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 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]] | ||
|5 | |6.2.1 | ||
|- | |||
|[[Rosetta]] | |||
|3.5 | |||
|- | |||
|[[ShengBTE]] | |||
|1.2.0 | |||
|- | |- | ||
|[[SIESTA]] | |[[SIESTA]] | ||
| | |4.0.1 | ||
|- | |- | ||
|[[TeraChem]] | |[[TeraChem]] | ||
Line 92: | Line 104: | ||
|- | |- | ||
|[[VASP]] | |[[VASP]] | ||
|5.4. | |5.4.4 | ||
|- | |- | ||
|[[VMD]] | |[[VMD]] | ||
|1.9 | |1.9 | ||
|- | |||
|[[Wannier90]] | |||
|2.1.0 | |||
|} | |} | ||
== | == Math/Matrix/Algebra == | ||
{| class=wikitable | {| class=wikitable | ||
Line 105: | Line 120: | ||
|'''Latest Installed Version | |'''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. | |3.4.4 | ||
|- | |- | ||
|[[ | |[[SageMath]] | ||
| | |7.5.1 | ||
|- | |- | ||
|[[ | |[[SCIP]] | ||
|6.0.0a | |||
|6.0 | |||
|} | |} | ||
Line 185: | Line 162: | ||
|- | |- | ||
|[[ANSYS]] | |[[ANSYS]] | ||
| | |2021R1 | ||
|- | |- | ||
|[[COMSOL]] | |[[COMSOL]] | ||
| | |6.0 | ||
|- | |- | ||
|[[DL_POLY]] | |[[DL_POLY]] | ||
Line 197: | Line 174: | ||
|- | |- | ||
|[[OpenFOAM]] | |[[OpenFOAM]] | ||
|2. | |2.3.1 | ||
|- | |||
|[[SPECFEM3D]] | |||
|3.0 | |||
|- | |- | ||
|[[STAR-CCM+]] | |[[STAR-CCM+]] | ||
| | |15.06.007 | ||
|} | |} | ||
== | == RF/Microwave/Networking == | ||
{| class=wikitable | {| class=wikitable | ||
Line 210: | Line 190: | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[ | |[[Ansoft Designer]] | ||
| | |6.0 | ||
|- | |- | ||
|[[ | |[[ANSYS EDT (formerly HFSS)]] | ||
| | |2021R1 | ||
|- | |- | ||
|[[ | |[[CST Studio Suite]] | ||
|2016 | |2016 | ||
|- | |- | ||
|[[ | |[[GprMax]] | ||
| | |3.0.0b24 | ||
|- | |- | ||
|[[ | |[[Keysight ADS]] | ||
| | |2016_01 | ||
|- | |- | ||
|[[ | |[[Sonnet]] | ||
| | |13.54 | ||
|- | |- | ||
|[[ | |[[NS-3]] | ||
|3.24.1 | |||
|3. | |||
|} | |} | ||
Line 301: | Line 226: | ||
|- | |- | ||
|[[Cadence Tools]] | |[[Cadence Tools]] | ||
| | |09/15/2017 | ||
|- | |- | ||
|[[Mentor Graphics]] | |[[Mentor Graphics]] | ||
Line 307: | Line 232: | ||
|- | |- | ||
|[[SIS|SIS TELS/MALS]] | |[[SIS|SIS TELS/MALS]] | ||
|1. | |1.3.6 | ||
|- | |- | ||
|[[Synopsys]] | |[[Synopsys]] | ||
| | |11/03/2017 | ||
|} | |} | ||
Line 322: | Line 247: | ||
|[[AERMOD]] | |[[AERMOD]] | ||
|15181 | |15181 | ||
|- | |||
|[[CESM]] | |||
|2.2.0 | |||
|- | |- | ||
|[[CMAQ]] | |[[CMAQ]] | ||
Line 356: | Line 284: | ||
|- | |- | ||
|[[GMT]] | |[[GMT]] | ||
|5. | |5.4.0 | ||
|- | |- | ||
|[[GrADS]] | |[[GrADS]] | ||
Line 365: | Line 293: | ||
|- | |- | ||
|[[proj.4]] | |[[proj.4]] | ||
