Provide popular PRACE packages, ensure they are available as a meta-module

[boegel]

(originally by @fgeorgatos)

most of the content on this has been shamelessly copied^H^H^H^H^H^H borrowed from:
https://openwiki.uninett.no/metacenter:reference:noturcpe

[boegel]

Moved from easybuilders/easybuild-framework#333

[fgeorgatos]

Updating status as of v2.2.0:

Required Components

Application name and remarks follow:

• FEniCS fenics ## FG: I understand DOLFIN covers this fine, any objections? Seems no.
• FFTW fftw ## version 2 pending and 3 OK
• GSL gsl
• MATLAB matlab
• PETSc petsc ## to check: built with double,complex,64-bit indices
• R R
• Trilinos trilinos
• CMake cmake
• GridFTP gridftp
• gnuplot gnuplot
• HDF5 hdf5
• hpn-ssh clients only
• Mayavi mayavi version 2 ## EPD might provide this
• NetCDF netcdf
• PAPI papi
• ParaView paraview
• pigz pigz multicore-parallel gzip
• Python python see the Python subsection
• TotalView totalview
• Visit visit by LLNL ## GJB may visit it
• VTK vtk

Python module

There is also an apparent need for an extended Python module, covering

• Cython
• gnuplot Python interface to gnuplot
• Ipython ## EPD might provide this
• matplotlib
• mpi4py requires MPI
• NumPy
• petsc4py requires PETSc
• Pypar
• PyTables requires hdf5
• PyTrilinos requires hdf5, trilinos
• ScientificPython
• SciPy
• SciTools ## EPD might provide this
• SymPy ## EPD might provide this

PRACE CPE Compatibility - issue objective

Finally, the PRACE CPE is the compatibility layer centers strive to be compliant against:

• Bash bash ## VP has this?
• BLACS blacs [1]
• BLAS blas [1]
• C compiler c [2]
• C++ compiler c++ [2]
• Emacs emacs
• Fortran compiler fortran [2]
• Java compiler java [1]
• LAPACK lapack [1]
• MPI mpi [1]
• ScaLAPACK scalapack [1]
• tcsh tcsh ## FG/VP has a version
• GNU Make gmake ## FG should fix this
• NEdit nedit ## FG needs this
• Perl perl
• Tcl tcl
• Tk tk
• OpenSSH openssh clients only
• PRACE CPE prace container module ## ie. this is a Toolchain per EasyBuild parlance!

As per the following, some aliasing work will be required (or it can be done via alt. namespace):

[1] provide an alias to the recommended, highest performance, library or utility, supporting the platform recommended compiler. In case of a library, this might be fully contained in another product. If a recommended vendor library does not fully contain the module file library (including its API), separate libraries must be provided (e.g. IBM ESSL).
[2] provide an alias to the recommended compiler, capable of compiling parallel (MPI) programs, with or without OpenMP.

btw. sources to bootstrap some easyconfigs needed above - some are working already

Mockup -untested- versions for some of the missing small items above can be found at:
https://github.com/fgeorgatos/easybuild.experimental/blob/master/contrib/pkgsrc/20121226/e/emacs-22.3.eb
https://github.com/fgeorgatos/easybuild.experimental/blob/master/contrib/pkgsrc/20121226/n/nedit--src.eb

Default PRACE module dependencies and variables

The PRACE module should automatically bring up as dependencies (ie. behave as an extended toolchain):
c c++ fortran mpi blas lapack blacs scalapack fftw/3 netcdf hdf5
and ensure it adjusts variables (ie. define modextravars in relation to $EBPRACEDEVEL?):

$PRACE_{FFLAGS,CFLAGS,LDFLAGS,STORE,SCRATCH,ARCH}

PRACE Applications - this is fyi. only

Finally, these apps have to be available as modules, too:

• mpiBLAST mpiblast
• LAMMPS lamps ## LS2/GF cares about this
• NAMD name ## LS2/GT is working on this
• ADF adf
• CPMD cpmd ## LS2 cares about this?
• Dalton dalton
• Gaussian gaussian ## LS2 cares about this? N/A
• VASP vasp ## LS2/GF cares about this?
• OpenFOAM openfoam

PRACE Benchmarks - this is fyi. only

For completeness -but not a prerequisite to resolve this issue-, here are the applications selected for the PRACE application benchmark suite:

