General software and libraries (Hexagon)

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This page contains software specific notes and is not a full list of software available on Hexagon.

For a full list please run module available on Hexagon login node.

Applications

Software Version Module Notes
Gaussian all gaussian/g16 1. You will need to ask for a CCM enabled account. Please contact Support

2. Please use this example script to learn how to get started

Matlab all matlab Can not be run on compute nodes, therefore must be used only to preview some data, but not massive calculations
NAMD all namd 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 $PBS_NNODES -cc cpu namd2
Python all python Only performance dependent, MPI and some basic packages are compiled into the Python modules, users are encouraged to use pip and their local folders to install extra Python packages.
Python miniconda python/miniconda3-4.4.10
R all R To run R in batch (on compute nodes) adjust your job script as follows:
#SBATCH --ntasks=32
#
# fix for temporary filesystem
export TMP=/work/users/$USER/
export TMPDIR=$TMP
#
aprun -n1 -N1 -m32000M R --no-save <./myscript.R
Trilinos all trilinos http://trilinos.sandia.gov/index.html
WRF all WRF 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)

Performance libraries

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

Scientific data libraries

Software Module Notes
NetCDF 3 netcdf
NetCDF 4 cray-netcdf Pay attention that netcdf4 modules have prefix cray- as well as hdf5 modules
NetCDF 4 parallel cray-netcdf-hdf5parallel
HDF5 cray-hdf5 Will be loaded automatically with the module cray-netcdf
HDF5 parallel cray-hdf5-parallel Will be loaded automatically with the module cray-netcdf-hdf5parallel