Difference between revisions of "Applications"
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|- | |- | ||
|[[Gromacs]] | |[[Gromacs]] | ||
|2016 | |2016.2 | ||
|- | |- | ||
|[[GULP]] | |[[GULP]] | ||
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|- | |- | ||
|[[LAMMPS]] | |[[LAMMPS]] | ||
| | |12Dec18 | ||
|- | |- | ||
|[[Lumerical FDTD]] | |[[Lumerical FDTD]] | ||
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|- | |- | ||
|[[NAMD]] | |[[NAMD]] | ||
|2. | |2.7 | ||
|- | |- | ||
|[[NWChem]] | |[[NWChem]] | ||
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|- | |- | ||
|[[OOMMF]] | |[[OOMMF]] | ||
|1. | |1.2b0 | ||
|- | |- | ||
|[[OpenMM]] | |[[OpenMM]] | ||
Line 83: | Line 83: | ||
|- | |- | ||
|[[Quantum Espresso]] | |[[Quantum Espresso]] | ||
| | |6.2.1 | ||
|- | |- | ||
|[[Rosetta]] | |[[Rosetta]] | ||
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|[[VMD]] | |[[VMD]] | ||
|1.9 | |1.9 | ||
|- | |||
|[[Wannier90]] | |||
|2.1.0 | |||
|} | |} | ||
Line 115: | Line 118: | ||
|- | |- | ||
|[[Gurobi]] | |[[Gurobi]] | ||
| | |9.0.2 | ||
|- | |- | ||
|[[MAGMA]] | |[[MAGMA]] | ||
|1 | |2.24-1 | ||
|- | |- | ||
|[[Maple]] | |[[Maple]] | ||
| | |2020 | ||
|- | |- | ||
|[[Mathematica]] | |[[Mathematica]] | ||
| | |12.0 | ||
|- | |- | ||
|[[Matlab]] | |[[Matlab]] | ||
| | |r2021a | ||
|- | |- | ||
|[[MOSEK]] | |[[MOSEK]] | ||
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|[[PETSc]] | |[[PETSc]] | ||
|3.4.4 | |3.4.4 | ||
|- | |||
|[[SageMath]] | |||
|7.5.1 | |||
|- | |- | ||
|[[SCIP]] | |[[SCIP]] | ||
| | |6.0.0a | ||
|} | |} | ||
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|- | |- | ||
|[[ANSYS]] | |[[ANSYS]] | ||
| | |2021R1 | ||
|- | |- | ||
|[[COMSOL]] | |[[COMSOL]] | ||
|5. | |5.6 | ||
|- | |- | ||
|[[DL_POLY]] | |[[DL_POLY]] | ||
Line 165: | Line 171: | ||
|- | |- | ||
|[[STAR-CCM+]] | |[[STAR-CCM+]] | ||
| | |15.06.007 | ||
|} | |} | ||
Line 174: | Line 180: | ||
|'''Application | |'''Application | ||
|'''Latest Installed Version | |'''Latest Installed Version | ||
|- | |- | ||
|[[Ansoft Designer]] | |[[Ansoft Designer]] | ||
Line 182: | Line 185: | ||
|- | |- | ||
|[[ANSYS EDT (formerly HFSS)]] | |[[ANSYS EDT (formerly HFSS)]] | ||
| | |2021R1 | ||
|- | |- | ||
|[[CST Studio Suite]] | |[[CST Studio Suite]] | ||
Line 189: | Line 192: | ||
|[[GprMax]] | |[[GprMax]] | ||
|3.0.0b24 | |3.0.0b24 | ||
|- | |||
|[[Keysight ADS]] | |||
|2016_01 | |||
|- | |- | ||
|[[Sonnet]] | |[[Sonnet]] | ||
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|- | |- | ||
|[[SIS|SIS TELS/MALS]] | |[[SIS|SIS TELS/MALS]] | ||
|1. | |1.3.6 | ||
|- | |- | ||
|[[Synopsys]] | |[[Synopsys]] | ||
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|[[AERMOD]] | |[[AERMOD]] | ||
