Difference between revisions of "Applications"
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Line 9: | Line 9: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[ABINIT]] | |[[ABINIT]] | ||
|7.10.5 | |7.10.5 | ||
|- | |- | ||
|[[Amber12]] | |[[Amber12]] | ||
|Update 21 | |Update 21 | ||
|- | |- | ||
|[[BoltzTraP]] | |[[BoltzTraP]] | ||
|1.2.3 | |1.2.3 | ||
|- | |- | ||
|[[CP2K]] | |[[CP2K]] | ||
|2.3.43 | |2.3.43 | ||
|- | |- | ||
|[[Dalton]] | |[[Dalton]] | ||
|2.0 | |2.0 | ||
|- | |- | ||
|[[Desmond]] | |[[Desmond]] | ||
|2016.2 | |2016.2 | ||
|- | |- | ||
|[[feram]] | |[[feram]] | ||
|0.19.06 | |0.19.06 | ||
|- | |- | ||
|[[GAMESS]] | |[[GAMESS]] | ||
|2012 | |2012 | ||
|- | |- | ||
|[[Gaussian]] | |[[Gaussian]] | ||
|09b01 | |09b01 | ||
|- | |- | ||
|[[GaussView]] | |[[GaussView]] | ||
|5.0 | |5.0 | ||
|- | |- | ||
|[[Gromacs]] | |[[Gromacs]] | ||
|2016 | |2016 | ||
|- | |- | ||
|[[GULP]] | |[[GULP]] | ||
|4.0 | |4.0 | ||
|- | |- | ||
|[[IQmol]] | |[[IQmol]] | ||
|2.2 | |2.2 | ||
|- | |- | ||
|[[Jmol]] | |[[Jmol]] | ||
|11.6.24 | |11.6.24 | ||
|- | |- | ||
|[[LAMMPS]] | |[[LAMMPS]] | ||
|16Feb16 | |16Feb16 | ||
|- | |- | ||
|[[Lumerical FDTD]] | |[[Lumerical FDTD]] | ||
|7.5.2 | |7.5.2 | ||
|- | |- | ||
|[[MassProfilerPro (MPP)]] | |[[MassProfilerPro (MPP)]] | ||
|1.4.4 | |1.4.4 | ||
|- | |- | ||
|[[Meep]] | |[[Meep]] | ||
|1.1.1 | |1.1.1 | ||
|- | |- | ||
|[[Molden]] | |[[Molden]] | ||
|4.9 | |4.9 | ||
|- | |- | ||
|[[MS Modeling]] | |[[MS Modeling]] | ||
|3.2 | |3.2 | ||
|- | |- | ||
|[[NAMD]] | |[[NAMD]] | ||
|2.7 | |2.7 | ||
|- | |- | ||
|[[NWChem]] | |[[NWChem]] | ||
|6.5 | |6.5 | ||
|- | |- | ||
|[[OOMMF]] | |[[OOMMF]] | ||
|1.1b2 | |1.1b2 | ||
|- | |- | ||
|[[OpenMM]] | |[[OpenMM]] | ||
|6.1 | |6.1 | ||
|- | |- | ||
|[[Quantum Espresso]] | |[[Quantum Espresso]] | ||
|5.1.2 | |5.1.2 | ||
|- | |- | ||
|[[SIESTA]] | |[[SIESTA]] | ||
|3.1 | |3.1 | ||
|- | |- | ||
|[[TeraChem]] | |[[TeraChem]] | ||
|1.0 | |1.0 | ||
|- | |- | ||
|[[VASP]] | |[[VASP]] | ||
|5.4.1 | |5.4.1 | ||
|- | |- | ||
|[[VMD]] | |[[VMD]] | ||
|1.9 | |1.9 | ||
|} | |} | ||
Line 134: | Line 104: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[ABySS]] | |[[ABySS]] | ||
|1.2.7 | |1.2.7 | ||
|- | |- | ||
|[[AutoDock]] | |[[AutoDock]] | ||
|4.2.3 | |4.2.3 | ||
|- | |- | ||
|[[BLAST]] | |[[BLAST]] | ||
|2.2.22 | |2.2.22 | ||
|- | |- | ||
|[[DOCK]] | |[[DOCK]] | ||
|6.5 | |6.5 | ||
|- | |- | ||
|[[ESPRIT]] | |[[ESPRIT]] | ||
|20090715 | |20090715 | ||
|- | |- | ||
|[[FASTX Toolkit]] | |[[FASTX Toolkit]] | ||
|0.0.13 | |0.0.13 | ||
|- | |- | ||
|[[MEGA]] | |[[MEGA]] | ||
|4.02 | |4.02 | ||
|- | |- | ||
|[[Meme]] | |[[Meme]] | ||
|3.5.7 | |3.5.7 | ||
|- | |- | ||
|[[MrBayes]] | |[[MrBayes]] | ||
|3.1.2 | |3.1.2 | ||
|- | |- | ||
|[[mpiBLAST]] | |[[mpiBLAST]] | ||
|1.6.0 | |1.6.0 | ||
|- | |- | ||
|[[Oases]] | |[[Oases]] | ||
|0.1.22 | |0.1.22 | ||
|- | |- | ||
