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/ |
The following list of applications is not complete. If you look in subdirectories of /usr/local/apps, you'll see many other packages. If you need an application you think would be appropriate for general use, or a more up-to-date version of an existing package, please sent an e-mail to "oit_help at help dot ncsu dot edu".
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 Element Package | |
| AMBER | Installed 8 9 10 11 12 |
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 Commercial Fluid Dyaamics Package | |
| 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 |
||
| 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. |
| VASP | Installed 5.2 |
| |
| 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. |