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Introduction

This page lists the software installed and available on Tandy. If the software you're interested in is not listed here, please email support@tandysupercomputing.org and let us know you'd like us to help you install it. You are welcome to install software in your own home directory. There is often an option to configure scripts such as --prefix=/home/username/softwarename that directs the program to install it in your preferred location.

TSC systems run CentOS, a Linux distribution. Software that is designed to run only on Windows will not run on the supercomputer.


Compilers

NameVersion(s)PurposeLocationModule file

Notes

GNU (gcc, gfort, g++)4.4.7
5.2.0 
Open source compiler
  • 4.4.7

    • /usr/bin/

  • 5.2.0

    • /opt/apps/gcc/5.2.0/bin/gcc 

  • gcc/4.4.7-3

  • gcc/5.2.0

gcc 4.4.7 is the default compiler
Intel (icc, ifort, icpc)13.0.1Commercial optimizing compiler
  • /opt/apps/intel/composer_xe_2013.1.117/bin/intel64/

icc/13.0.1

Only 2 users at a time

MPI packages

Name
Version
Available compilers
for this version 
MPI module file
Notes
Intel MPI4.1.0.024

icc/13.0.1

intel-mpi/4.1.0.024


MPICH1.5.0

gcc/4.4.7-3

mpich/1.5.0


MPICH3.1.1

icc/13.0.1

mpich/3.1.1


MPICH3.1.4

gcc/4.4.7-3

mpich/3.1.4


MPICH3.2icc/13.0.1mpich/3.2
OpenMPI1.6.5

icc/13.0.1
gcc/4.4.7-3

openmpi/1.6.5


OpenMPI1.8.1

gcc/4.4.7-3

openmpi/1.8.1


Software application packages which have "Core" listed as a prerequisite do not depend on any other module and can be loaded directly.

Software Application Packages 

Name (click for more information)
Purpose
Version
Command(s)
Prerequisite modules
Module file
Example bsub file*
Type of Parallelism
Notes
AbaqusFinite element analysis
  • 6.13-3





Commercial; requires license
AbinitMaterials science
  • 7.6.2
abinit
  • gcc/4.4.7-3
    • openmpi/1.6.5
abinit/7.6.2
abinit_parallel.bsub
MPI
abyssGene assembly (de novo, parallel, paired-end sequence assembler designed for short reads)
  • 1.3.7

  • icc/13.0.1
    • openmpi/1.6.5
abyss/1.3.7
MPI
alamodeAnharmonic LAttice MODEl, which is designed for estimating harmonic and anharmonic properties of lattice vibrations (phonons) in solids.
  • 0.9.3
  • 0.9.5

  • 0.9.3
    • icc/13.0.1
      • intel-mpi/4.1.0.024

      • openmpi/1.6.5

  • 0.9.5
    • icc/13.0.1
      • openmpi/1.6.5
  • alamode/0.9.3
  • alamode/0.9.5



AnsysSimulation software suite
  • 16.2.0





Commercial; requires license
ArmadilloC++ linear algebra (matrix math) library, with a syntax deliberately similar to MATLAB
  • 3.800.2




N/A
bdwgcThis module loads the libtool library.
  • 7.4.2

  • icc/13.0.1
  • gcc/4.4.7-3
  • gcc/5.2.0
bdwgc/7.4.2


beagle-libPhylogeny
  • 1.2.0
  • 1120

  • 1.2.0
    • gcc/4.4.7-3
  • 1120
    • icc/13.0.1
    • gcc/4.4.7-3
  • beagle-lib/1.2.0
  • beagle-lib/1120

N/A
beast/beast2Phylogeny
  • 1.7.5
  • 1.8.0
  • 2.1.1
  • 2.4.0
  • 2.4.0-snapp1.3.0
  • beast
  • beauti
  • gcc/4.4.7-3
  • beast/1.7.5
  • beast/1.8.0
  • beast/2.1.1
  • beast/2.4.0
  • beast/2.4.0-snapp1.3.0
beast.bsubSharedmem
BLASLinear algebra
  • 1

