  • add easyconfig for IPython (easyconfigs#485)

Discussion notes

(with Xavier, Fotis, Kenneth)

  • jail tool is bottom-up
  • FG: if you whitelist something, you may start missing stuff again (ie. not reporting osdependencies properly)
  • KH: only if you resolve it by allowing OS deps?
  • FG: it is probably very wise to adhere to the rule "osdependencies reported via deps, are redundant and not needed"
  • top-down: via ldd
  • but, then stuff like static libs, required header files, etc. are missed
  • XB: makeinstall tool to easily create packages, but doesn't take into account deps, etc.
  • FG: checkinstall is probably what we want to refer here; ref. http://asic-linux.com.mx/~izto/checkinstall/
  • FG: getting environment modules 3.2.10 into RHEL6
  • required to reel in grid people; FG has already been bugging Gergely Sipos since spring 2013 about EB.
  • EasyBuild is a (very) consistent way to roll out software, even cross-distro, and pretty possible cross-OS
  • technical reason for using only top (ictce/goolf/...) toolchains, and just rebuilding tools like CMake with those
  • recursive --try-toolchain will not work with other approaches to only obtain a minimal set of modules that easily allow switching MPI stacks
  • rebuilding software stack with another toolchain would require lots of manual work
  • [off-topic] discuss Valentin's (Uni.lu) work on using GAs to autotune configure options for best performance
  • using EasyBuild to rebuild software packages with different setup
  • mainly for GROMACS, QuantumESPRESSO (and considering RaxML for its fancy MPI with pthreads hybrid model)
  • should be really strict about testing and validating correctness of resulting binaries
  • also consider using modules to predict outcomes and let that steer the GA, to significantly speed up search process
  • FG: RaxML is a special case; it is significantly tuned to specific processor architectures (eg. x86 L1/2/3 caches)
  • which makes it extremely sensitive to the value of particular config options and run-time MPI stack tuning
  • can machine learning models catch/learn something like that? what can we extract and automate out of this?