Difference between revisions of "UFRC Help and Documentation"

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Welcome to the <span class="plainlinks">[http://www.ufl.edu/ University of Florida] [http://www.hpc.ufl.edu High Performance Computing Center] Wiki. This site provides documentation for various software applications and hardware configurations provided by the UF HPC Center. Please submit a request in our [http://support.hpc.ufl.edu Support System] or send email to [mailto://support@hpc.ufl.edu HPC support].</span>
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[[Category:Software]]
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=== Getting Started ===
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The following is a list of the installed software at the UF HPC Center.
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{|  
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 +
List updated '''12 October 2011'''.
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==Software==
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{| border="1"
 +
! Software !! Version !! Home Website !! Category !! Notes
 +
|-
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| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html Abaqus] || Simulation||
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|-
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| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ ADMB] || Modeling, math ||
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|-
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| [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ Amber] || Simulation, chemistry ||
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|-
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| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] || Biology, Genomics ||
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|-
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| [[Ansys]] || 10.0 || [http://www.ansys.com/ Ansys] || Simulation, Engineering ||
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|-
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| [[antlr]] || 3.1.3 || [http://www.antlr.org/ Antlr] || Linguistics, Parser ||
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|-
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| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational- Arachne] || Biology, Genomics ||
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|-
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| [[bioscope]] || 1.0.1, 1.2.1 || [http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/ngs-data-analysis-software/bioscope.html ABI BioScope] || Biology, NGS ||
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|-
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| [[Blast]] || 2.2.24, 2.2.25 || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download  NCBI] || Biology, Sequence alignment ||
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|-
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| [[Boost]] || 1.37.0, 1.46.1 || [http://www.boost.org/ Boost] || C++, Library ||
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|-
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| [[tuxedo|Bowtie]] || 0.12.7 || [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] || Biology, NGS ||
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|-
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| [[Charmm]] || 35b2 || [http://www.charmm.org/ Charmm] || Simulation, Chemistry ||
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|-
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| [[Circuit]] || &nbsp; || [http://www.circuitscape.org/Circuitscape/Welcome.html Circuitscape] || GIS ||
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|-
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| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ CPMD] || Simulation, Chemistry ||
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|-
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| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30
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|-
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| [[tuxedo|Cufflinks]] || 1.0.3 || [http://cufflinks.cbcb.umd.edu/ Cufflinks] || Biology, NGS ||
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|-
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| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ Dar] || Backup ||
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|-
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| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html Desmond] || Simulation, Biology, Chemistry ||
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|-
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| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml DL_POLY]  || Simulation, Biology, Chemistry ||
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|-
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| [[dock]] || 6.3, 6.4 || [http://dock.compbio.ucsf.edu/ Dock] || Chemistry, ligand binding prediction ||
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|-
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| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ Emboss] || Biology, multi-tool suite ||
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|-
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| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ Espresso] || Modeling, Physics ||
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|-
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| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC] || Biology, NGS ||
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|-
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| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ FFTW Gaussian] || Math, Library, C++ ||
 