|[[QIIME]] | |[[QIIME]] | ||
|1.9.1 | |1.9.1 | ||
|- | |- | ||
|[[Trans-ABySS]] | |[[Trans-ABySS]] | ||
|1.4.4 | |1.4.4 | ||
|- | |- | ||
|[[Velvet]] | |[[Velvet]] | ||
|1.1.05 | |1.1.05 | ||
|} | |} | ||
Line 199: | Line 154: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[Agilent ADS]] | |[[Agilent ADS]] | ||
|2009u1 | |2009u1 | ||
|- | |- | ||
|[[Ansoft Designer]] | |[[Ansoft Designer]] | ||
|6.0 | |6.0 | ||
|- | |- | ||
|[[ANSYS EDT (formerly HFSS)]] | |[[ANSYS EDT (formerly HFSS)]] | ||
|15.0, 2014, 16.2 | |15.0, 2014, 16.2 | ||
|- | |- | ||
|[[CST Studio Suite]] | |[[CST Studio Suite]] | ||
|2016 | |2016 | ||
|- | |- | ||
|[[GprMax]] | |[[GprMax]] | ||
|3.0.0b24 | |3.0.0b24 | ||
|- | |- | ||
|[[Sonnet]] | |[[Sonnet]] | ||
|13.54 | |13.54 | ||
|- | |- | ||
|[[NS-3]] | |[[NS-3]] | ||
|3.24.1 | |3.24.1 | ||
|} | |} | ||
Line 236: | Line 183: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[ANSYS]] | |[[ANSYS]] | ||
|17.1 | |17.1 | ||
|- | |- | ||
|[[COMSOL]] | |[[COMSOL]] | ||
|5.2a | |5.2a | ||
|- | |- | ||
|[[DL_POLY]] | |[[DL_POLY]] | ||
|2.16, 3.06 | |2.16, 3.06 | ||
|- | |- | ||
|[[iso2mesh]] | |[[iso2mesh]] | ||
|0.8.0 | |0.8.0 | ||
|- | |- | ||
|[[OpenFOAM]] | |[[OpenFOAM]] | ||
|2.2.1 | |2.2.1 | ||
|- | |- | ||
|[[STAR-CCM+]] | |[[STAR-CCM+]] | ||
|9.04.011 | |9.04.011 | ||
|} | |} | ||
Line 269: | Line 209: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[COIN-OR]] | |[[COIN-OR]] | ||
|1.6.0 | |1.6.0 | ||
|- | |- | ||
|[[CUDA Toolkit and Compilers]] | |[[CUDA Toolkit and Compilers]] | ||
|7.5 | |7.5 | ||
|- | |- | ||
|[[GLPK]] | |[[GLPK]] | ||
|4.54 | |4.54 | ||
|- | |- | ||
|[[Intel Parallel Studio XE]] | |[[Intel Parallel Studio XE]] | ||
|2015 | |2015 | ||
|- | |- | ||
|[[Julia]] | |[[Julia]] | ||
|0.5.0-rc3 | |0.5.0-rc3 | ||
|- | |- | ||
|[[PGI Compilers]] | |[[PGI Compilers]] | ||
|7.x, 12.10 | |7.x, 12.10 | ||
|} | |} | ||
Line 302: | Line 235: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[GAMS]] | |[[GAMS]] | ||
|24.2.1 | |24.2.1 | ||
|- | |- | ||
|[[GNU Octave]] | |[[GNU Octave]] | ||
|3.8.2 | |3.8.2 | ||
|- | |- | ||
|[[Gurobi]] | |[[Gurobi]] | ||
|6.5.2 | |6.5.2 | ||
|- | |- | ||
|[[MAGMA]] | |[[MAGMA]] | ||
|1.6.2 | |1.6.2 | ||
|- | |- | ||
|[[Maple]] | |[[Maple]] | ||
|2016 | |2016 | ||
|- | |- | ||
|[[Mathematica]] | |[[Mathematica]] | ||
|11.0 | |11.0 | ||
|- | |- | ||
|[[Matlab]] | |[[Matlab]] | ||
|r2016b | |r2016b | ||
|- | |- | ||
|[[MOSEK]] | |[[MOSEK]] | ||
|7.1.15 | |7.1.15 | ||
|- | |- | ||
|[[PETSc]] | |[[PETSc]] | ||
|3.4.4 | |3.4.4 | ||
|- | |- | ||
|[[SCIP]] | |[[SCIP]] | ||
|3.1.1 | |3.1.1 | ||
|} | |} | ||
Line 351: | Line 273: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[Fiji]] | |[[Fiji]] | ||
|1.49c | |1.49c | ||
|- | |- | ||
|[[IDL]] | |[[IDL]] | ||
|8.2 | |8.2 | ||
|- | |- | ||
|[[Maya]] | |[[Maya]] | ||
|2013 | |2013 | ||
|- | |- | ||
|[[ParaView]] | |[[ParaView]] | ||
