Difference between revisions of "Applications"
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Line 30: | Line 30: | ||
|[[feram]] | |[[feram]] | ||
|0.19.06 | |0.19.06 | ||
|- | |||
|[[FLEUR]] | |||
|MaX-6.0 | |||
|- | |- | ||
|[[GAMESS]] | |[[GAMESS]] | ||
Line 41: | Line 44: | ||
|- | |- | ||
|[[Gromacs]] | |[[Gromacs]] | ||
|2016 | |2016.2 | ||
|- | |- | ||
|[[GULP]] | |[[GULP]] | ||
Line 53: | Line 56: | ||
|- | |- | ||
|[[LAMMPS]] | |[[LAMMPS]] | ||
| | |12Dec18 | ||
|- | |- | ||
|[[Lumerical FDTD]] | |[[Lumerical FDTD]] | ||
|8.5.3 | |8.5.3 | ||
|- | |- | ||
|[[Meep]] | |[[Meep]] | ||
Line 71: | Line 71: | ||
|- | |- | ||
|[[NAMD]] | |[[NAMD]] | ||
|2. | |2.7 | ||
|- | |- | ||
|[[NWChem]] | |[[NWChem]] | ||
Line 77: | Line 77: | ||
|- | |- | ||
|[[OOMMF]] | |[[OOMMF]] | ||
|1. | |1.2b0 | ||
|- | |- | ||
|[[OpenMM]] | |[[OpenMM]] | ||
|6.1 | |6.1 | ||
|- | |||
|[[ORCA]] | |||
|5.0.3 | |||
|- | |||
|[[PSI4]] | |||
|1.8.1 | |||
|- | |- | ||
|[[Quantum Espresso]] | |[[Quantum Espresso]] | ||
| | |6.2.1 | ||
|- | |- | ||
|[[Rosetta]] | |[[Rosetta]] | ||
|3.5 | |3.5 | ||
|- | |||
|[[ShengBTE]] | |||
|1.2.0 | |||
|- | |- | ||
|[[SIESTA]] | |[[SIESTA]] | ||
| | |4.0.1 | ||
|- | |- | ||
|[[TeraChem]] | |[[TeraChem]] | ||
Line 99: | Line 108: | ||
|[[VMD]] | |[[VMD]] | ||
|1.9 | |1.9 | ||
|- | |||
|[[Wannier90]] | |||
|2.1.0 | |||
|} | |} | ||
Line 115: | Line 127: | ||
|- | |- | ||
|[[Gurobi]] | |[[Gurobi]] | ||
| | |9.0.2 | ||
|- | |- | ||
|[[MAGMA]] | |[[MAGMA]] | ||
|1 | |2.24-1 | ||
|- | |- | ||
|[[Maple]] | |[[Maple]] | ||
| | |2021 | ||
|- | |- | ||
|[[Mathematica]] | |[[Mathematica]] | ||
| | |13.0 | ||
|- | |- | ||
|[[Matlab]] | |[[Matlab]] | ||
| | |r2022a | ||
|- | |- | ||
|[[MOSEK]] | |[[MOSEK]] | ||
Line 134: | Line 146: | ||
|[[PETSc]] | |[[PETSc]] | ||
|3.4.4 | |3.4.4 | ||
|- | |||
|[[SageMath]] | |||
|7.5.1 | |||
|- | |- | ||
|[[SCIP]] | |[[SCIP]] | ||
| | |6.0.0a | ||
|} | |} | ||
Line 147: | Line 162: | ||
|- | |- | ||
|[[ANSYS]] | |[[ANSYS]] | ||
| | |2021R1 | ||
|- | |- | ||
|[[COMSOL]] | |[[COMSOL]] | ||
| | |6.0 | ||
|- | |- | ||
|[[DL_POLY]] | |[[DL_POLY]] | ||
Line 160: | Line 175: | ||
|[[OpenFOAM]] | |[[OpenFOAM]] | ||
|2.3.1 | |2.3.1 | ||
|- | |||
|[[SPECFEM3D]] | |||
|3.0 | |||
|- | |- | ||
|[[STAR-CCM+]] | |[[STAR-CCM+]] | ||
| | |15.06.007 | ||
|} | |} | ||
Line 171: | Line 189: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[Ansoft Designer]] | |[[Ansoft Designer]] | ||
Line 179: | Line 194: | ||
|- | |- | ||
|[[ANSYS EDT (formerly HFSS)]] | |[[ANSYS EDT (formerly HFSS)]] | ||
