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 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
6.4.1
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
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

bcMPI
LAMMPS Installed
16Jul08
Installed
17Apr09
15Jan10
A parallel molecular dynamics program
Matlab Installed
6.5,7.1,7.5

bcMPI   Installed Allows MPI calls in Matlab scripts (to parallelize)
www.bluecollarcomputing.org/applications/bcMPI/index.shtml
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
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
3.6.2
Installed
3.6.0-p1
3.6.1
3.6.2
3.6.3
4.1.1
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
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 11 2012 09:38:30.
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