|4.3.1 | |4.3.1 | ||
|} | |} | ||
Line 376: | Line 293: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[ABC|ABC Sequential Synthesis]] | |[[ABC|ABC Sequential Synthesis]] | ||
|161025 | |161025 | ||
|- | |- | ||
|[[Aldec]] | |[[Aldec]] | ||
|2013.06 SR1 | |2013.06 SR1 | ||
|- | |- | ||
|[[Cadence Tools]] | |[[Cadence Tools]] | ||
|12/15/2015 | |12/15/2015 | ||
|- | |- | ||
|[[Mentor Graphics]] | |[[Mentor Graphics]] | ||
|2014.4_18.13 | |2014.4_18.13 | ||
|- | |- | ||
|[[SIS|SIS TELS/MALS]] | |[[SIS|SIS TELS/MALS]] | ||
|1.2 | |1.2 | ||
|- | |- | ||
|[[Synopsys]] | |[[Synopsys]] | ||
|04/25/2012 | |04/25/2012 | ||
|} | |} | ||
Line 409: | Line 319: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[AERMOD]] | |[[AERMOD]] | ||
|15181 | |15181 | ||
|- | |- | ||
|[[CMAQ]] | |[[CMAQ]] | ||
|4.7 | |4.7 | ||
|- | |- | ||
|[[Delft3D]] | |[[Delft3D]] | ||
|5.01.00.2163 | |5.01.00.2163 | ||
|- | |- | ||
|[[ESMF]] | |[[ESMF]] | ||
|5.2.0 | |5.2.0 | ||
|- | |- | ||
|[[MOVES]] | |[[MOVES]] | ||
|2014 | |2014 | ||
|- | |- | ||
|[[PEST]] | |[[PEST]] | ||
|13.6 | |13.6 | ||
|- | |- | ||
|[[Vapor]] | |[[Vapor]] | ||
|2.1.0 | |2.1.0 | ||
|- | |- | ||
|[[WRF]] | |[[WRF]] | ||
|3.3 | |3.3 | ||
|} | |} | ||
Line 450: | Line 351: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[GMT]] | |[[GMT]] | ||
|5.1.0 | |5.1.0 | ||
|- | |- | ||
|[[GrADS]] | |[[GrADS]] | ||
|2.0.1 | |2.0.1 | ||
|- | |- | ||
|[[GRASS GIS]] | |[[GRASS GIS]] | ||
|6.4.0 | |6.4.0 | ||
|- | |- | ||
|[[proj.4]] | |[[proj.4]] | ||
|4.7.1 | |4.7.1 | ||
|- | |- | ||
|[[TITAN2D]] | |[[TITAN2D]] | ||
|2.0.1 | |2.0.1 | ||
|} | |} | ||
Line 479: | Line 374: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[JAGS]] | |[[JAGS]] | ||
|3.3.0 | |3.3.0 | ||
|- | |- | ||
|[[OpenBUGS]] | |[[OpenBUGS]] | ||
|3.2.2 | |3.2.2 | ||
|- | |- | ||
|[[R and Rmpi]] | |[[R and Rmpi]] | ||
|3.1.2 | |3.1.2 | ||
|- | |- | ||
|[[SAS]] | |[[SAS]] | ||
|9.4 | |9.4 | ||
|- | |- | ||
|[[IBM SPSS Statistics]] | |[[IBM SPSS Statistics]] | ||
|21 | |21 | ||
|} | |} | ||
Line 510: | Line 399: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[BamTools]] | |[[BamTools]] | ||
|2.4.0 | |2.4.0 | ||
|- | |- | ||
|[[BCFtools]] | |[[BCFtools]] | ||
|1.2 | |1.2 | ||
|- | |- | ||
|[[Burrows-Wheeler Alignment (BWA)]] | |[[Burrows-Wheeler Alignment (BWA)]] | ||
|0.7.12 | |0.7.12 | ||
|- | |- | ||
|[[Delly2]] | |[[Delly2]] | ||
|0.7.2 | |0.7.2 | ||
|- | |- | ||
|[[FreeBayes]] | |[[FreeBayes]] | ||
|1.0.1 | |1.0.1 | ||
|- | |- | ||
|[[Gemini]] | |[[Gemini]] | ||
|0.18.0 | |0.18.0 | ||
|- | |- | ||
|[[Genome Analysis ToolKit (GATK)]] | |[[Genome Analysis ToolKit (GATK)]] | ||
|3.5 | |3.5 | ||
|- | |- | ||
|[[GotCloud]] | |[[GotCloud]] | ||
|1.17.5 | |1.17.5 | ||
|- | |- | ||
|[[grabix]] | |[[grabix]] | ||
|0.1.6 | |0.1.6 | ||
|- | |- | ||
|[[htslib]] | |[[htslib]] | ||
|1.2.1 | |1.2.1 | ||
|- | |- | ||