  • gcc/4.4.7-3
blas/1

MKL is usually faster on Tandy
BOOSTMulti-purpose C++ libraries
  • 1.41.0
  • 1.57.0

  • 1.58.0


  • 1.41.0
    • gcc/4.4.7-3
      • openmpi/1.8.1
  • 1.57.0

    • icc/13.0.1
      • intel-mpi/4.1.0.024
  • 1.58.0

    • icc/13.0.1
      • openmpi/1.6.5
  • boost/1.41.0
  • boost/1.57.0
  • boost/1.58.0

MPI
bzip2File compression
  • 1.0.6

  • gcc/4.4.7-3
bzip2/1.0.6


cmakeOpen source build system
  • 2.8.11.2
  • 3.0.2
  • 3.3.2
  • 3.6.0
cmake
  • 2.8.11.2, 3.0.2, 3.6.0
    • Core
  • 3.3.2
    • gcc/5.2.0
  • cmake/2.8.11.2

  • cmake/3.0.2

  • cmake/3.3.2

  • cmake/3.6.0



CWP/SU: Seismic UnixA free open seismic processing, research, and educational software package.
  • 44R1

  • icc/13.0.1
  • cwp/44R1



EON

The EON software package contains a set of algorithms used primarily to model the evolution of atomic scale systems over long time scales. Standard molecular dynamics algorithms, based upon solving Newton’s equations, are limited by the femtosecond time scale of atomic vibrations. EON simulations are designed for rare event systems where the interesting dynamics can be described by fast transition between stable states. In each algorithm, the residence time in the stable states is modeled with statistical mechanics, and the important state-to-state dynamics are modeled stochastically.

http://theory.cm.utexas.edu/eon/index.html

  • April 2017


  • eon/20170418
eon_mpi.bsubMPI
Quantum Espresso (espresso)

Integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

  • 4.0.3
  • 5.0.1
  • 5.3.0

  • 4.0.3
    • icc/13.0.1
      • intel-mpi/4.1.0.024
  • 5.0.1
    • gcc/4.4.7-3
      • openmpi/1.6.5
  • 5.3.0
    • icc/13.0.1
      • openmpi/1.6.5
  • espresso/4.0.3
  • espresso/5.0.1
  • espresso/5.3.0



FastQCGene sequence quality control
  • 0.10.1
fastqc
 
fastqc/0.10.1
Serial
ffmpegMultimedia library
  • 2.1.4

 

ffmpeg/2.1.4




fftwThis module loads the fftw library.
  • 3.3.4

  • icc/13.0.1
    • openmpi/1.6.5
fftw/3.3.4


gamessThis module loads gamess into the user environment.
  • 20141205


gamess/20141205


gdalGeospatial data
  • 1.11.0
  • 2.0.0

  • 1.11.0
    • Core
  • 2.0.0
    • gcc/4.4.7-3
  • gdal/1.11.0
  • gdal/2.0.0



geos
  • 3.4.2

  • gcc/4.4.7-3
geos/3.4.2


gmp
  • 6.0.0
  • 6.1.0

  • 6.0.0
    • icc/13.0.1
    • gcc/4.4.7-3
  • 6.1.0
    • gcc/5.2.0
  • gmp/6.0.0
  • gmp/6.1.0



GNU Linear Programming Kit (GNU LPK)Linear programming
  • 4.52

  • gcc/4.4.7-3

glpk/4.52


N/A
GNU Multiple Precision Floating Point (GNU MPFR)Arbitrary precision arithmetic
  • 3.1.2
  • 3.1.3

  • 3.1.2

    • gcc/4.4.7-3

  • 3.1.3
    • gcc/5.2.0
  • mpfr/3.1.2
  • mpfr/3.1.3

N/A
GNU Scientific Library (GSL)Numerical library for C and C++ programmers
  • 1.13




