General software and libraries (Hexagon)

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Full up to date list is available at NOTUR

Application software by discipline:

Bio-informatics

Software Version Module Resources Notes
NAMD 2.8b1 namd Homepage Recommended env variables (loaded with module):
export MPICH_PTL_SEND_CREDITS=-1
export MPICH_MAX_SHORT_MSG_SIZE=8000
export MPICH_PTL_UNEX_EVENTS=100000
export MPICH_UNEX_BUFFER_SIZE=100M
aprun -n $PBS_NNODES -cc cpu namd2

Use Support for support.

MEME 4.4.0 meme Homepage NOTE: linking was forced on this installation. Please compare output with previous (non-forced) runs for correctness.

Use Support for support.

Chemistry

Software Version Module Resources Notes
ADF NA NA NA Not supported on Hexagon
Daulton User installation NA NA Use Support for support
Gamess NA NA NA Not supported on Hexagon
Gaussian NA NA NA Not supported on Hexagon
Molpro NA NA NA Not supported on Hexagon
NWChem 5.1.1 nwchem-cnl The module sets necessary variables
VASP User installation NA NA Use Support for support

Fluid dynamics

Software Version Module Resources Notes
OpenFOAM 1.5, 1.6, 1.7.1 openfoam Homepage Limited amount of solvers are available due to static linking

Geosciences

Software Version Module Resources Notes
BOM User installation NA Bergen Ocean Model Use Support for support
EnKF User installation NA Use Support for support
HYCOM User installation NA Homepage Use Support for support
MYCOM User installation NA MICOM group homepage Parallel MICOM page Use Support for support
NCL 5.1.1, 5.2 ncl_ncarg Default version is aprun compatible. If you are missing some features, you can use ncl_ncarg/##-login version
NCO 3.9.6, 4.0.0 nco-cnl
ROMS User installation NA Homepage Use Support for support
UDUNITS2 2.1.7 udunits-cnl
WPS 3.0.1, 3.1, 3.1.1, 3.2, 3.2.1, 3.3 WPS-cnl WPS site NOTE: some results can be different (it depends on the input files) if WRF module is loaded. In this case please ensure that WRF module is not loaded
WRF 2.2.1, 3.0.1.1, 3.1, 3.1.1, 3.2, 3.2.1, 3.3 WRF-cnl WRF site If you are using spectral nudging you will need to use 8000MB of memory per core. Otherwise despite of message that spectral nudging was enabled the output netcdf file will not be properly produced (see case #21869)
WRF (special version) 3.1.1, 3.2 WRFquiet-cnl This version of WRF is not producing rsl* files during execution, but send all output to STDOUT&STDERR. You can use this module to avoid producing big amount of rsl files.

Remember! aprun wrf.exe > /dev/null

WRFDA 3.1.1, 3.2 WRFDA
WRFNL 3.2 WRFNL
WRFPLUS 3.2 WRFPLUS
WRFchem 3.0.1.1, 3.1, 3.1.1, 3.2, 3.2.1, 3.3 WRFchem-cnl WRFchem site
WRFpolar-cnl 3.1.1 WRFpolar-cnl

Performance libraries

Software Version Module Resources Notes
BLAS
LAPACK
ScaLAPACK
BLACS
IRT
SuperLU sparse solver routines
CRAFFT
System xt-libsci CrayXT Programming Environment User Guide BLAS and LAPACK include routines from the 64-bit libGoto library from the University of Texas (GotoBLAS).
PETSc:
MUMPS
SuperLU
ParMETIS
HYPRE
System petsc CrayXT Programming Environment User Guide
ACML System acml CrayXT Programming Environment User Guide
FFTW System fftw CrayXT Programming Environment User Guide
Fast_mv System libfast CrayXT Programming Environment User Guide

Scientific data libraries

Software Version Module Resources Notes
NetCDF 3 System netCDF
NetCDF 4 System netcdf CrayXT Programming Environment User Guide
NetCDF 4 parallel System netcdf-hdf5parallel
HDF5 System hdf5 CrayXT Programming Environment User Guide Will be loaded automatically with the module netcdf
HDF5 parallel System hdf5-parallel Will be loaded automatically with the module netcdf-hdf5parallel

General

Software Version Module Resources Notes
Matlab 2007b, 2008b, 2009a matlab Can not be run on compute nodes, therefore must be used only to preview some data, but not massive calculations
Gnuplot 4.2.5 gnuplot-login
GSL 1.11 gsl-cnl
Perl 5.8.8 perl-cnl
Python 2.6.2, 2.6.5 python-cnl Version 2.6.2 is statically linked and contains only essential Python modules, numpy, netCDF4, Cython, mpi4py
Version 2.6.5 is dynamically linked, contains mostly all Python modules, NumPy, netCDF4, SciPy, Matplotlib, lxml, pyYaml
Paraview 3.6.1 paraview-cnl, paraview-login Statically compiled, supports only pvbatch, with MPI enabled
R 2.15.0, 3.0.2 R To run R in batch (on compute nodes) adjust your job script as follows:
#PBS -l mppwidth=1,mppnppn=1,mppmem=32000mb
#
# fix for temporary filesystem
export TMP=/work/$USER/
export TMPDIR=$TMP
#
aprun -B R --no-save <./myscript.R
Trilinos System trilinos http://trilinos.sandia.gov/index.html