HPC Software

This page lists software installed on the Redhawk cluster.  Use the table controls to search and sort.  Follow the links in the first column to learn more about a particular software package.  Use the module name in the fourth column to load the software. Visit the modules page to learn more about software management on the cluster.  Where a module name is not listed, view the details to learn more about using the package.

The pages describing individual software tools support comments.  Feel free to use these to add information about a package.

Contact the RCS group to request installation of additional packages or with other questions about software on the cluster.

Package NameCategoryVersionModule NameUsage Restrictions?Acknowledgement 
ComsolEngineering3.5a
4.0
4.1
4.2
4.2a
4.3
4.3a
comsol-3.5a
comsol-4.0
comsol-4.1
comsol-4.2
comsol-4.2a
comsol-4.3
comsol
YesNone
RStatistics2.10.1, 2.15.0, 3.0.2, RStudio-0.96 (2.15.3 based)R, R-x.y.z, RStudio-0.96NoAvailable
AbaqusEngineering6.12-1
6.12-3 (Teaching license only)
6.13
6.14
6.14-AP with Isight and Tosca
abaqusYesNone
BlastBioinformatics2.2.22blastNoNone
MatlabGeneralR2008a until R2014a (a releases)
R2015a
R2016a
matlab-r2008a - matlab-r2014a

matlab-r2015a (=matlab)
matlab-r2016a
YesNone
PerlGeneral5.8.8perlNoNone
BioPerlBioinformatics1.6.1bioperlNoAvailable
DDD DebuggerDevelopment3.3.12dddNoNone
Open MPIGeneral1.4.1openmpi-gnu (for gnu)
openmpi-intel (for Intel)
NoNone
Macaulay2Mathematics1.3.1macaulya2NoAvailable
COIN-ORMathematics1.3.1coin-orNoAvailable
BoostDevelopment1_43_0
1_42_0

1_53_0
boost (1_43 for GNU)
boost-1_42_0-gnu
boost-1_42_o-intel
boost-1_53-gnu
NoNone
BelvuBioinformatics2.31belvuNoRequested
CAP3Bioinformatics03122012cap3YesRequested
ClustalBioinformaticsclustalw/x - 2.0.12

clustal Omega - 1.0.3
clustal

clustal-omega
NoAvailable
EmbossBioinformatics6.2.0 (fails on rocks 6)
6.6.0
embossNoAvailable
Blast+Bioinformatics2.2.26+, 2.2.25+, 2.2.26+, 2.2.29+blast+NoNone
InterProScanBioinformatics4.8iprscan-4.8
iprscan
NoAvailable
FastaBioinformatics35.4.11fastaNoAvailable
HmmerBioinformatics3.0hmmerNoAvailable
HmmtopBioinformatics2.1hmmtopYesRequired
MrBayesBioinformatics3.1.2mrbayesNoAvailable
MuscleBioinformatics3.7
4.0 (experimental)
muscle
muscle-4.0
NoAvailable
PCAPBioinformatics7/5/07pcapNoNone
CD-HITBioinformatics4.5.5cd-hitNoRequested
Primer3Bioinformatics2.2.3primerNoAvailable
PaupBioinformatics4b10paupYesAvailable
PhylipBioinformatics3.69phylipNoAvailable
R8sBioinformatics1.71r8sNoNone
VelvetBioinformatics1.2.03velvetNoAvailable
PythonGeneral2.6
2.5
2.7.2
2.7.6
anaconda 1.9.2
python
python-2.7(fails on rocks6)
python-2.5
python-2.7.6