N/A
GraphVizGraph visualization
  • 2.26.0
  • dot
  • neato
  • gcc/4.4.7-3
graphviz/2.26.0
Serial
gti
  • 1.2.0

  • gcc/4.4.7-3
    • mpich/1.5.0
gti/1.2.0


guile
  • 2.0.11

  • gcc/4.4.7-3
  • icc/13.0.1
guile/2.0.11


ICUText encoding (Unicode)
  • 54.1

  • gcc/4.4.7-3
icu/54.1


Intel Math Kernel Library (MKL)Optimized math routine library: BLAS, LAPACK, FFT, FFTW
  • 2013.1.117

  • icc/13.0.1

  • gcc/4.4.7-3

mkl/2013.1.117


N/A

Only 2 users at a time
Intel Trace Analyzer and Collector (ITAC)Graphical profiling tool for analyzing parallel code.
  • 2013.1.117
  • traceanalyzer
  • itcconfig
  • itcpin

itac/2013.1.117


N/AOnly 2 users at a time
ISPVerification tool for MPI programs
  • 0.3.1

  • gcc/4.4.7-3
    • openmpi/1.8.1
  • icc/13.0.1
    • mpich/3.1.1
isp/0.3.1
MPI
Java - JRE (runtime) & JDK (development)Object-oriented programming language
  • 1.7.0_55
  • 1.8.0_11
  • java (JRE)
  • javac (JDK)

  • jdk/1.7.0_55
  • jdk/1.8.0_11
  • jre/1.7.0_55
  • jdk/1.8.0_11



LaGrangeLikelihood analysis of geographic range evolution
  • 20131111

 

lagrange/20131111




LAPACKLinear algebra
  • 3.5.0

  • gcc/4.4.7-3
lapack/3.5.0

MKL is usually faster on Tandy
libtool
  • 2.4.6

  • icc/13.0.1
  • gcc/4.4.7-3
  • gcc/5.2.0
libtool/2.4.6


libunistring
  • 0.9.5

  • icc/13.0.1
  • gcc/4.4.7-3
  • gcc/5.2.0
libunistring/0.9.5


libXt
  • 1.1.4

  • gcc/4.4.7-3
libXt/1.1.4


libzData compression library
  • 1.2.3
  • 1.2.8






llvm
  • 3.3


llvm/3.3


Mathematica
  • setup-mathematica
  • mathematica
  • math

See the wiki
SharedmemCommercial; requires license
Matlab Distributed Computing ServerParallel environment for supercomputing with MATLAB
  • 2012a
  • 2012b
  • 2013a
  • 2015aSP1
  • 2016a

N/AN/A
Distributed (proprietary)Available to properly licensed Academic MATLAB license holders.
metis
  • 5.1.0

  • gcc/4.4.7-3
  • icc/13.0.1
metis/5.1.0


mpc
  • 1.0.3

  • gcc/4.4.7-3
  • gcc/5.2.0
mpc/1.0.3


MrBayesPhylogeny
  • 3.2.1
mb
  • icc/13.0.1

    • openmpi/1.6.5

mrbayes/3.2.1

mrbayes.bsubMPI
MUMPS
  • 5.0.1

  • icc/13.0.1
    • intel-mpi/4.1.0.024
mumps/5.0.1


must
  • 1.2.0

  • gcc/4.4.7-3
    • mpich/1.5.0
must/1.2.0


mybsub
  • 0


mybsub/0


octave
  • 3.8.2
  • 3.8.2-jit


  • octave/3.8.2
  • octave/3.8.2-jut



opengrads (Grid Analysis and Display System)Weather - Access, manipulation, and visualization of earth science data
  • 2.0.1.oga.1
opengrads

opengrads/2.0.1.oga.1


ParaViewData visualization
  • 4.2.0
paraview
  • gcc/4.4.7-3

    • openmpi/1.8.1

paraview/4.2.0
MPIRequires X11
parmetis
  • 4.0.3

  • icc/13.0.1
    • mpich/3.2
parmetis/4.0.3


pcre
  • 8.35

  • gcc/4.4.7-3
pcre/8.35


perlInterpreted programming language
  • 5.10.1
  • 5.18.1
perl
  • Perl 5.10.1 supplied by OS
  • perl/5.18.1