|-
 
|-
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|
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| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT ANSYS FLUENT] || Simulation ||
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* [[Getting Started]]
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|-
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* [[Getting Help]]
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| [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets] || Software Development ||
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* [[Policies]]
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|-
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||
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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ GAMESS]|| Quantum Chemistry||
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* [[Frequently Asked Questions]]
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|-
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* [[Password | Changing your Password]]
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| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
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* [[Samba Access]]
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|-
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| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ Gromacs]||Physics, Modeling||
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|-
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| [[HDF5]] || 1.8.7 || [http://www.hdfgroup.org/HDF5/ HDF5]||Library, Data||
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|-
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| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics||
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|-
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| [[Inelastica]] || 1.1 || [http://sourceforge.net/projects/inelastica/ Inelastica]||Quantum Chemistry||
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|-
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| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/ IE3D]||Simulation, Design||
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|-
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| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
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|-
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| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS]||Math, DIff. Equation solving||
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|-
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| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
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|-
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| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS]||Biology, ChIP-Seq||
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|-
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| [[Matlab]] || 2009b || [http://www.mathworks.com MathWorks]||Math, Simulation, Programming||
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|-
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| [[meep]] || 0.10.0, 0.20.3 || || Will be removed on 2011-10-30
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|-
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| [[meme]] || 3.0.13, 4.3.0 || [http://meme.nbcr.net/meme/intro.html MEME]||Biology, Motifs, Sequence analysis||
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|-
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| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis Metis]||Math, Graph partitioning||
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|-
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| [[mira]] || 3.2.0 || [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_intro_whatismira MIRA Guide]||Biology, NGS||
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|-
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| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ MrBayes]||Biology, Phylogenetics||
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|-
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| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
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|-
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| [[netcdf]] || 3.6.3, 4.1.2, 4.1.3 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools || HDF5 support in 4.1.3 only
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|-
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| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
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|-
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| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page NWChem]||Simulation, Chemistry||
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|-
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| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/ OpenFoam]||Molecular Dynamics||
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|-
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| [[papi]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html PAPI]||CPU API||
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|-
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| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
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|-
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| [[pdt]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php PDT]||Programming, Profiler||
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|-
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| [[petsc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/ PETSc]||MPI toolkit||
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|-
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| [[pqs]] || 3.3-19 ||[http://www.pqs-chem.com/software.php PQS]||Modeling, Chemistry||
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|-
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| [[pyopencl]] || 0.92 || [http://mathema.tician.de/software/pyopencl PyOpenCL]||python, parallel programming||
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|-
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| [[python]] || 2.5.1, 2.6.4, 2.6.5 || [http://python.org Python]||Programming, scripting, language||
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|-
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| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
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|-
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| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
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|-
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| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]||Biology, Genomics||
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|-
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| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ Rosetta]||Biology, Structural, Modeling||
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|-
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| [[rsm]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm RSM]||Math, Modeling, Geometry||
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|-
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| [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ Samtools]||Biology, NGS||
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|-
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| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]||Statistics, Graphing||
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|-
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| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.icmab.es/siesta/ Siesta]||Simulation, physics, ab-initio||
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|-
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| [[Stata]] || 10 || [http://www.stata.com/ Stata]||Statistics, Data analysis||
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|-
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| [[tau]] || 2.20.1 ||[http://www.cs.uoregon.edu/Research/tau/home.php TAU]||Profiling, Tracing, Programming, Toolkit||
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|-
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| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics||
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|-
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| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS||
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|-
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| [[tuxedo]] ||colspan="3"|The "tuxedo suite," Bowtie, Tophat, and Cufflinks||
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|-
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| [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ VASP]||Quantum Chemistry, ab initio||
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|-
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| [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet]||Biology, NGS||
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|-
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| [[vmd]] || 1.9 ||[http://ftp.ks.uiuc.edu/Research/vmd/ VMD]||Biology, Visualization||
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|-
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| [[weka]] || 3.6.2 ||[http://www.cs.waikato.ac.nz/ml/weka/ WEKA]||Data mining algorithms||
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|-
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| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast]||Biology, Sequence Alignment||
 
|}
 
|}
  
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=== System Information ===
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* Many versions available.  <code>/scratch/hpc/osg/app/etc/grid3-locations.txt</code> may have an up-to-date list. Or look underneath <code>/scratch/hpc/osg/app/cmssoft</code>.
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Information on how to utilize our systems as well as technical information about the different hardware. There is also information for users on how to perform basic tasks on our systems.
 
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* [[Schedulers]]
 
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* [[Job Submission Queues]]
 
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* [[Sample Scripts | Sample Submission Script]]
 
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* [[Cluster Monitoring]]
 
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* [[Operating Environment]]
 
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* [[Node Performance]]
 
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* [[Hardware Testing]]
 
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=== Software and Libraries ===
 
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* [[Installed Software]]
 
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* [[CUDA]] Programming Guides
 
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* [[Command List]]
 
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* [[OpenMPI]]
 
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* [[OpenMP]]
 
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* [[Installing Perl Modules]] Installing Perl Modules as a Normal User
 
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* [[Compilers]]
 
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* [[Modules]]
 
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* [[Galaxy]]
 
  
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=== Specific Research Areas ===
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{{App Add Page}}
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* [[Biology|Biological Research Computing]]
 

Revision as of 03:52, 13 October 2011

The following is a list of the installed software at the UF HPC Center.

List updated 12 October 2011.