|[[LASER]] | |[[LASER]] | ||
|2.02 | |2.02 | ||
|- | |- | ||
|[[LUMPY]] | |[[LUMPY]] | ||
|0.2.11 | |0.2.11 | ||
|- | |- | ||
|[[samtools]] | |[[samtools]] | ||
|1.2 | |1.2 | ||
|- | |- | ||
|[[speedseq]] | |[[speedseq]] | ||
|0.1.0 | |0.1.0 | ||
|- | |- | ||
|[[vcflib]] | |[[vcflib]] | ||
|1.0.0 | |1.0.0 | ||
|- | |- | ||
|[[VCFtools]] | |[[VCFtools]] | ||
|0.1.14 | |0.1.14 | ||
|- | |- | ||
|[[vt]] | |[[vt]] | ||
|0.577 | |0.577 | ||
|} | |} | ||
Line 587: | Line 458: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[Hadoop]] | |[[Hadoop]] | ||
|2.7.1 | |2.7.1 | ||
|- | |- | ||
|[[RapidMiner Studio|RapidMiner Studio]] | |[[RapidMiner Studio|RapidMiner Studio]] | ||
|6.5.002 | |6.5.002 | ||
|- | |- | ||
|[[WEKA]] | |[[WEKA]] | ||
|3.7.12 | |3.7.12 | ||
|} | |} |
Revision as of 14:10, 21 February 2017
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 |
ABINIT | 7.10.5 |
Amber12 | Update 21 |
BoltzTraP | 1.2.3 |
CP2K | 2.3.43 |
Dalton | 2.0 |
Desmond | 2016.2 |
feram | 0.19.06 |
GAMESS | 2012 |
Gaussian | 09b01 |
GaussView | 5.0 |
Gromacs | 2016 |
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 | 6.1 |
Quantum Espresso | 5.1.2 |
SIESTA | 3.1 |
TeraChem | 1.0 |
VASP | 5.4.1 |
VMD | 1.9 |
Bioinformatics
Application | Latest Installed Version |
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 |
mpiBLAST | 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 |
Agilent ADS | 2009u1 |
Ansoft Designer | 6.0 |
ANSYS EDT (formerly HFSS) | 15.0, 2014, 16.2 |
CST Studio Suite | 2016 |
GprMax | 3.0.0b24 |
Sonnet | 13.54 |
NS-3 | 3.24.1 |
Multi-physics/FEM
Application | Latest Installed Version |
ANSYS | 17.1 |
COMSOL | 5.2a |
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 | 7.5 |
GLPK | 4.54 |
Intel Parallel Studio XE | 2015 |
Julia | 0.5.0-rc3 |
PGI Compilers | 7.x, 12.10 |
Math/Matrix/Algebra
Application | Latest Installed Version |
GAMS | 24.2.1 |
GNU Octave | 3.8.2 |
Gurobi | 6.5.2 |
MAGMA | 1.6.2 |
Maple | 2016 |
Mathematica | 11.0 |
Matlab | r2016b |
MOSEK | 7.1.15 |
PETSc | 3.4.4 |
SCIP | 3.1.1 |
Visualization/3D Rendering
Application | Latest Installed Version |
Fiji | 1.49c |
IDL | 8.2 |
Maya | 2013 |
ParaView | 4.3.1 |
VLSI/HDL/Circuit Design
Application | Latest Installed Version |
ABC Sequential Synthesis | 161025 |
Aldec | 2013.06 SR1 |
Cadence Tools | 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 |
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 |
GMT | 5.1.0 |
GrADS | 2.0.1 |
GRASS GIS | 6.4.0 |
proj.4 | 4.7.1 |
TITAN2D | 2.0.1 |
Statistics
Application | Latest Installed Version |
JAGS | 3.3.0 |
OpenBUGS | 3.2.2 |
R and Rmpi | 3.1.2 |
SAS | 9.4 |
IBM 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 |
BamTools | 2.4.0 |
BCFtools | 1.2 |
Burrows-Wheeler Alignment (BWA) | 0.7.12 |
Delly2 | 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 |
Hadoop | 2.7.1 |
RapidMiner Studio | 6.5.002 |
WEKA | 3.7.12 |