Applications

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Below is a list of available applications installed on the High-Performance cluster, or available for download.

Additionally, a list of software that is queued for installation, updates, or maintenace is available at the following link: Current Software Projects.

Physics/Chemistry

Application	Latest Installed Version	Run with CWA
ABINIT	7.10.5	n/a
Amber12	Update 21	n/a
cp2k	2.3.43	n/a
BoltzTraP	1.2.3	Run
Dalton	2.0	n/a
feram	0.19.06	n/a
GAMESS	2012	n/a
Gaussian	09b01	n/a
GaussView	5.0	n/a
Gromacs	5.0.4	n/a
Gulp	4.0	n/a
IQmol	2.2	n/a
Jmol	11.6.24	n/a
LAMMPS	16Feb16	n/a
[[Fdtd	Lumerical FDTD]]	7.5.2
MassProfilerPro (MPP)	1.4.4	n/a
Meep	1.1.1	n/a
Molden	4.9	n/a
MS Modeling	3.2	n/a
NAMD	2.7	n/a
NWChem	6.5	n/a
OOMMF	1.1b2	n/a
OpenMM	4.0	n/a
Quantum Espresso	5.1.2	n/a
SIESTA	3.1	n/a
TeraChem	1.0	n/a
VASP	5.4.1	n/a
VMD	1.9	n/a

Bioinformatics

Application	Latest Installed Version	Run with CWA
ABySS	1.2.7	n/a
AutoDock	4.2.3	n/a
Blast	2.2.22	n/a
DOCK	6.5	n/a
ESPRIT	20090715	n/a
FASTX Toolkit	0.0.13	n/a
MEGA	4.02	n/a
Meme	3.5.7	n/a
MrBayes	3.1.2	n/a
MPI BLAST	1.6.0	n/a
Oases	0.1.22	n/a
QIIME	1.9.1	n/a
Trans-ABySS	1.4.4	n/a
Velvet	1.1.05	n/a

RF/Microwave/Networking

Application	Latest Installed Version	Run with CWA
ADS	2009u1	n/a
[[Designer	Ansoft Designer]]	6.0
[[HFSS	Ansys EDT (formerly HFSS)]]	15.0, 2014, 16.2
Sonnet	13.54	n/a
NS-3	3.24.1	n/a

Multi-physics/FEM

Application	Latest Installed Version	Run with CWA
Ansys	17.1	Run
Comsol	5.2	Run
DL_POLY	2.16, 3.06	n/a
iso2mesh	0.8.0	n/a
OpenFOAM	2.2.1	n/a
[[star_ccm	STAR-CCM+]]	9.04.011

Compilers/Development

Application	Latest Installed Version
COIN-OR	1.6.0
[[CUDA	CUDA Toolkit and Compilers]]
GLPK	4.54
[[IntelCS	Intel Compilers]]
Julia	0.3.7-pre1
PGI Compilers	7.x, 12.10

Math/Matrix/Algebra

Application	Latest Installed Version	Run with CWA
GAMS	24.2.1	n/a
MAGMA	1.6.2	n/a
Maple	2016	n/a
Mathematica	10.3	Run
Matlab	R2016a	Run
MOSEK	7.1.15	n/a
Octave	3.8.2	n/a
PETSc	3.4.4	n/a
SCIP	3.1.1	n/a

Visualization/3D Rendering

Application	Latest Installed Version	Run with CWA
Fiji	1.49c	n/a
IDL	8.2	n/a
Maya	2013	Run
ParaView	4.3.1	n/a

VLSI/HDL/Circuit Design

Application	Latest Installed Version	Run with CWA
Aldec	2013.06 SR1	n/a
Cadence	12/15/2015	n/a
Mentor Graphics	2014.4_18.13	n/a
[[SIS	SIS TELS/MALS]]	1.2
Synopsys	04/25/2012	n/a

Weather/Climate/Atmosphere/Emissions

Application	Latest Installed Version	Run with CWA
AERMOD	15181	n/a
CMAQ	4.7	n/a
Delft3D	5.01.00.2163	n/a
ESMF	5.2.0	n/a
MOVES	2014	n/a
PEST	13.6	n/a
Vapor	2.1.0	n/a
WRF	3.3	n/a

GIS/Geology

Application	Latest Installed Version	Run with CWA
GMT	5.1.0	n/a
GrADS	2.0.1	Run
Grass GIS	6.4.0	n/a
PROJ.4	4.7.1	n/a
TITAN2D	2.0.1	n/a

Statistics

Application	Latest Installed Version	Run with CWA
JAGS	3.3.0	n/a
OpenBUGS	3.2.2	n/a
[[Rmpi	R and Rmpi]]	3.1.2, 0.6-5
SAS	9.4	Run
[[SPSS	SPSS Statistics]]	21

Genomics

NOTE: Many of the tools below are intertwined such that multiple versions may be present if more than one tool is used at a time (i.e. GotCloud contains bwa, bgzip, tabix (from htslib), samtools, tabix, and vt which are also stand alone packages). This means that different versions may be in your path and you should either check which binary you are using (type ‘which samtools’ for instance) and/or get in the habit of resetting your environment with each new tools (module purge, module add PACKAGE).

Application	Latest Installed Version	Run with CWA
bamtools	2.4.0	n/a
bcftools	1.2	n/a
[[BWA	Burrows-Wheeler Alignment (BWA)]]	0.7.12
delly	0.7.2	n/a
FreeBayes	1.0.1	n/a
Gemini	0.18.0	n/a
[[GATK	Genome Analysis ToolKit (GATK)]]	3.5
GotCloud	1.17.5	n/a
grabix	0.1.6	n/a
htslib	1.2.1	n/a
LASER	2.02	n/a
lumpy	0.2.11	n/a
samtools	1.2	n/a
speedseq	0.1.0	n/a
vcflib	1.0.0	n/a
vcftools	0.1.14	n/a
vt	0.577	n/a

Miscellaneous

Application	Latest Installed Version	Run with CWA
Hadoop	2.7.1	n/a
[[RapidMinerStudio	RapidMiner Studio]]	6.5.002
WEKA	3.7.12	n/a