PhonTS
  • 1.1.5

  • icc/13.0.1
    • intel-mpi/4.1.0.024
    • openmpi/1.6.5
phonts/1.1.5


pnmpi
  • 1.2.0

  • gcc/4.4.7-3
    • mpich/1.5.0
pnmpi/1.2.0


PowerFlowComputational fluid dynamics
  • 5.0b





Commercial; requires license
Python 2High productivity language
  • 2.6.6
  • 2.7.5
  • 2.7.6
  • 2.7.12
pythonCore
  • python/2.6.6
  • python/2.7.5
  • python/2.7.6
  • python/2.7.12


Python 2.7.6 includes Numpy and Scipy
Python 3High productivity system language
  • 3.5.2
python3Core
  • python3/3.5.2



qt
  • 4.8.6

  • gcc/4.4.7-3
qt/4.8.6


QUASTQuality assessment for genome assemblies
  • 2.3
quast

quast/2.3
Sharedmem
RStatistical computing language
  • 3.0.1
R

R/3.0.1




readline
  • 6.3


readline/6.3


ShengBTEMaterials science (solving the Boltzmann Transport Equation)
  • 0.9.13-58a4ca4
ShengBTE
  • icc/13.0.1

ShengBTE/0.9.13-58a4ca4

shengbte_mpi.bsub
MPI
SOAPdenovoGene assembly - short-read assembly method that can build a de novo draft assembly for the human-sized genomes
  • r240

  • icc/13.0.1

soapdenovo/r240


Sharedmem
SODTool for the computer modelling of periodic systems with site disorder, using the supercell method.
  • 0.26
Various

sod/0.26

sod.bsubSerial
sparsehash
  • 2.0.2

  • icc/13.0.1
sparsehash/2.0.2


spglibCrystal symmetry handling library
  • 1.6.0
N/A
  • icc/13.0.1
  • gcc/4.4.7-3

spg/1.6.0




stacks

A user-friendly bioinformatics pipeline.

  • 1.19

  • icc/13.0.1
stacks/1.19


Star-CCM+Industrial simulation software.
  • 11.04.010-R8





Commercial; requires license
SuperLULinear algebra library (large, sparse, nonsymmetric systems of linear equations)
  • 2.1
N/A
  • icc/13.0.1
superlu-mt/2.1
Sharedmem
TclProgramming language for tools and rapid prototyping
  • 8.5.7
tcl
  • gcc/4.4.7-3
tcl/8.5.7
Serial
testmodule
  • 1.7.5

  • icc/13.0.1
    • openmpi/1.6.5
testmodule/1.7.5


thirdorder
  • 0.9.4-22be7e7

  • gcc/4.4.7-3
thirdorder/0.9.4-22be7e7


unclutter
  • 1.09


unclutter/1.09


VelvetSequence assembler for very short reads
  • 2.1.1
velvet
  • gcc/4.4.7-3

velvet/2.1.1


Sharedmem
VTKVisualization toolkit
  • 6.1.0

  • gcc/4.4.7-3

vtk/6.1.0




wannier90
  • 2.0

  • icc/13.0.1
    • intel-mpi/4.1.0.024
wannier90/2.0


wgribWeather - Y2K friendly gridded binary manipulation
  • 2.0
wgrib

wgrib2/2.0


x264
  • 2409


x264/2409


zlib
  • 1.2.8
  • x86.1.2.8

  • 1.2.8
    • icc/13.0.1
    • gcc/4.4.7-3
  • x86.1.2.8
    • icc/13.0.1
    • gcc/4.4.7-3
  • zlib/1.2.8
  • zlib/x86.1.2.8



*Note: Example bsub files are located at /opt/apps/common/example_bsubs/

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