Difference between revisions of "Applications"
 
(165 intermediate revisions by 6 users not shown)
Line 9: Line 9:
|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[ABINIT]]
|[[ABINIT]]
|7.10.5
|7.10.5
|
|-
|-
|[[Amber12]]
|[[Amber12]]
|Update 21
|Update 21
|
|-
|[[cp2k]]
|2.3.43
|
|-
|-
|[[BoltzTraP]]
|[[BoltzTraP]]
|1.2.3
|1.2.3
|[https://cwa.rc.usf.edu/cwa_applications/research-computing/34|Run]
|-
|[[CP2K]]
|2.3.43
|-
|-
|[[Dalton]]
|[[Dalton]]
|2.0
|2.0
|
|-
|[[Desmond]]
|2016.2
|-
|-
|[[feram]]
|[[feram]]
|0.19.06
|0.19.06
|
|-
|[[FLEUR]]
|MaX-6.0
|-
|-
|[[GAMESS]]
|[[GAMESS]]
|2012
|2012
|
|-
|-
|[[Gaussian]]
|[[Gaussian]]
|09b01
|09b01
|
|-
|-
|[[GaussView]]
|[[GaussView]]
|5.0
|5.0
|
|-
|-
|[[Gromacs]]
|[[Gromacs]]
|5.0.4
|2016.2
|
|-
|-
|[[Gulp]]
|[[GULP]]
|4.0
|4.0
|
|-
|-
|[[IQmol]]
|[[IQmol]]
|2.2
|2.2
|
|-
|-
|[[Jmol]]
|[[Jmol]]
|11.6.24
|11.6.24
|
|-
|-
|[[LAMMPS]]
|[[LAMMPS]]
|16Feb16
|12Dec18
|
|-
|-
|[[Lumerical FDTD]]
|[[Lumerical FDTD]]
|7.5.2
|8.5.3
|-
|[[MassProfilerPro (MPP)]]
|1.4.4
|
|-
|-
|[[Meep]]
|[[Meep]]
|1.1.1
|1.3
|
|-
|-
|[[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
|1.2b0
|
|-
|-
|[[OpenMM]]
|[[OpenMM]]
|4.0
|6.1
|
|-
|[[ORCA]]
|5.0.3
|-
|[[PSI4]]
|1.8.1
|-
|-
|[[Quantum Espresso]]
|[[Quantum Espresso]]
|5.1.2
|6.2.1
|
|-
|[[Rosetta]]
|3.5
|-
|[[ShengBTE]]
|1.2.0
|-
|-
|[[SIESTA]]
|[[SIESTA]]
|3.1
|4.0.1
|
|-
|-
|[[TeraChem]]
|[[TeraChem]]
|1.0
|1.0
|
|-
|-
|[[VASP]]
|[[VASP]]
|5.4.1
|5.4.4
|
|-
|-
|[[VMD]]
|[[VMD]]
|1.9
|1.9
|
|-
|[[Wannier90]]
|2.1.0
|}
|}


== Bioinformatics ==
== Math/Matrix/Algebra ==


{| class=wikitable
{| class=wikitable
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|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[ABySS]]
|[[GAMS]]
|1.2.7
|24.2.1
|
|-
|-
|[[AutoDock]]
|[[GNU Octave]]
|4.2.3
|3.8.2
|
|-
|-
|[[Blast]]
|[[Gurobi]]
|2.2.22
|9.0.2
|
|-
|-
|[[DOCK]]
|[[MAGMA]]
|6.5
|2.24-1
|
|-
|-
|[[ESPRIT]]
|[[Maple]]
|20090715
|2021
|
|-
|-
|[[FASTX Toolkit]]
|[[Mathematica]]
|0.0.13
|13.0
|
|-
|-
|[[MEGA]]
|[[Matlab]]
|4.02
|r2022a
|
|-
|-
|[[Meme]]
|[[MOSEK]]
|3.5.7
|7.1.15
|
|-
|-
|[[MrBayes]]
|[[PETSc]]
|3.1.2
|3.4.4
|
|-
|-
|[[MPI BLAST]]
|[[SageMath]]
|1.6.0
|7.5.1
|
|-
|-
|[[Oases]]
|[[SCIP]]
|0.1.22
|6.0.0a
|
|-
|[[QIIME]]
|1.9.1
|
|-
|[[Trans-ABySS]]
|1.4.4
|
|-
|[[Velvet]]
|1.1.05
|
|}
|}