anaconda-python
NoNone
RepeatMaskerBioinformatics3.3.0RepeatMaskerYesAvailable
SignalSleuthBioinformatics1.0alphasignalsleuthNoAvailable
wxWidgets (wxGTK)Library2.8.10wxGTXNoNone
TreeviewxBioinformatics0.5.1treeviewxNoAvailable
VMDChemistry1.9.1vmdYesAvailable
VmatchBioinformatics2.0vmatchYesAvailable
GmapBioinformatics2010-10-26gmapNoNone
PhredBioinformatics0.020425.cphredYesAvailable
PhrapBioinformatics0.990329phrapYesAvailable
Phd2fastaBioinformatics0.990622.fphd2fastaYesAvailable
GMPLibrary4.3.2gmpNoNone
PariMathematics2.3.5pariNoRequested
NTLMathematics5.5.2ntlNoNone
MwrankMathematics2008-07-20mwrankNoNone
RatpointsMathematics2.1.3ratpointsNoRequested
CL_MatcontEngineering2.5.1cl_matcontNoNone
AutoEngineering07p v 0.7.3autoNoNone
GamessChemistry1/12/2009gamessYesRequired
SASStatistics9.3, 9.4sasYesNone
AutoAssignChemistry - NMR2.3.0autoassignYesRequired
CyanaChemistry - NMR2.1
2.1 Parallel
3.0
cyana
cyana-2.1-mpi
cyana-3.0
YesRequired
CCP4Chemistry - NMR6.1.3, 6.4.0YesRequested
CNSChemistry - NMR1.3YesRequired
APBSChemistry1.2.1apbsNoAvailable
Solve/ResolveChemistry - NMR2.13solveYesRequested
RasMolChemistry - NMR2.7.4rasmolNoAvailable
ShelxChemistry97shelxYesRequired
AutoDockChemistry - NMR4.2.3autodockNoAvailable
JmolChemistry11.8.22jmolNoAvailable
DockChemistry - NMR6.3dockYesRequired
DSSPChemistry - NMRApril 1, 2000dsspYesRequested
MolMolChemistry - NMR2k.2.0molmolNoRequested
HKL2MAPChemistry - NMR0.2hkl2mapNoRequested
MDDNMRChemistry - NMR1.6_27Jan10NoRequested
memeBioinformatics4.3
4.9.1
memeYesAvailable
Xplor-NIHChemistry - NMR2.25
2.33
xplor-nihYesRequested
XtalViewChemistry - NMR4.1YesRequested
IMSLStatistics7.0YesNone
SparkyChemistry - NMR3.113sparkyNoAvailable
PymolChemistry - NMR1.2pymolNoAvailable
QueenChemistry - NMR1.1queenNoAvailable
PhenixChemistry - NMR1.7.1
1.8.2
YesRequested
AutoStructureChemistry - NMR2.2.1autostructureYesRequired
NMRPipeChemistry - NMR5.1 Rev 2010.073.21.00YesAvailable
MorassChemistry - NMR2.51morassYesNone
CootChemistry - NMR0.6.1cootNoAvailable
MUMmerBioinformatics3.22mummerNoAvailable
MetaSimBioinformatics0.95metasimYesRequested
SoapBioinformatics2.20soapNoAvailable
TGICLBioinformatics2.31tgiclNoNone
RosettaChemistry - NMR3.1
3.2
3.2-parallel
2014.16.56682
rosetta
rosetta-3.2
rosetta-3.2-mpi
2014.16.56682
YesRequired
ARP/wARPChemistry - NMR7.0.1YesAvailable
LAMMPSChemistry1Jul11
30Sept13
1Feb14
lammpsNoAvailable
CS_RosettaChemistry - NMR1.01NoAvailable
MiraBioinformatics3.4.0.1miraNoAvailable
MPFRLibrary2.4.2mpfrNoNone
MPCLibrary0.82mpcNoNone
GCCDevelopment4.1.2
4.4.4
4.8.2
default
gcc-4.4.4
NoNone
NeditGeneral5.5neditNoNone
LADRMathematics2009-11AladrNoNone
SageMathematics4.4.4sageNoRequested
MathematicaGeneral8.0mathematicaNoNone
XalanGeneralXalan-Java 2.7.1xalanNoNone
