Difference between revisions of "Applications"
Line 3: Line 3:
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: [[AppsQueue|Current Software Projects]].
Additionally, a list of software that is queued for installation, updates, or maintenace is available at the following link: [[Apps Queue|Current Software Projects]].


== Physics/Chemistry ==
== Physics/Chemistry ==
Line 14: Line 14:
|[[ABINIT]]
|[[ABINIT]]
|7.10.5
|7.10.5
|n/a
|
|-
|-
|[[Amber12]]
|[[Amber12]]
|Update 21
|Update 21
|n/a
|
|-
|-
|[[cp2k]]
|[[cp2k]]
|2.3.43
|2.3.43
|n/a
|
|-
|-
|[[BoltzTraP]]
|[[BoltzTraP]]
Line 30: Line 30:
|[[Dalton]]
|[[Dalton]]
|2.0
|2.0
|n/a
|
|-
|-
|[[feram]]
|[[feram]]
|0.19.06
|0.19.06
|n/a
|
|-
|-
|[[GAMESS]]
|[[GAMESS]]
|2012
|2012
|n/a
|
|-
|-
|[[Gaussian]]
|[[Gaussian]]
|09b01
|09b01
|n/a
|
|-
|-
|[[GaussView]]
|[[GaussView]]
|5.0
|5.0
|n/a
|
|-
|-
|[[Gromacs]]
|[[Gromacs]]
|5.0.4
|5.0.4
|n/a
|
|-
|-
|[[Gulp]]
|[[Gulp]]
|4.0
|4.0
|n/a
|
|-
|-
|[[IQmol]]
|[[IQmol]]
|2.2
|2.2
|n/a
|
|-
|-
|[[Jmol]]
|[[Jmol]]
|11.6.24
|11.6.24
|n/a
|
|-
|-
|[[LAMMPS]]
|[[LAMMPS]]
|16Feb16
|16Feb16
|n/a
|
|-
|-
|[[Lumerical FDTD]]
|[[Lumerical FDTD]]
Line 73: Line 73:
|[[MassProfilerPro (MPP)]]
|[[MassProfilerPro (MPP)]]
|1.4.4
|1.4.4
|n/a
|
|-
|-
|[[Meep]]
|[[Meep]]
|1.1.1
|1.1.1
|n/a
|
|-
|-
|[[Molden]]
|[[Molden]]
|4.9
|4.9
|n/a
|
|-
|-
|[[MS Modeling]]
|[[MS Modeling]]
|3.2
|3.2
|n/a
|
|-
|-
|[[NAMD]]
|[[NAMD]]
|2.7
|2.7
|n/a
|
|-
|-
|[[NWChem]]
|[[NWChem]]
|6.5
|6.5
|n/a
|
|-
|-
|[[OOMMF]]
|[[OOMMF]]
|1.1b2
|1.1b2
|n/a
|
|-
|-
|[[OpenMM]]
|[[OpenMM]]
|4.0
|4.0
|n/a
|
|-
|-
|[[Quantum Espresso]]
|[[Quantum Espresso]]
|5.1.2
|5.1.2
|n/a
|
|-
|-
|[[SIESTA]]
|[[SIESTA]]
|3.1
|3.1
|n/a
|
|-
|-
|[[TeraChem]]
|[[TeraChem]]
|1.0
|1.0
|n/a
|
|-
|-
|[[VASP]]
|[[VASP]]
|5.4.1
|5.4.1
|n/a
|
|-
|-
|[[VMD]]
|[[VMD]]
|1.9
|1.9
|n/a
|
|}
|}


Line 133: Line 133:
|[[ABySS]]
|[[ABySS]]
|1.2.7
|1.2.7
|n/a
|
|-
|-
|[[AutoDock]]
|[[AutoDock]]
|4.2.3
|4.2.3
|n/a
|
|-
|-
|[[Blast]]
|[[Blast]]
|2.2.22
|2.2.22
|n/a
|
|-
|-
|[[DOCK]]
|[[DOCK]]
|6.5
|6.5
|n/a
|
|-
|-
|[[ESPRIT]]
|[[ESPRIT]]
|20090715
|20090715
|n/a
|
|-
|-
|[[FASTX Toolkit]]
|[[FASTX Toolkit]]
|0.0.13
|0.0.13
|n/a
|
|-
|-
|[[MEGA]]
|[[MEGA]]
|4.02
|4.02
|n/a
|
|-
|-
|[[Meme]]
|[[Meme]]
|3.5.7
|3.5.7
|n/a
|
|-
|-
|[[MrBayes]]
|[[MrBayes]]
|3.1.2
|3.1.2
|n/a
|
|-
|-
|[[MPI BLAST]]
|[[MPI BLAST]]
|1.6.0
|1.6.0
|n/a
|
|-
|-
|[[Oases]]
|[[Oases]]
|0.1.22
|0.1.22
|n/a
|
|-
|-
|[[QIIME]]
|[[QIIME]]
|1.9.1
|1.9.1
|n/a
|
|-
|-
|[[Trans-ABySS]]
|[[Trans-ABySS]]
|1.4.4
|1.4.4
|n/a
|
|-
|-
|[[Velvet]]
|[[Velvet]]
|1.1.05
|1.1.05
|n/a
|
|}
|}