== RF/Microwave/Networking ==
== Multi-physics/FEM ==


{| class=wikitable
{| class=wikitable
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|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[ADS]]
|[[ANSYS]]
|2009u1
|2021R1
|
|-
|-
|[[Ansoft Designer]]
|[[COMSOL]]
|6.0
|6.0
|
|-
|[[Ansys EDT | Ansys EDT (formerly HFSS)]]
|15.0, 2014, 16.2
|
|-
|[[Sonnet]]
|13.54
|
|-
|[[NS-3]]
|3.24.1
|
|}
== Multi-physics/FEM ==
{| class=wikitable
|- style="background-color:#f1edbe;"
|'''Application
|'''Latest Installed Version
|'''Run with CWA
|-
|[[Ansys]]
|17.1
|[[cwa_applications/research-computing/22|Run]]
|-
|[[Comsol]]
|5.2
|[[cwa_applications/research-computing/54|Run]]
|-
|-
|[[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
|2.3.1
|
|-
|-
|[[STAR-CCM|STAR-CCM+]]
|[[SPECFEM3D]]
|9.04.011
|3.0
|}
 
== Compilers/Development ==
 
{| class=wikitable
|- style="background-color:#f1edbe;"
|'''Application
|'''Latest Installed Version
|'''Run with CWA
|-
|[[COIN-OR]]
|1.6.0
|
|-
|[[CUDA Toolkit and Compilers]]
|7.5
|
|-
|[[GLPK]]
|4.54
|
|-
|[[Intel Compilers]]
|2015
|
|-
|[[Julia]]
|0.3.7-pre1
|
|-
|-
|[[PGI Compilers]]
|[[STAR-CCM+]]
|7.x, 12.10
|15.06.007
|
|}
|}


== Math/Matrix/Algebra ==
== RF/Microwave/Networking ==


{| class=wikitable
{| class=wikitable
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|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[GAMS]]
|[[Ansoft Designer]]
|24.2.1
|6.0
|
|-
|-
|[[MAGMA]]
|[[ANSYS EDT (formerly HFSS)]]
|1.6.2
|2021R1
|
|-
|-
|[[Maple]]
|[[CST Studio Suite]]
|2016
|2016
|
|-
|-
|[[Mathematica]]
|[[GprMax]]
|10.3
|3.0.0b24
|[[cwa_applications/research-computing/51|Run]]
|-
|-
|[[Matlab]]
|[[Keysight ADS]]
|R2016a
|2016_01
|[[cwa_applications/research-computing/53|Run]]
|-
|-
|[[MOSEK]]
|[[Sonnet]]
|7.1.15
|13.54
|
|-
|-
|[[Octave]]
|[[NS-3]]
|3.8.2
|3.24.1
|
|-
|[[PETSc]]
|3.4.4
|
|-
|[[SCIP]]
|3.1.1
|
|}
|}


== Visualization/3D Rendering ==
== VLSI/HDL/Circuit Design ==


{| class=wikitable
{| class=wikitable
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|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|[[Fiji]]
|1.49c
|
|-
|[[IDL]]
|8.2
|
|-
|[[Maya]]
|2013
|[[cwa_applications/research-computing/21|Run]]
|-
|-
|[[ParaView]]
|[[ABC|ABC Sequential Synthesis]]
|4.3.1
|161025
|
|}
 
== VLSI/HDL/Circuit Design ==
 
{| class=wikitable
|- style="background-color:#f1edbe;"
|'''Application
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[Aldec]]
|[[Aldec]]
|2013.06 SR1
|2013.06 SR1
|
|-
|-
|[[Cadence]]
|[[Cadence Tools]]
|12/15/2015
|09/15/2017
|
|-
|-
|[[Mentor Graphics]]
|[[Mentor Graphics]]
|2014.4_18.13
|2014.4_18.13
|
|-
|-
|[[SIS|SIS TELS/MALS]]
|[[SIS|SIS TELS/MALS]]
|1.2
|1.3.6
|-
|-
|[[Synopsys]]
|[[Synopsys]]
|04/25/2012
|11/03/2017
|
|}
|}


