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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 analysis6.13-3     Commercial; requires license
AbinitMaterials science7.6.2abinit
  • 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 suite16.2.0     Commercial; requires license
ArmadilloC++ linear algebra (matrix math) library, with a syntax deliberately similar to MATLAB3.800.2    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 algebra1 
  • 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 compression1.0.6 
  • 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
   
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 control0.10.1
fastqc
 
fastqc/0.10.1 Serial 
ffmpegMultimedia library2.1.4 
 

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 programming4.52 
  • 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++ programmers1.13    N/A 
GraphVizGraph visualization2.26.0
  • 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, FFTW2013.1.117 
  • 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 programs0.3.1 
  • 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 evolution20131111 
 

lagrange/20131111

   
LAPACKLinear algebra3.5.0 
  • 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   
MrBayesPhylogeny3.2.1mb
  • 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 data2.0.1.oga.1
opengrads
 opengrads/2.0.1.oga.1   
ParaViewData visualization4.2.0
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 dynamics5.0b 

 

   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 assemblies2.3
quast
 quast/2.3 Sharedmem 
RStatistical computing language3.0.1R 

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 genomesr240 
  • icc/13.0.1

soapdenovo/r240

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

sod/0.26

sod.bsubSerial 
sparsehash 2.0.2 
  • icc/13.0.1
sparsehash/2.0.2   
spglibCrystal symmetry handling library1.6.0N/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   
SuperLULinear algebra library (large, sparse, nonsymmetric systems of linear equations)2.1N/A
  • icc/13.0.1
superlu-mt/2.1 Sharedmem 
TclProgramming language for tools and rapid prototyping8.5.7
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 reads2.1.1
velvet
  • gcc/4.4.7-3

velvet/2.1.1

 Sharedmem 
VTKVisualization toolkit6.1.0 
  • 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 manipulation2.0
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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