| | |6.2.0 | ||
|- | |- | ||
|[[TITAN2D]] | |[[TITAN2D]] | ||
|2.0. | |2.0.1b | ||
|} | |} | ||
Line 384: | Line 312: | ||
|3.2.2 | |3.2.2 | ||
|- | |- | ||
|[[R and Rmpi]] | |[[R and Rmpi|R and Rstudio]] | ||
|3.1 | |3.6.1 | ||
|- | |- | ||
|[[SAS]] | |[[SAS]] | ||
|9.4 | |9.4 | ||
|- | |- | ||
|[[IBM SPSS Statistics]] | |[[IBM SPSS Statistics|SPSS Statistics]] | ||
|22 | |22 | ||
|- | |||
|[[STATA]] | |||
|14 | |||
|} | |||
== Bioinformatics == | |||
{| class=wikitable | |||
|- style="background-color:#f1edbe;" | |||
|'''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 | |||
|- | |||
|[[QIIME|QIIME2 Studio]] | |||
|2019.10 | |||
|- | |||
|[[SPAdes]] | |||
|3.11.1 | |||
|- | |||
|[[Trans-ABySS]] | |||
|1.4.4 | |||
|- | |||
|[[TrimGalore|Trim Galore!]] | |||
|0.4.4 | |||
|- | |||
|[[Velvet]] | |||
|1.1.05 | |||
|} | |} | ||
Line 408: | Line 416: | ||
|[[BCFtools]] | |[[BCFtools]] | ||
|1.2 | |1.2 | ||
|- | |||
|[[Bowtie2]] | |||
|2.3.4.1 | |||
|- | |- | ||
|[[Burrows-Wheeler Alignment (BWA)]] | |[[Burrows-Wheeler Alignment (BWA)]] | ||
Line 420: | 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)]] | ||
|3. | |3.7 | ||
|- | |- | ||
|[[GotCloud]] | |[[GotCloud]] | ||
Line 438: | Line 452: | ||
|[[LUMPY]] | |[[LUMPY]] | ||
|0.2.11 | |0.2.11 | ||
|- | |||
|[[MaSuRCA]] | |||
|3.2.2 | |||
|- | |||
|[[MaxQuant]] | |||
|2.0.3.1 | |||
|- | |||
|[[MHC|MHC_I]] | |||
|2.17 | |||
|- | |||
|[[MHC|MHC_II]] | |||
|2.17.3 | |||
|- | |||
|[[MSMC2|MSMC2]] | |||
|2.1.4 | |||
|- | |||
|[[plink]] | |||
|1.07 | |||
|- | |- | ||
|[[samtools]] | |[[samtools]] | ||
Line 444: | Line 477: | ||
|[[speedseq]] | |[[speedseq]] | ||
|0.1.0 | |0.1.0 | ||
|- | |||
|[[Stacks]] | |||
|2.62 | |||
|- | |||
|[[subread]] | |||
|1.6.0 | |||
|- | |||
|[[TraCeR]] | |||
|0.15.2 | |||
|- | |- | ||
|[[vcflib]] | |[[vcflib]] | ||
Line 453: | Line 495: | ||
|[[vt]] | |[[vt]] | ||
|0.577 | |0.577 | ||
|- | |||
|[[xHLA]] | |||
|10.04.2017 | |||
|} | |||
== Visualization/3D Rendering == | |||
{| class=wikitable | |||
|- style="background-color:#f1edbe;" | |||
|'''Application | |||
|'''Latest Installed Version | |||
|- | |||
|[[Fiji]] | |||
|1.49c | |||
|- | |||
|[[IDL]] | |||
|8.2 | |||
|- | |||
|[[Maya]] | |||
|2013 | |||
|- | |||
|[[ParaView]] | |||
|4.3.1 | |||
|} | |||
== Compilers/Development == | |||
{| class=wikitable | |||
|- style="background-color:#f1edbe;" | |||
|'''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|LLVM/Clang]] | |||
|4.0.1 | |||
|- | |||
|[[PGI Compilers]] | |||
|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 |