Line 197: Line 197:
|[[ADS]]
|[[ADS]]
|2009u1
|2009u1
|n/a
|
|-
|-
|[[Ansoft Designer]]
|[[Ansoft Designer]]
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|[[Sonnet]]
|[[Sonnet]]
|13.54
|13.54
|n/a
|
|-
|-
|[[NS-3]]
|[[NS-3]]
|3.24.1
|3.24.1
|n/a
|
|}
|}


Line 231: Line 231:
|[[DL_POLY]]
|[[DL_POLY]]
|2.16, 3.06
|2.16, 3.06
|n/a
|
|-
|-
|[[iso2mesh]]
|[[iso2mesh]]
|0.8.0
|0.8.0
|n/a
|
|-
|-
|[[OpenFOAM]]
|[[OpenFOAM]]
|2.2.1
|2.2.1
|n/a
|
|-
|-
|[[STAR-CCM|STAR-CCM+]]
|[[STAR-CCM|STAR-CCM+]]
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|[[GAMS]]
|[[GAMS]]
|24.2.1
|24.2.1
|n/a
|
|-
|-
|[[MAGMA]]
|[[MAGMA]]
|1.6.2
|1.6.2
|n/a
|
|-
|-
|[[Maple]]
|[[Maple]]
|2016
|2016
|n/a
|
|-
|-
|[[Mathematica]]
|[[Mathematica]]
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|[[MOSEK]]
|[[MOSEK]]
|7.1.15
|7.1.15
|n/a
|
|-
|-
|[[Octave]]
|[[Octave]]
|3.8.2
|3.8.2
|n/a
|
|-
|-
|[[PETSc]]
|[[PETSc]]
|3.4.4
|3.4.4
|n/a
|
|-
|-
|[[SCIP]]
|[[SCIP]]
|3.1.1
|3.1.1
|n/a
|
|}
|}


Line 321: Line 321:
|[[Fiji]]
|[[Fiji]]
|1.49c
|1.49c
|n/a
|
|-
|-
|[[IDL]]
|[[IDL]]
|8.2
|8.2
|n/a
|
|-
|-
|[[Maya]]
|[[Maya]]
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|[[ParaView]]
|[[ParaView]]
|4.3.1
|4.3.1
|n/a
|
|}
|}


Line 345: Line 345:
|[[Aldec]]
|[[Aldec]]
|2013.06 SR1
|2013.06 SR1
|n/a
|
|-
|-
|[[Cadence]]
|[[Cadence]]
|12/15/2015
|12/15/2015
|n/a
|
|-
|-
|[[Mentor Graphics]]
|[[Mentor Graphics]]
|2014.4_18.13
|2014.4_18.13
|n/a
|
|-
|-
|[[SIS|SIS TELS/MALS]]
|[[SIS|SIS TELS/MALS]]
Line 360: Line 360:
|[[Synopsys]]
|[[Synopsys]]
|04/25/2012
|04/25/2012
|n/a
|
|}
|}


Line 372: Line 372:
|[[AERMOD]]
|[[AERMOD]]
|15181
|15181
|n/a
|
|-
|-
|[[CMAQ]]
|[[CMAQ]]
|4.7
|4.7
|n/a
|
|-
|-
|[[Delft3D]]
|[[Delft3D]]
|5.01.00.2163
|5.01.00.2163
|n/a
|
|-
|-
|[[ESMF]]
|[[ESMF]]
|5.2.0
|5.2.0
|n/a
|
|-
|-
|[[MOVES]]
|[[MOVES]]
|2014
|2014
|n/a
|
|-
|-
|[[PEST]]
|[[PEST]]
|13.6
|13.6
|n/a
|
|-
|-
|[[Vapor]]
|[[Vapor]]
|2.1.0
|2.1.0
|n/a
|
|-
|-
|[[WRF]]
|[[WRF]]
|3.3
|3.3
|n/a
|
|}
|}


Line 412: Line 412:
|[[GMT]]
|[[GMT]]
|5.1.0
|5.1.0
|n/a
|
|-
|-
|[[GrADS]]
|[[GrADS]]
Line 420: Line 420:
|[[Grass GIS]]
|[[Grass GIS]]
|6.4.0
|6.4.0
|n/a
|
|-
|-
|[[PROJ.4]]
|[[PROJ.4]]
|4.7.1
|4.7.1
|n/a
|
|-
|-
|[[TITAN2D]]
|[[TITAN2D]]
|2.0.1
|2.0.1
|n/a
|
|}
|}


