Software

A variety of commercial and open-source software is available to facilitate computational research at the University of Louisville. Software for bioinformatics, computational chemistry, fluid dynamics, molecular dynamcs, quantum physics and chemistry, and solid mechancics is available. In addition compilers are available for local code development including GNU, IBM, Intel, and the Portland Group suites of compilers. Oracle and MySQL database managment systems are available as well. The list below provides a high-level overview of general-purpose software that is available on the CRC.

However, due to time limitations, IT's research computing staff can only actively support a subset of the software below. In general it is the user's responsibility to understand how to use the applications listed in a distributed computing environment but training sessions are available upon request - contact us for more information.

In addition IT's research computing consultants can assist in the installation, debugging and use of additional software when requested via a consulting project.

Compilers, Debuggers, and Profilers

• Intel C, C++, and FORTRAN

• Portland Group C, C++ and FORTRAN Compilers

• GNU C, C++, and FORTRAN

• TotalView Debugger (Version 8.6.2-2)

Parallel Environments

• OpenMPI

   (Versions 1.2.8 and 1.3.1)

• MPICH

   (Version 1.2.7), MPICH2 (Version 1.0.8)

• MVAPICH, MVAPICH2

   ()

• Intel MPI

   (Version 3.2.0)

Computational Chemistry Software

• Gaussian 09

   rev c01

• GAMESS

   (Version Jan. 12, 2009 R3)

• PC GAMESS/Firefly

   (Version Dec. 4, 2009)

• Amber 12

• NWCHEM

   (Version 5.1.1)

Mathematical and Statistical Software

• MATLAB

   and MATLAB Distributed Computing Server with the Parallel Computing Toolbox

• R

   (Version 2.8.1), Rmpi (Version 0.5-7), Rpy2

Visualization and Plotting

• GNUPlot

   (Version 4.0)

• Grace/Xmgr

• Jmol

   (Version 11.6.19)

• Molden

   (Version 4.6)

• XCrySDen

   (Version 1.5.17)

• VESTA

• GaussView 5

Libraries, Python, Java and Perl packages

• fftw

   (Fast Fourier Transform library, Version 3.2.1)

• ATLAS

  , LAPACK, BLAS, and ScaLAPACK - linear algebra libraries

• Intel MKL libraries (optimized versions of the above for Intel compilers)

• GSL

  , the GNU Scientific Library

• HDF5

• NumPy

  , SciPy, BioPy, and various other Python scientific libraries

• BioPerl

   (Version 1.6.0)

• boost C++ Libraries

   (Version 1.40.0)

• Java

   (Sun/Oracle Versions 1.4.x-1.7.x)

Bioinformatics and biostatistics Software

• ClustalW

   (Version 2.0.11)

• Blast (Version 2.2.19), WU-Blast (Blast2 Version 2.6)

• Blat

• RepeatMasker

   (Version 3.2.8)

• MUMmer

   (Version 3.2.1)

• Exalin

Engineering Analysis Software

• Abaqus

   (Version 6.9-2)

Data-, Text-, and Web-Mining Software

• Weka

   (Version 3.6.1)

• Lucene

Contact us at it-hpc@louisville.edu with any questions or for additional information.