3rd EasyBuild hackathon meeting minutes day 2
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(Tuesday Mar. 12th 2013, 10am-6pm)
The second day of the 3rd EasyBuild hackathon was the first day of the actual 2-day hackathon. The attendees got to know EasyBuild better by installing it and getting hands-on experience on building software. Some already even got to adding support for new software by producing their own easyconfig files, or started fixing outdated easyblocks/easyconfigs for software they care about.
These notes were mainly taken by Kenneth and Jens, with contributions by Fotis.
- Kenneth Hoste (HPC-UGent, EasyBuild developer and release manager)
- Jens Timmerman (HPC-UGent, EasyBuild developer)
- Fotis Georgatos (University of Luxembourg, HPC sysadmin and active contributor)
- Thekla Loizou (The Cyprus Institute, HPC user support)
- George Tsouloupas (The Cyprus Institute, HPC sysadmin and user support)
- Mohamed Gafaar (Bibliotheca Alexandrina, HPC sysadmin/user support)
- Dina Mahmoud Ibrahim (Cairo University, HPC sysadmin/user support)
- Alan O'Cais (Jülich Supercomputing Centre, HPC user support & LinkSCEEM)
- Alexander Schnurpfeil (Jülich Supercomputing Center, HPC user suppot)
- Nicolas Kanaris (The Cyprus Institute, HPC user (OpenFOAM))
- George Fanourgakis (The Cyprus Institute, HPC user, molecular dynamics)
- Stelios Erotokritou (The Cyprus Institute, HPC user support/PRACE)
- [10am-6pm] 1st day of actual hackathon
- [6pm-8.00pm] aftermath: discussathon with George T., Fotis, Jens T. and Kenneth
- discuss a way to make modules conflict for compilers, MPI, BLAS/LAPACK, ...(?)
- ie. it makes not much sense to have 2 different MPI stacks loaded together, better spit a warning
- KH?: one way would be to add ghost modules being loaded as e.g. a compiler is needed
- add extra
conflict COMPILERline in GCC, icc, ifort modules
- shows up in
ifortneeds special attention, they're both compilers
- no way of easily combining GCC and Intel compilers anymore if you wanted to
- George F.: Ferret
- ported outdated easyblock and easyconfig for Ferret
- patch out hardcoded from *.mk file used by Ferret
- add missing dependencies in easyconfig (zlib, ncurses, cURL, ...)
- OpenFOAM / pyFOAM
- look into OpenFOAM 'extensions' (commercial ThirdParty stuff)
- getting EasyBuild to work on JUROPA (SLES/x86-64)
- with Tcl environment modules
- interested in building NWChem
- work on training exercises and Getting Started wiki page (gzip, ...)
- build GCC in VM on her laptop
- build OpenMPI with dummy toolchain during waiting
- building basic libraries
- look into UNITE and its dependencies
- George & Fotis
- CUDA toolkit 5.0.35; DONE.
- GROMACS v4.6 (w/o CUDA); DONE.
- FFTW 3.3.3; DONE.
- OpenMPI v1.7 for DMA to GPU support
- only 1.7rc8 is available; DONE.
- Fortran libraries were renamed in this version
- requires GCC newer than v4.8 (which hasn't been released yet)
- see http://www.open-mpi.org/software/ompi/versions/ (bottom of page)
The incorrect interface was removed in Open MPI v1.7. To be clear: applications that use the old/incorrect MPI_SCATTERV binding will no longer be able to compile properly (*). Developers must fix their applications or use an older version of Open MPI. (*) Note that using this incorrect MPI_SCATTERV interface will not be recongized in v1.7 if you are using gfortran (as of gfortran v4.8). This is because gfortran <=v4.8 does not (yet) have the support Open MPI needs for its new, full-featured "mpi" and "mpi_f08" modules. Hence, Open MPI falls back to the same "mpi" module from the v1.6 series, but the "large" size of that module -- which contains the MPI_SCATTERV interface -- been disabled because it is broken. Further, this "large" sized (old) "mpi" module has been deemed unworthy of fixing because it has been wholly replaced by a new, full-featured "mpi" module. We anticipate supporting gfortran in the new, full-featured module in the future.
- OpenMPI v1.6.3 & v1.6.4 (Fotis); DONE.
- with slightly more relaxed sanity check paths
- goolf 1.4.10; ~DONE (deviations: FFTW is the default version, so far)
- GCC 4.7.2
- OpenMPI 1.6.4
- OpenBLAS 0.2.6
- LAPACK 3.4.2
- FFTW 3.3.3 (single/double)
- ScaLAPACK 2.0.2
- goolf 1.5.10; same as above, except with OpenMPI v1.7rc8; existing just as a prototype really
- gmolf: no much progress on that yet
- CUDA toolkit 5.0.35
- GROMACS v4.6 w/ CUDA support
- Jens T.
- help out with several people
- write easyconfig for OpenBLAS
- help out with several people