• QCD, particle physics
• Quantum_Espresso, computational chemistry
• NAMD, computational chemistry
• CPMD, computational chemistry
• Code_Saturne, computational fluid dynamics
• GADGET, astronomy and cosmology
• TORB/EUTERPE, plasma physics
• WRF, atmospheric modelling
• NEMO, ocean modelling
• CP2K, computational chemistry
• GROMACS, computational chemistry # WJ/FG/GT/KH have been working on this, including CUDA support
• NS3D, computational fluid dynamics
• AVBP, computational fluid dynamics
• HELIUM, computational physics
• TRIPOLI-4, computational engineering
• PEPC, plasma physics
• GPAW, computational chemistry
• ALYA, computational mechanics
• OCTOPUS, computational chemistry
• BSIT, computational geophysics
• ELMER, computational engineering
• SPECFEM3D, computational geophysics

Ref: http://www.hpcwire.com/hpcwire/2010-02-15/prace_benchmark_suite_finalised.html

[fgeorgatos]

Hoi *,

Getting ready to contribute the first iteration of the PRACE environment during the hackathon @ Cyprus:
https://github.com/fgeorgatos/easybuild.experimental/tree/master/users/fgeorgatos/PRACE

Toolchains tested: goalf/1.1.0, ictce/4.1.13, ictce/5.2.0

We still have some way to go as regards minor tools and also variables, as defined here:
http://www.prace-ri.eu/PRACE-Common-Production

Overall, it's looking good but gives some errors with the $EBDEVELPRACE
(it has to be tuned, because the whole point of the PRACE CPE is to eliminate such issues)

The upcoming hackathon in Nicosia next week is a prime opportunity to follow up on the issues,
before we hit the trigger for the grand pull request.

Don't be dismayed to give it a try, its status is already pretty good for the majority of users;

fgeorgatos@gaia-10:~/easybuild.experimental/users/fgeorgatos/PRACE$ module load PRACE
fgeorgatos@gaia-10:~/easybuild.experimental/users/fgeorgatos/PRACE$ module list
Currently Loaded Modulefiles:
  1) EasyBuild/1.2.0               5) imkl/11.0.2.146               9) Bash/4.2-ictce-5.2.0         13) zlib/1.2.7-ictce-5.2.0       17) Bison/2.5-ictce-5.2.0
  2) icc/2013.2.146                6) ictce/5.2.0                  10) tcsh/6.18.01-ictce-5.2.0     14) Szip/2.1-ictce-5.2.0         18) Doxygen/1.8.1.1-ictce-5.2.0
  3) ifort/2013.2.146              7) make/3.82-ictce-5.2.0        11) Tcl/8.5.12-ictce-5.2.0       15) HDF5/1.8.9-ictce-5.2.0       19) netCDF/4.1.3-ictce-5.2.0
  4) impi/4.1.0.030                8) Java/1.7.0_10                12) Tk/8.5.12-ictce-5.2.0        16) flex/2.5.35-ictce-5.2.0      20) PRACE/20130306-ictce-5.2.0
fgeorgatos@gaia-10:~/easybuild.experimental/users/fgeorgatos/PRACE$
fgeorgatos@gaia-10:~/easybuild.experimental/users/fgeorgatos/PRACE$ echo $EBDEVELPRACE
/home/users/fgeorgatos/.local/easybuild/software/PRACE/20130306-ictce-5.2.0/easybuild/PRACE-20130306-ictce-5.2.0-easybuild-devel

enjoy,
Fotis

[fgeorgatos]

Progress report:
We now have 2 PRACE toolchains, which cover both recent Intel and GNU compiler toolkits:
https://github.com/fgeorgatos/easybuild.experimental/tree/master/users/fgeorgatos/PRACE
PrgEnv business requires more work but the structure I think is relatively correct.

[fgeorgatos]

this feels like necroposting, nevertheless here is some newer information in relation to $subject:
https://repository.prace-ri.eu/git/UEABS/ueabs#the-application-codes-that-constitute-the-ueabs-are

It basically has explicit instructions/info about the PRACE benchmark suite's components:

• ALYA
• Code_Saturne
• CP2K
• GADGET
• GPAW
• GROMACS
• NAMD
• NEMO
• PFARM
• QCD
• Quantum Espresso
• SHOC
• SPECFEM3D

[boegel]

Oh they even added TensorFlow recently to it, see https://repository.prace-ri.eu/git/UEABS/ueabs#tensorflow .

Now it's getting interesting... I've been looking for a decent TensorFlow benchmark for a while now.