Line 440: Line 440:
|[[JAGS]]
|[[JAGS]]
|3.3.0
|3.3.0
|n/a
|
|-
|-
|[[OpenBUGS]]
|[[OpenBUGS]]
|3.2.2
|3.2.2
|n/a
|
|-
|-
|[[R and Rmpi]]
|[[R and Rmpi]]
Line 468: Line 468:
|[[bamtools]]
|[[bamtools]]
|2.4.0
|2.4.0
|n/a
|
|-
|-
|[[bcftools]]
|[[bcftools]]
|1.2
|1.2
|n/a
|
|-
|-
|[[BWA|Burrows-Wheeler Alignment (BWA)]]
|[[BWA|Burrows-Wheeler Alignment (BWA)]]
Line 479: Line 479:
|[[delly]]
|[[delly]]
|0.7.2
|0.7.2
|n/a
|
|-
|-
|[[FreeBayes]]
|[[FreeBayes]]
|1.0.1
|1.0.1
|n/a
|
|-
|-
|[[Gemini]]
|[[Gemini]]
|0.18.0
|0.18.0
|n/a
|
|-
|-
|[[GATK|Genome Analysis ToolKit (GATK)]]
|[[GATK|Genome Analysis ToolKit (GATK)]]
Line 494: Line 494:
|[[GotCloud]]
|[[GotCloud]]
|1.17.5
|1.17.5
|n/a
|
|-
|-
|[[grabix]]
|[[grabix]]
|0.1.6
|0.1.6
|n/a
|
|-
|-
|[[htslib]]
|[[htslib]]
|1.2.1
|1.2.1
|n/a
|
|-
|-
|[[LASER]]
|[[LASER]]
|2.02
|2.02
|n/a
|
|-
|-
|[[lumpy]]
|[[lumpy]]
|0.2.11
|0.2.11
|n/a
|
|-
|-
|[[samtools]]
|[[samtools]]
|1.2
|1.2
|n/a
|
|-
|-
|[[speedseq]]
|[[speedseq]]
|0.1.0
|0.1.0
|n/a
|
|-
|-
|[[vcflib]]
|[[vcflib]]
|1.0.0
|1.0.0
|n/a
|
|-
|-
|[[vcftools]]
|[[vcftools]]
|0.1.14
|0.1.14
|n/a
|
|-
|-
|[[vt]]
|[[vt]]
|0.577
|0.577
|n/a
|
|}
|}


Line 542: Line 542:
|[[Hadoop]]
|[[Hadoop]]
|2.7.1
|2.7.1
|n/a
|
|-
|-
|[[RapidMiner Studio|RapidMiner Studio]]
|[[RapidMiner Studio|RapidMiner Studio]]
Line 549: Line 549:
|[[WEKA]]
|[[WEKA]]
|3.7.12
|3.7.12
|n/a
|
|}
|}

Revision as of 18:00, 24 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
Amber12 Update 21
cp2k 2.3.43
BoltzTraP 1.2.3 Run
Dalton 2.0
feram 0.19.06
GAMESS 2012
Gaussian 09b01
GaussView 5.0
Gromacs 5.0.4
Gulp 4.0
IQmol 2.2
Jmol 11.6.24
LAMMPS 16Feb16
Lumerical FDTD 7.5.2
MassProfilerPro (MPP) 1.4.4
Meep 1.1.1
Molden 4.9
MS Modeling 3.2
NAMD 2.7
NWChem 6.5
OOMMF 1.1b2
OpenMM 4.0
Quantum Espresso 5.1.2
SIESTA 3.1
TeraChem 1.0
VASP 5.4.1
VMD 1.9

Bioinformatics

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

RF/Microwave/Networking

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

Multi-physics/FEM

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

Compilers/Development

Application Latest Installed Version
COIN-OR 1.6.0
CUDA Toolkit and Compilers
GLPK 4.54
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
MAGMA 1.6.2
Maple 2016
Mathematica 10.3 Run
Matlab R2016a Run
MOSEK 7.1.15
Octave 3.8.2
PETSc 3.4.4
SCIP 3.1.1

Visualization/3D Rendering

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

VLSI/HDL/Circuit Design

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

Weather/Climate/Atmosphere/Emissions

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

GIS/Geology

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

Statistics

Application Latest Installed Version Run with CWA
JAGS 3.3.0
OpenBUGS 3.2.2
R and Rmpi 3.1.2, 0.6-5
SAS 9.4 Run
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
bcftools 1.2
Burrows-Wheeler Alignment (BWA) 0.7.12
delly 0.7.2
FreeBayes 1.0.1
Gemini 0.18.0
Genome Analysis ToolKit (GATK) 3.5
GotCloud 1.17.5
grabix 0.1.6
htslib 1.2.1
LASER 2.02
lumpy 0.2.11
samtools 1.2
speedseq 0.1.0
vcflib 1.0.0
vcftools 0.1.14
vt 0.577

Miscellaneous

Application Latest Installed Version Run with CWA
Hadoop 2.7.1
RapidMiner Studio 6.5.002
WEKA 3.7.12
Retrieved from "https://wiki.rc.usf.edu/index.php?title=Applications&oldid=238"