Difference between revisions of "Applications"
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Below is a list of available applications installed on the High-Performance cluster, or available for download.
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: [[Apps Queue|Current Software Projects]].
Additionally, a list of software that is queued for installation, updates, or maintenace is available at the following link: [[AppsQueue|Current Software Projects]].


== Physics/Chemistry ==
== Physics/Chemistry ==


{| class=wikitable
{| class=wikitable class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Bioinformatics ==
== Bioinformatics ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== RF/Microwave/Networking ==
== RF/Microwave/Networking ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Multi-physics/FEM ==
== Multi-physics/FEM ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Compilers/Development ==
== Compilers/Development ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Math/Matrix/Algebra ==
== Math/Matrix/Algebra ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Visualization/3D Rendering ==
== Visualization/3D Rendering ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== VLSI/HDL/Circuit Design ==
== VLSI/HDL/Circuit Design ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Weather/Climate/Atmosphere/Emissions ==
== Weather/Climate/Atmosphere/Emissions ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== GIS/Geology ==
== GIS/Geology ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Statistics ==
== Statistics ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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'''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).
'''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).


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version
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== Miscellaneous ==
== Miscellaneous ==


{|
{| class=wikitable
!Application
!Application
!Latest Installed Version
!Latest Installed Version

Revision as of 18:27, 23 June 2016

Applications

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
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