SaxonGeneralSaxon HE 9.2.1.2saxonNoNone
GaussianChemistryGaussian 09g09YesRequired
StataStatistics12.1stataYesAvailable
SAMtoolsBioinformatics0.1.12asamtoolsNoAvailable
AMOSBioinformatics3.0.0amosNoNone
alien_hunterBioinformatics1.7alien_hunterNoAvailable
ArtemisBioinformatics13.0artemisNoAvailable
ActiveTclGeneral8.4.5ActiveState-TclNoNone
MosflmChemistry - NMR7.0.7mosflmNoAvailable
iMosflmChemistry - NMR1.0.5imosflmNoNone
Intel CompilersDevelopment11.1
12.0
intel
intel-12
NoNone
Intel MKLLibrary10.2
10.3
mkl
mkl-10.3
NoNone
JAGSStatistics2.20jagsNoNone
ParaviewGeneral3.10.1paraviewNoNone
PdbStatChemistry - NMR5.4pdbstatYesNone
SeqCleanBioinformaticsseqcleanNoNone
LucyBioinformatics1.20plucyNoAvailable
GAMSMathematics23.7.1gamsNoNone
SSAHA2Bioinformatics2.5.4ssaha2NoAvailable
KcachegrindDevelopment0.4.6kcachegrindNoNone
ASDPChemistry - NMR1.0asdpYesRequired
ValgrindDevelopment3.6.1
3.8.1
valgrindNoNone
StadenBioinformatics2.0.0b8stadenNoNone
SeqtrimBioinformatics0.110seqtrimNoRequested
GMT - Generic Mapping ToolsGeneral4.5.7gmtNoAvailable
NetCDFLibrary4.1.3netCDFNoNone
OpenCVLibrary2.3.1opencvNoNone
CmakeDevelopment2.8.3, 2.8.12cmakeNoNone
RCIChemistry - NMRNoNone
PalesChemistry - NMR2.1palesYesRequired
BtrimBioinformaticsbtrimNoAvailable
FastxBioinformatics0.0.13fastxNoNone
SWIGDevelopment2.0.4swigNoNone
GHMMLibrary0.9-rc1ghmmNoNone
ArgtableLibrary2.13argtableNoNone
MothurBioinformatics1.22.2, 1.32.1mothur, mothur-1.32.1NoAvailable
DelphiChemistry6.1delphiYesRequested
FastTreeBioinformatics2.1.4fasttreeNoNone
WebMOChemistry12.0YesNone
OOMMFPhysics1.2a3oommfNoRequested
ImageJGeneral1.45imagejNoAvailable
GNU Scientific LibraryLibrary1.15gslNoNone
MAFFTBioinformatics6.864mafftNoAvailable
AmpliconNoiseBioinformatics1.25AmpliconNoiseNoNone
GATEText Processing7.0gateNoRequested
MetaVelvetBioinformatics1.2.02meta-velvetNoAvailable
YaehmopChemistry3.0.3yaehmopNoNone
StarBioinformatics2.2.0starNoNone
GnuplotGeneral4.6.1gnuplotNoNone
EmanChemistry1.9emanNoAvailable
ChimeraAudacityChemistry1.6.2chimeraYesRequired
AudacityAudio File Processing2.03audacityNoAvailable
GNU EmacsText editing24.2emacs-24.1NoAvailable
Spheral++Numerical Simulation2.0.4spheralNoAvailable
vmd-xplorNMR Visualization1.7.2vmd-xplorNo Available
GromacsMolecular Dynamics4.6.3gromacsNoAvailable
Grace2D plotting5.1.23graceNoAvailable
AvogadroMolecule editor and visualizer1.1.0avogadroNoAvailable
AmberTools13Molecular Dynamics13ambertoolsNoAvailable
PhaverGeometry0.38N/ANo Available
QiimeMicrobio1.7.0qiimeNoAvailable
eLSA python moduleGeologyNoAvailable
ChGeneral7.0.0chNoNone
RootData analysis, C++ Interpreters6Root-6NoAvailable
MapleGeneral purpose scientific computing17,
2016
mapleNoAvailable
NuSMVSymbolic model checker2.5.4NuSMV-2.5.4NoAvailable