| | |2021R1 | ||
|- | |- | ||
|[[CST Studio Suite]] | |[[CST Studio Suite]] | ||
Line 186: | Line 201: | ||
|[[GprMax]] | |[[GprMax]] | ||
|3.0.0b24 | |3.0.0b24 | ||
|- | |||
|[[Keysight ADS]] | |||
|2016_01 | |||
|- | |- | ||
|[[Sonnet]] | |[[Sonnet]] | ||
Line 208: | Line 226: | ||
|- | |- | ||
|[[Cadence Tools]] | |[[Cadence Tools]] | ||
| | |09/15/2017 | ||
|- | |- | ||
|[[Mentor Graphics]] | |[[Mentor Graphics]] | ||
Line 214: | Line 232: | ||
|- | |- | ||
|[[SIS|SIS TELS/MALS]] | |[[SIS|SIS TELS/MALS]] | ||
|1. | |1.3.6 | ||
|- | |- | ||
|[[Synopsys]] | |[[Synopsys]] | ||
| | |11/03/2017 | ||
|} | |} | ||
Line 229: | Line 247: | ||
|[[AERMOD]] | |[[AERMOD]] | ||
|15181 | |15181 | ||
|- | |||
|[[CESM]] | |||
|2.2.0 | |||
|- | |- | ||
|[[CMAQ]] | |[[CMAQ]] | ||
Line 272: | Line 293: | ||
|- | |- | ||
|[[proj.4]] | |[[proj.4]] | ||
| | |6.2.0 | ||
|- | |- | ||
|[[TITAN2D]] | |[[TITAN2D]] | ||
|2.0. | |2.0.1b | ||
|} | |} | ||
Line 291: | Line 312: | ||
|3.2.2 | |3.2.2 | ||
|- | |- | ||
|[[R and Rmpi]] | |[[R and Rmpi|R and Rstudio]] | ||
|3.1 | |3.6.1 | ||
|- | |- | ||
|[[SAS]] | |[[SAS]] | ||
Line 316: | Line 337: | ||
|[[AutoDock]] | |[[AutoDock]] | ||
|4.2.3 | |4.2.3 | ||
|- | |||
|[[bcbio-nextgen]] | |||
|1.0.5 | |||
|- | |- | ||
|[[bcl2fastq]] | |[[bcl2fastq]] | ||
|2.19.1 | |2.19.1 | ||
|- | |||
|[[biopython]] | |||
|1.71 | |||
|- | |- | ||
|[[BLAST]] | |[[BLAST]] | ||
Line 328: | Line 355: | ||
|[[ESPRIT]] | |[[ESPRIT]] | ||
|20090715 | |20090715 | ||
|- | |||
|[[FastQC]] | |||
|0.11.5 | |||
|- | |- | ||
|[[FASTX Toolkit]] | |[[FASTX Toolkit]] | ||
Line 333: | Line 363: | ||
|- | |- | ||
|[[MEGA]] | |[[MEGA]] | ||
| | |7.0.26-1 | ||
|- | |- | ||
|[[Meme]] | |[[Meme]] | ||
|3.5.7 | |3.5.7 | ||
|- | |||
|[[Mothur]] | |||
|1.42.3 | |||
|- | |||
|[[mpiBLAST]] | |||
|1.6.0 | |||
|- | |- | ||
|[[MrBayes]] | |[[MrBayes]] | ||
|3.1.2 | |3.1.2 | ||
|- | |- | ||
|[[ | |[[MUSCLE]] | ||
| | |3.8.31 | ||
|- | |- | ||
|[[Oases]] | |[[Oases]] | ||
Line 349: | Line 385: | ||
|[[QIIME]] | |[[QIIME]] | ||
|1.9.1 | |1.9.1 | ||
|- | |||
|[[QIIME|QIIME2 Studio]] | |||
|2019.10 | |||
|- | |||
|[[SPAdes]] | |||
|3.11.1 | |||
|- | |- | ||
|[[Trans-ABySS]] | |[[Trans-ABySS]] | ||
|1.4.4 | |1.4.4 | ||
|- | |||
|[[TrimGalore|Trim Galore!]] | |||
|0.4.4 | |||
|- | |- | ||
|[[Velvet]] | |[[Velvet]] | ||
Line 371: | Line 416: | ||
|[[BCFtools]] | |[[BCFtools]] | ||
|1.2 | |1.2 | ||
|- | |||
|[[Bowtie2]] | |||
|2.3.4.1 | |||
|- | |- | ||
|[[Burrows-Wheeler Alignment (BWA)]] | |[[Burrows-Wheeler Alignment (BWA)]] | ||