Line 386: Line 244:
|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[AERMOD]]
|[[AERMOD]]
|15181
|15181
|
|-
|[[CESM]]
|2.2.0
|-
|-
|[[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 427: Line 279:
|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|[[CircuitScape]]
|4.0.5
|-
|-
|[[GMT]]
|[[GMT]]
|5.1.0
|5.4.0
|
|-
|-
|[[GrADS]]
|[[GrADS]]
|2.0.1
|2.0.1
|[[cwa_applications/research-computing/24|Run]]
|-
|-
|[[Grass GIS]]
|[[GRASS GIS]]
|6.4.0
|6.4.0
|
|-
|-
|[[PROJ.4]]
|[[proj.4]]
|4.7.1
|6.2.0
|
|-
|-
|[[TITAN2D]]
|[[TITAN2D]]
|2.0.1
|2.0.1b
|
|}
|}


Line 456: Line 305:
|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[JAGS]]
|[[JAGS]]
|3.3.0
|3.3.0
|
|-
|-
|[[OpenBUGS]]
|[[OpenBUGS]]
|3.2.2
|3.2.2
|
|-
|-
|[[R and Rmpi]]
|[[R and Rmpi|R and Rstudio]]
|3.1.2, 0.6-5
|3.6.1
|-
|-
|[[SAS]]
|[[SAS]]
|9.4
|9.4
|[[cwa_applications/research-computing/20|Run]]
|-
|-
|[[SPSS|SPSS Statistics]]
|[[IBM SPSS Statistics|SPSS Statistics]]
|21
|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
|}
|}


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|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[bamtools]]
|[[BamTools]]
|2.4.0
|2.4.0
|
|-
|-
|[[bcftools]]
|[[BCFtools]]
|1.2
|1.2
|
|-
|-
|[[BWA|Burrows-Wheeler Alignment (BWA)]]
|[[Bowtie2]]
|2.3.4.1
|-
|[[Burrows-Wheeler Alignment (BWA)]]
|0.7.12
|0.7.12
|-
|-
|[[delly]]
|[[Delly2]]
|0.7.2
|0.7.2
|
|-
|-
|[[FreeBayes]]
|[[FreeBayes]]
|1.0.1
|1.0.1
|
|-
|-
|[[Gemini]]
|[[Gemini]]
|0.18.0
|0.18.0
|
|-
|-
|[[GATK|Genome Analysis ToolKit (GATK)]]
|[[GDC-client|GDC Data Transfer Tool]]
|3.5
|1.4.0
|-
|[[Genome Analysis ToolKit (GATK)]]
|3.7
|-
|-
|[[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
|
|-
 
|[[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]]
|1.2
|1.3.1
|
|-
|-
|[[speedseq]]
|[[speedseq]]
|0.1.0
|0.1.0
|
|-
|[[Stacks]]
|2.62
|-
|[[subread]]
|1.6.0
|-
|[[TraCeR]]
|0.15.2
|-
|-
|[[vcflib]]
|[[vcflib]]
|1.0.0
|1.0.0
|
|-
|-
|[[vcftools]]
|[[VCFtools]]
|0.1.14
|0.1.14
|
|-
|-
|[[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
|}
|}


Line 560: Line 564:
|'''Application
|'''Application
|'''Latest Installed Version
|'''Latest Installed Version
|'''Run with CWA
|-
|-
|[[Hadoop]]
|[[Hadoop]]
|2.7.1
|2.7.1
|
|-
|-
|[[RapidMiner Studio|RapidMiner Studio]]
|[[RapidMiner Studio|RapidMiner Studio]]
Line 571: Line 573:
|[[WEKA]]
|[[WEKA]]
|3.7.12
|3.7.12
|
|}
|}

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
Retrieved from "https://wiki.rc.usf.edu/index.php?title=Applications&oldid=2835"