Software

Software Version Home Website Category Notes
Abaqus 6.6-1, 6.9-2 Abaqus Simulation
ADMB 9.1, 10.0 ADMB Modeling, math
Amber 10,11.old, 11 Amber Simulation, chemistry
Amos 3.0.0 AMOS Biology, Genomics
Ansys 10.0 Ansys Simulation, Engineering
antlr 3.1.3 Antlr Linguistics, Parser
arachne 37618 Arachne Biology, Genomics
bioscope 1.0.1, 1.2.1 ABI BioScope Biology, NGS
Blast 2.2.24, 2.2.25 NCBI Biology, Sequence alignment
Boost 1.37.0, 1.46.1 Boost C++, Library
Bowtie 0.12.7 Bowtie Biology, NGS
Charmm 35b2 Charmm Simulation, Chemistry
Circuit   Circuitscape GIS
CPMD 3.11.1 CPMD Simulation, Chemistry
Crystal 1.0.2 Will be removed on 2011-10-30
Cufflinks 1.0.3 Cufflinks Biology, NGS
dar 2.3.9 Dar Backup
Desmond 2.4.2.1 Desmond Simulation, Biology, Chemistry
dlpoly 3.0.9 DL_POLY Simulation, Biology, Chemistry
dock 6.3, 6.4 Dock Chemistry, ligand binding prediction
emboss 6.4.0 Emboss Biology, multi-tool suite
espresso 3.0, 3.2.2, 4.0.4 Espresso Modeling, Physics
fastqc 0.10.0 FastQC Biology, NGS
fftw 2.1.5, 3.1.2 FFTW Gaussian Math, Library, C++
fluent 6.3.26 ANSYS FLUENT Simulation
gadget 2.0.4, 2.0.5 Atlassian Gadgets Software Development
gamess 11-Aug11 GAMESS Quantum Chemistry
gaussian 03,09 Gaussian Modeling, Physics
Gromacs 4.0.4, 4.0.7 Gromacs Physics, Modeling
HDF5 1.8.7 HDF5 Library, Data
hypre 2.0.0 HYPRE Library, Math, Physics
Inelastica 1.1 Inelastica Quantum Chemistry
IE3D 15.1 IE3D Simulation, Design
lammps 17-Sept11 LAMPPS Simulation
madness 0.9 MADNESS Math, DIff. Equation solving
mafft 6.859 MAFFT Biology, Multiple sequence alignment
MACS 1.4.1 MACS Biology, ChIP-Seq
Matlab 2009b MathWorks Math, Simulation, Programming
meep 0.10.0, 0.20.3 Will be removed on 2011-10-30
meme 3.0.13, 4.3.0 MEME Biology, Motifs, Sequence analysis
metis 4.0 Metis Math, Graph partitioning
mira 3.2.0 MIRA Guide Biology, NGS
MrBayes 3.1.2 MrBayes Biology, Phylogenetics
NAMD 2.7b2 NAMD Simulation, Chemistry, Biology
netcdf 3.6.3, 4.1.2, 4.1.3 NetCDF Data exchange, Tools HDF5 support in 4.1.3 only
Newbler 2.5.3, 2.6 Newbler Biology, NGS
NWChem 6.0 NWChem Simulation, Chemistry
OpenFOAM 1.7.1 OpenFoam Molecular Dynamics
papi 4.1.2.1 PAPI CPU API
PeakSplitter 1.0 PeakSplitter Biology, Chip-Seq
pdt 3.16 PDT Programming, Profiler
petsc 2.3.3-p8, 3.0.0-p12 PETSc MPI toolkit
pqs 3.3-19 PQS Modeling, Chemistry
pyopencl 0.92 PyOpenCL python, parallel programming
python 2.5.1, 2.6.4, 2.6.5 Python Programming, scripting, language
RAxML 7.3.0 RAxML Biology, Phylogenetics
RAxML-Light 1.0.5 RAxML Biology, Phylogenetics
RepeatMasker 3.3.0 Repeat Masker Biology, Genomics
Rosetta 2.1.1, 2.1.2 Rosetta Biology, Structural, Modeling
rsm 2961 RSM Math, Modeling, Geometry
samtools 0.1.16 Samtools Biology, NGS
SAS 9.2, 9.3 SAS Statistics, Graphing
Siesta 2.0, 2.0.2, 3.0b Siesta Simulation, physics, ab-initio
Stata 10 Stata Statistics, Data analysis
tau 2.20.1 TAU Profiling, Tracing, Programming, Toolkit
TRF 4.04 TRF Biology, Genomics
Tophat 1.3.0 Tophat Biology, NGS
tuxedo The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP 4.6.34,5.2.0 VASP Quantum Chemistry, ab initio
velvet 1.1.05 Velvet Biology, NGS
vmd 1.9 VMD Biology, Visualization
weka 3.6.2 WEKA Data mining algorithms
wublast 2.0 WU-Blast Biology, Sequence Alignment
  • Many versions available. /scratch/hpc/osg/app/etc/grid3-locations.txt may have an up-to-date list. Or look underneath /scratch/hpc/osg/app/cmssoft.


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