Line 383: | Line 431: | ||
|[[Gemini]] | |[[Gemini]] | ||
|0.18.0 | |0.18.0 | ||
|- | |||
|[[GDC-client|GDC Data Transfer Tool]] | |||
|1.4.0 | |||
|- | |- | ||
|[[Genome Analysis ToolKit (GATK)]] | |[[Genome Analysis ToolKit (GATK)]] | ||
Line 402: | Line 453: | ||
|0.2.11 | |0.2.11 | ||
|- | |- | ||
|[[MaSuRCA]] | |[[MaSuRCA]] | ||
|3.2.2 | |3.2.2 | ||
|- | |||
|[[MaxQuant]] | |||
|2.0.3.1 | |||
|- | |- | ||
|[[MHC|MHC_I]] | |[[MHC|MHC_I]] | ||
|2.17 | |2.17 | ||
|- | |||
|[[MHC|MHC_II]] | |||
|2.17.3 | |||
|- | |||
|[[MSMC2|MSMC2]] | |||
|2.1.4 | |||
|- | |- | ||
|[[plink]] | |[[plink]] | ||
Line 416: | Line 477: | ||
|[[speedseq]] | |[[speedseq]] | ||
|0.1.0 | |0.1.0 | ||
|- | |||
|[[Stacks]] | |||
|2.62 | |||
|- | |||
|[[subread]] | |||
|1.6.0 | |||
|- | |- | ||
|[[TraCeR]] | |[[TraCeR]] | ||
Line 428: | Line 495: | ||
|[[vt]] | |[[vt]] | ||
|0.577 | |0.577 | ||
|- | |||
|[[xHLA]] | |||
|10.04.2017 | |||
|} | |} | ||
Line 464: | Line 534: | ||
|- | |- | ||
|[[CUDA Toolkit and Compilers]] | |[[CUDA Toolkit and Compilers]] | ||
| | |11.3.1 | ||
|- | |- | ||
|[[GLPK]] | |[[GLPK]] | ||
Line 470: | Line 540: | ||
|- | |- | ||
|[[Intel Parallel Studio XE]] | |[[Intel Parallel Studio XE]] | ||
| | |2019 | ||
|- | |- | ||
|[[Julia]] | |[[Julia]] | ||
|0.5.2 | |0.5.2 | ||
|- | |||
|[[JupyterLab]] | |||
|User-dependent | |||
|- | |- | ||
|[[LLVM-Clang|LLVM/Clang]] | |[[LLVM-Clang|LLVM/Clang]] | ||
Line 480: | Line 553: | ||
|[[PGI Compilers]] | |[[PGI Compilers]] | ||
|7.x, 12.10 | |7.x, 12.10 | ||
|- | |||
|[[Valgrind]] | |||
|3.13.0 | |||
|} | |} | ||
Latest revision as of 15:14, 31 August 2023
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 |
FLEUR | MaX-6.0 |
GAMESS | 2012 |
Gaussian | 09b01 |
GaussView | 5.0 |
Gromacs | 2016.2 |
GULP | 4.0 |
IQmol | 2.2 |
Jmol | 11.6.24 |
LAMMPS | 12Dec18 |
Lumerical FDTD | 8.5.3 |
Meep | 1.3 |
Molden | 4.9 |
MS Modeling | 3.2 |
NAMD | 2.7 |
NWChem | 6.5 |
OOMMF | 1.2b0 |
OpenMM | 6.1 |
ORCA | 5.0.3 |
PSI4 | 1.8.1 |
Quantum Espresso | 6.2.1 |
Rosetta | 3.5 |
ShengBTE | 1.2.0 |
SIESTA | 4.0.1 |
TeraChem | 1.0 |
VASP | 5.4.4 |
VMD | 1.9 |
Wannier90 | 2.1.0 |
Math/Matrix/Algebra
Application | Latest Installed Version |
GAMS | 24.2.1 |
GNU Octave | 3.8.2 |
Gurobi | 9.0.2 |
MAGMA | 2.24-1 |
Maple | 2021 |
Mathematica | 13.0 |
Matlab | r2022a |
MOSEK | 7.1.15 |
PETSc | 3.4.4 |
SageMath | 7.5.1 |
SCIP | 6.0.0a |
Multi-physics/FEM
Application | Latest Installed Version |
ANSYS | 2021R1 |
COMSOL | 6.0 |
DL_POLY | 2.16, 3.06 |
iso2mesh | 0.8.0 |
OpenFOAM | 2.3.1 |
SPECFEM3D | 3.0 |
