Installed Software

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The following is a list of the installed software packages maintained at the UF HPC Center.

List updated 15 June 2011.

Software

Software Version Home Website
Abaqus 6.6-1, 6.9-2
ADMB 9.1, 10.0 admb-project.org
Amber 8,9,10,11 amber.scripps.edu
Amos 3.0.0 AMOS SourceForge
Ansys 10.0 www.ansys.com
antlr 3.1.3 http://www.antlr.org/
arachne 37618
bioscope 1.0.1, 1.2.1
Blast 2.2.24
Boost 1.37.0, 1.46.1
Bowtie 0.12.7 http://bowtie-bio.sourceforge.net/
Charmm 35b2
Circuit  
CPMD 3.11.1 www.cpmd.org
Crystal 1.0.2  
Cufflinks 1.0.3 http://cufflinks.cbcb.umd.edu/
dar 2.3.9
denovo 2.5.3, 2.6
Desmond 2.4.2.1 www.deshawresearch.com/resources_desmond.html
dlpoly 3.0.9 www.cse.clrc.ac.uk
dock 6.3, 6.4 dock.compbio.ucsf.edu
emboss 6.4.0 emboss.sourceforge.net
espresso 3.0, 3.2.2, 4.0.4
fftw 2.1.5, 3.1.2 www.gaussian.com
fluent 6.3.26
gadget 2.0.4, 2.0.5
gaussian 03,09 www.gaussian.com
Gromacs 4.0.4, 4.0.7 www.gromacs.org
hypre 2.0.0 Lawrence Livermore National Labs
Inelastica 1.1
IE3D 15.1
madness  
Matlab 2009b www.mathworks.com
meep 0.10.0, 0.20.3
meme 3.0.13, 4.3.0
metis 4.0 glaros.dtc.umn.edu
mira 3.2.0
MrBayes 3.1.2 mrbayes.scs.fsu.edu
NAMD 2.7b2 www.ks.uiuc.edu
netcdf 3.6.3, 4.1.2
Newbler 2.5.3, 2.6
NWChem 6.0 http://www.nwchem-sw.org
OpenFOAM 1.7.1
papi 4.1.2.1
pdt 3.16
petsc 2.3.3-p8, 3.0.0-p12
pqs 3.3-19
pyopencl 0.92
python 2.5.1, 2.6.4, 2.6.5
RepeatMasker 3.3.0 Repeat Masker
Rosetta 2.1.1, 2.1.2 www.rosettacommons.org
rsm 2961
samtools 0.1.16 http://samtools.sourceforge.net/
SAS 9.1, 9.2, 9.3 SAS
Siesta 2.0, 2.0.2, 3.0b www.uam.es
Stata 10 Stata
tau 2.20.1
TRF 4.04 Tandem Repeats Finder
Tophat 1.3.0 http://tophat.cbcb.umd.edu/
tuxedo The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP 4.6.34,5.2.0 cms.mpi.univie.ac.at
vmd 1.9
weka 3.6.2
wublast 2.0 WU-Blast WU-BLAST Readme file
  • Many versions available. /scratch/hpc/osg/app/etc/grid3-locations.txt may have an up-to-date list. Or look underneath /scratch/hpc/osg/app/cmssoft.