UFRC Help and Documentation

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

List updated 12 October 2011.

Software

Software	Version	Home Website	Category	Notes
Abaqus	6.6-1, 6.9-2	Abaqus	Simulation
ADMB	9.1, 10.0	ADMB	Modeling, math
Amber	10,11.old, 11	Amber	Simulation, chemistry
Amos	3.0.0	AMOS	Biology, Genomics
Ansys	10.0	Ansys	Simulation, Engineering
antlr	3.1.3	Antlr	Linguistics, Parser
arachne	37618	Arachne	Biology, Genomics
bioscope	1.0.1, 1.2.1	ABI BioScope	Biology, NGS
Blast	2.2.24, 2.2.25	NCBI	Biology, Sequence alignment
Boost	1.37.0, 1.46.1	Boost	C++, Library
Bowtie	0.12.7	Bowtie	Biology, NGS
Charmm	35b2	Charmm	Simulation, Chemistry
Circuit		Circuitscape	GIS
CPMD	3.11.1	CPMD	Simulation, Chemistry
Crystal	1.0.2			Will be removed on 2011-10-30
Cufflinks	1.0.3	Cufflinks	Biology, NGS
dar	2.3.9	Dar	Backup
Desmond	2.4.2.1	Desmond	Simulation, Biology, Chemistry
dlpoly	3.0.9	DL_POLY	Simulation, Biology, Chemistry
dock	6.3, 6.4	Dock	Chemistry, ligand binding prediction
emboss	6.4.0	Emboss	Biology, multi-tool suite
espresso	3.0, 3.2.2, 4.0.4	Espresso	Modeling, Physics
fastqc	0.10.0	FastQC	Biology, NGS
fftw	2.1.5, 3.1.2	FFTW Gaussian	Math, Library, C++
fluent	6.3.26	ANSYS FLUENT	Simulation
gadget	2.0.4, 2.0.5	Atlassian Gadgets	Software Development
gamess	11-Aug11	GAMESS	Quantum Chemistry
gaussian	03,09	Gaussian	Modeling, Physics
Gromacs	4.0.4, 4.0.7	Gromacs	Physics, Modeling
HDF5	1.8.7	HDF5	Library, Data
hypre	2.0.0	HYPRE	Library, Math, Physics
Inelastica	1.1	Inelastica	Quantum Chemistry
IE3D	15.1	IE3D	Simulation, Design
lammps	17-Sept11	LAMPPS	Simulation
madness	0.9	MADNESS	Math, DIff. Equation solving
mafft	6.859	MAFFT	Biology, Multiple sequence alignment
MACS	1.4.1	MACS	Biology, ChIP-Seq
Matlab	2009b	MathWorks	Math, Simulation, Programming
meep	0.10.0, 0.20.3		Will be removed on 2011-10-30
meme	3.0.13, 4.3.0	MEME	Biology, Motifs, Sequence analysis
metis	4.0	Metis	Math, Graph partitioning
mira	3.2.0	MIRA Guide	Biology, NGS
MrBayes	3.1.2	MrBayes	Biology, Phylogenetics
NAMD	2.7b2	NAMD	Simulation, Chemistry, Biology
netcdf	3.6.3, 4.1.2, 4.1.3	NetCDF	Data exchange, Tools	HDF5 support in 4.1.3 only
Newbler	2.5.3, 2.6	Newbler	Biology, NGS
NWChem	6.0	NWChem	Simulation, Chemistry
OpenFOAM	1.7.1	OpenFoam	Molecular Dynamics
papi	4.1.2.1	PAPI	CPU API
PeakSplitter	1.0	PeakSplitter	Biology, Chip-Seq
pdt	3.16	PDT	Programming, Profiler
petsc	2.3.3-p8, 3.0.0-p12	PETSc	MPI toolkit
pqs	3.3-19	PQS	Modeling, Chemistry
pyopencl	0.92	PyOpenCL	python, parallel programming
python	2.5.1, 2.6.4, 2.6.5	Python	Programming, scripting, language
RAxML	7.3.0	RAxML	Biology, Phylogenetics
RAxML-Light	1.0.5	RAxML	Biology, Phylogenetics
RepeatMasker	3.3.0	Repeat Masker	Biology, Genomics
Rosetta	2.1.1, 2.1.2	Rosetta	Biology, Structural, Modeling
rsm	2961	RSM	Math, Modeling, Geometry
samtools	0.1.16	Samtools	Biology, NGS
SAS	9.2, 9.3	SAS	Statistics, Graphing
Siesta	2.0, 2.0.2, 3.0b	Siesta	Simulation, physics, ab-initio
Stata	10	Stata	Statistics, Data analysis
tau	2.20.1	TAU	Profiling, Tracing, Programming, Toolkit
TRF	4.04	TRF	Biology, Genomics
Tophat	1.3.0	Tophat	Biology, NGS
tuxedo	The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP	4.6.34,5.2.0	VASP	Quantum Chemistry, ab initio
velvet	1.1.05	Velvet	Biology, NGS
vmd	1.9	VMD	Biology, Visualization
weka	3.6.2	WEKA	Data mining algorithms
wublast	2.0	WU-Blast	Biology, Sequence Alignment

• 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.