STAR-CCM+ | 15.06.007 |
RF/Microwave/Networking
Application | Latest Installed Version |
Ansoft Designer | 6.0 |
ANSYS EDT (formerly HFSS) | 2021R1 |
CST Studio Suite | 2016 |
GprMax | 3.0.0b24 |
Keysight ADS | 2016_01 |
Sonnet | 13.54 |
NS-3 | 3.24.1 |
VLSI/HDL/Circuit Design
Application | Latest Installed Version |
ABC Sequential Synthesis | 161025 |
Aldec | 2013.06 SR1 |
Cadence Tools | 09/15/2017 |
Mentor Graphics | 2014.4_18.13 |
SIS TELS/MALS | 1.3.6 |
Synopsys | 11/03/2017 |
Weather/Climate/Atmosphere/Emissions
Application | Latest Installed Version |
AERMOD | 15181 |
CESM | 2.2.0 |
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 |
CircuitScape | 4.0.5 |
GMT | 5.4.0 |
GrADS | 2.0.1 |
GRASS GIS | 6.4.0 |
proj.4 | 6.2.0 |
TITAN2D | 2.0.1b |
Statistics
Application | Latest Installed Version |
JAGS | 3.3.0 |
OpenBUGS | 3.2.2 |
R and Rstudio | 3.6.1 |
SAS | 9.4 |
SPSS Statistics | 22 |
STATA | 14 |
Bioinformatics
Application | Latest Installed Version |
ABySS | 1.2.7 |
AutoDock | 4.2.3 |
bcbio-nextgen | 1.0.5 |
bcl2fastq | 2.19.1 |
biopython | 1.71 |
BLAST | 2.2.22 |
DOCK | 6.5 |
ESPRIT | 20090715 |
FastQC | 0.11.5 |
FASTX Toolkit | 0.0.13 |
MEGA | 7.0.26-1 |
Meme | 3.5.7 |
Mothur | 1.42.3 |
mpiBLAST | 1.6.0 |
MrBayes | 3.1.2 |
MUSCLE | 3.8.31 |
Oases | 0.1.22 |
QIIME | 1.9.1 |
QIIME2 Studio | 2019.10 |
SPAdes | 3.11.1 |
Trans-ABySS | 1.4.4 |
Trim Galore! | 0.4.4 |
Velvet | 1.1.05 |
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 |
Bowtie2 | 2.3.4.1 |
Burrows-Wheeler Alignment (BWA) | 0.7.12 |
Delly2 | 0.7.2 |
FreeBayes | 1.0.1 |
Gemini | 0.18.0 |
GDC Data Transfer Tool | 1.4.0 |
Genome Analysis ToolKit (GATK) | 3.7 |
GotCloud | 1.17.5 |
grabix | 0.1.6 |
htslib | 1.2.1 |
LASER | 2.02 |
LUMPY | 0.2.11 |
MaSuRCA | 3.2.2 |
MaxQuant | 2.0.3.1 |
MHC_I | 2.17 |
MHC_II | 2.17.3 |
MSMC2 | 2.1.4 |
plink | 1.07 |
samtools | 1.3.1 |
speedseq | 0.1.0 |
Stacks | 2.62 |
subread | 1.6.0 |
TraCeR | 0.15.2 |
vcflib | 1.0.0 |
VCFtools | 0.1.14 |
vt | 0.577 |
xHLA | 10.04.2017 |
Visualization/3D Rendering
Application | Latest Installed Version |
Fiji | 1.49c |
IDL | 8.2 |
Maya | 2013 |
ParaView | 4.3.1 |
Compilers/Development
Application | Latest Installed Version |
Apache Maven | 3.5.0 |
COIN-OR | 1.6.0 |
CUDA Toolkit and Compilers | 11.3.1 |
GLPK | 4.54 |
Intel Parallel Studio XE | 2019 |
Julia | 0.5.2 |
JupyterLab | User-dependent |
LLVM/Clang | 4.0.1 |
PGI Compilers | 7.x, 12.10 |
Valgrind | 3.13.0 |
Miscellaneous
Application | Latest Installed Version |
Hadoop | 2.7.1 |
RapidMiner Studio | 6.5.002 |
WEKA | 3.7.12 |