|15181 | |15181 | ||
|- | |||
|[[CESM]] | |||
|2.2.0 | |||
|- | |- | ||
|[[CMAQ]] | |[[CMAQ]] | ||
Line 275: | Line 284: | ||
|- | |- | ||
|[[proj.4]] | |[[proj.4]] | ||
| | |6.2.0 | ||
|- | |- | ||
|[[TITAN2D]] | |[[TITAN2D]] | ||
|2.0. | |2.0.1b | ||
|} | |} | ||
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|- | |- | ||
|[[R and Rmpi|R and Rstudio]] | |[[R and Rmpi|R and Rstudio]] | ||
|3. | |3.6.1 | ||
|- | |- | ||
|[[SAS]] | |[[SAS]] | ||
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|3.5.7 | |3.5.7 | ||
|- | |- | ||
|[[ | |[[Mothur]] | ||
| | |1.42.3 | ||
|- | |- | ||
|[[mpiBLAST]] | |[[mpiBLAST]] | ||
|1.6.0 | |1.6.0 | ||
|- | |||
|[[MrBayes]] | |||
|3.1.2 | |||
|- | |- | ||
|[[MUSCLE]] | |[[MUSCLE]] | ||
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|- | |- | ||
|[[QIIME|QIIME2 Studio]] | |[[QIIME|QIIME2 Studio]] | ||
| | |2019.10 | ||
|- | |- | ||
|[[SPAdes]] | |[[SPAdes]] | ||
Line 397: | Line 409: | ||
|- | |- | ||
|[[Bowtie2]] | |[[Bowtie2]] | ||
| | |2.3.4.1 | ||
|- | |- | ||
|[[Burrows-Wheeler Alignment (BWA)]] | |[[Burrows-Wheeler Alignment (BWA)]] | ||
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|- | |- | ||
|[[GDC-client|GDC Data Transfer Tool]] | |[[GDC-client|GDC Data Transfer Tool]] | ||
|1. | |1.4.0 | ||
|- | |- | ||
|[[Genome Analysis ToolKit (GATK)]] | |[[Genome Analysis ToolKit (GATK)]] | ||
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|0.2.11 | |0.2.11 | ||
|- | |- | ||
|[[MaSuRCA]] | |[[MaSuRCA]] | ||
|3.2.2 | |3.2.2 | ||
|- | |||
|[[MaxQuant]] | |||
|1.6.2.3 | |||
|- | |- | ||
|[[MHC|MHC_I]] | |[[MHC|MHC_I]] | ||
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|[[speedseq]] | |[[speedseq]] | ||
|0.1.0 | |0.1.0 | ||
|- | |||
|[[Stacks]] | |||
|2.3e | |||
|- | |- | ||
|[[subread]] | |[[subread]] | ||
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|- | |- | ||
|[[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]] |
Revision as of 17:53, 19 October 2021
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 | 2016.2 |
GULP | 4.0 |
IQmol | 2.2 |
Jmol | 11.6.24 |
LAMMPS | 12Dec18 |
Lumerical FDTD | 8.5.3 |
MassProfilerPro (MPP) | 1.4.4 |
Meep | 1.3 |
Molden | 4.9 |
MS Modeling | 3.2 |
NAMD | 2.7 |
NWChem | 6.5 |
OOMMF | 1.2b0 |
OpenMM | 6.1 |
Quantum Espresso | 6.2.1 |
Rosetta | 3.5 |
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 | 2020 |
Mathematica | 12.0 |
Matlab | r2021a |
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 | 5.6 |
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 | 1.6.2.3 |
MHC_I | 2.17 |
MHC_II | 2.17.3 |
plink | 1.07 |
samtools | 1.3.1 |
speedseq | 0.1.0 |
Stacks | 2.3e |
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 | 8.0 |
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 |