HPC - Software

Software

The following tables show the status of software that has been requested and/or installed on HPC systems for general use. Tables are divided between Compilers, Applications, and Libraries. Most of the applications require group membership for access. If you encounter a "permission denied" error for one of the packages, please contact oit_hpc@help.ncsu.edu and we will (if the software license permits), add you to the list of users. For ANSYS and ANSYS CFD (previously CFX), please request access using the button provided below (you have to agree to some software licensing terms). For Gaussian a license acknowledgement needs to be signed and returned to obtain access.

Compilers

Name	Status sam cluster	Status henry2 cluster	Notes
Intel		Installed 7.1, 8.0, 8.1 9.1, 10.1, 11.1	Intel Linux Compilers Web Site
Portland Group	Installed 7.2-2, 9.0-4	Installed 5.0, 5.2, 6.0 6.1, 7.0-6 7.2-2, 9.0-4 10.5	http://www.pgroup.com/

Applications

Name	Status sam cluster	Status henry2 cluster	Notes
Abinit		Installed 7.2.1	An ab initio quantum chemistry package
ABAQUS		Installed 6.7-5 6.8-4 6.9-EF	http://www.abaqus.com/ Commercial Finite Elment Package
AMBER		Installed 8 9 10	http://amber.scripps.edu/
ANSYS		Installed 12.1	http://www.ansys.com/ Commercial Finite Elment Package
ANSYS CFX		Installed 10.0, 11.0	http://www.ansys.com/cfx
bioperl		Installed 1.4.1, 1.6.1	BioPerl
mpiBLAST		Installed	A parallel version of the NCBI program BLAST
CHARMM		Installed c35b3	A molecular dynamics program
CPLEX		Installed 9.0,10.1, 11.2, 12.1	Linear, Mixed-integer and Quadratic solvers http://www.ilog.com/products/cplex/
CPMD		Installed 3.13.2	Ab initio molecular dynamics
DL_POLY_4		Installed 4.01	http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
Elmer		Installed 5.4.1	Open Source Finite Element Software for Multiphysical Problems http://www.csc.fi/english/pages/elmer
ESPRESSO		Installed 4.2.1	Electronic-structure calculations and materials modeling package (including PWscf, PHONON, CP90, FPMD, Wannier)
Gamess		Installed 22_Feb_06	http://www.msg.ameslab.gov/GAMESS/
Gaussian		Installed g03, g09	http://gaussian.com
Java		Installed
LAMMPS	Installed 16Jul08	Installed 17Apr09 15Jan10	A parallel molecular dynamics program
Matlab		Installed 6.5,7.1,7.5,8.0
Mr Bayes	Installed 3.1.2	Installed 3.1.1 3.1.2	http://mrbayes.csit.fsu.edu
NAMD Molecular Dynamics		32 bit version 2.6	http://www.ks.uiuc.edu/Research/namd/
NCAR Graphics		Installed	http://ngwww.ucar.edu/ng4.3/
NCBI Toolbox		Installed	Includes BLAST, SEQUIN, FA2HTGS, ENTREZ, and CN3D
NWChem			www.emsl.pnl.gov/docs/nwchem/doc/user/index.html
Octave		Installed 3.6.3
OpenFOAM		Installed 25_Feb 2009	Open Source Finite Element Software http://www.opencfd.co.uk/openfoam/doc/tutorials.html
Paup		Installed	Phylogenetic trees http://paup.csit.fsu.edu/about.html
PerlTk		Installed	Constructing GUIs http://www.perl.com/pub/1999/10/perltk/
PETSc	Installed	Installed	http://www-unix.mcs.anl.gov/petsc/petsc-as/index.html
Python	Installed 2.4.3	Installed 2.4.3 2.6.5	2.4.3 installed as part of Linux distribution 2.6.5 includes numpy, scipy, and some additional modules
R	Installed 2.11.1 2.9.0	Installed 2.4.0 2.4.1 2.5.0 2.6.1	Open Source Statistics Package
RAxML		Installed 7.2.6
SAS		Installed
Stata		Installed (UNCG Users only)
TotalView	Installed 8.6.1-1	Installed 8.4.1-4	http://www.etnus.com/ Another full-featured parallel debugger is the pgdbg debugger for codes compiled with the Portland Group compilers.
Vis5D		Installed 5.1
VMD		Installed 1.8.6	http://www.ks.uiuc.edu/Research/vmd/
WRF			Forecasting Lab Guide to Using WRF
Wien2K		Installed wien2k_08	/usr/local/apps/wien2k/wien2k_08/intel32-81 http://www.wien2k.at/
send email to request other application software for HPC systems

Libraries

Name	Status sam cluster	Status henry2 cluster	Notes
ACML	Installed 3.6.0 3.6.1 4.3.0	Installed 3.6.0 3.6.1 4.3.0	subdirectories of /usr/local/apps/acml Numerical libraries provided by AMD (64 bit only). Versions for pgi, intel, and gnu compilers. Separate directories for 64 bit integer and multithreaded versions. http://developer.amd.com/cpu/Libraries/acml/Pages/default.aspx
Atlas	Installed 3.8.0		http://math-atlas.sourceforge.net/
BLAS	Installed	Installed	Part of the AMD and mkl libraries
fftw	Installed 2.1.5 3.2	Installed 2.1.5 3.2.2	subdirectories of /usr/local/apps/fftw Fast Fourier Transforms -- includes parallel versions
hdf		Installed 4.1r5 5-1.4.5 5_1.6.0 5-1.6.8 5-1.8.5-patch1	subdirectories of /usr/local/apps/hdf4.1r5 /usr/local/apps/hdf5-1.4.5 /usr/local/apps/hdf5_1.6.0 /usr/local/apps/hdf5_1.6.8 /usr/local/apps/hdf/64hydra-pgi105
Intel MKL		Installed 7.0, 7.2.1, 9.1.023 11.1.072	mklXXX subdirectores of /usr/local/intel See also /usr/local/apps/intel/cmkl/8.0/lib and /usr/local/intel/fce/11.1.072/mkl Newer versions include threaded and 64 bit integer libraries http://software.intel.com/en-us/articles/intel-math-kernel-library-documentation/
LAPACK	Installed 3.2	Installed	Part of the AMD and mkl libraries
MPICH-1	Installed 1.2.7p1	Installed 1.2.7p1	usage deprecated (transitioning to mpich2)
MPICH-2		Installed 1.3a2	Using "add pgi64_hydra" or "add intel64_hydra" allows compilation by mpif90, mpicc, linking to the mpich2 library. See henry 2 HowTO
NetCDF	Installed	Installed 3.6.0-p1 3.6.1 3.6.2 3.6.3 4.1.1 4.1.3 4.2.1.1	subdirectories of /usr/local/apps/netcdf /usr/local/apps/netcdf-3.6.0-p1 /usr/local/apps/netcdf-3.6.1 /usr/local/apps/netcdf-3.6.3 /usr/local/apps/netcdf-4.1.1 /usr/local/apps/netcdf-4.1.3 /usr/local/apps/netcdf-4.2.1.1
PETsc		Installed	http://www.mcs.anl.gov/petsc/petsc-as/ Parallel numeric library from Argonne
ScaLAPACK		Installed MKL 10.2	Distributed memory dense dense linear algebra www.netlib.org/scalapack/
Trilinos		Installed	http://software.sandia.gov/trilinos/ Parallel numeric library from Sandia
slatec		Installed	slatec is a standard numerical fortran library developed by DOE through the 1990s. Subdirectories of /usr/local/apps/slatec have pgi, intel, and gnu compiled versions.

Last modified: April 19 2013 13:54:50.