Difference between revisions of "UFRC Help and Documentation"

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[[Category:Software]]
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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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The following is a list of the installed software at the UF HPC Center.
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=== Getting Started ===
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{|  
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List updated '''12 October 2011'''.
 
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==Software==
 
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{|  border="1" cellspacing="0" cellpadding="2"
 
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! Software !! Version !! Home Website !! Category !! Notes
 
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|-
 
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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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| [[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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| [[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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| [[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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| [[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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| [[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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|-
 
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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ GAMESS]|| Quantum Chemistry||
 
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|-
 
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| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
 
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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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| [[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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| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
 
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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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| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
 
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| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS]||Biology, ChIP-Seq||
 
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| [[Matlab]] || 2009b || [http://www.mathworks.com MathWorks]||Math, Simulation, Programming||
 
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| [[meep]] || 0.10.0, 0.20.3 || || Will be removed on 2011-10-30
 
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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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| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis Metis]||Math, Graph partitioning||
 
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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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| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ MrBayes]||Biology, Phylogenetics||
 
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| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
 
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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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| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
 
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| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page NWChem]||Simulation, Chemistry||
 
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| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/ OpenFoam]||Molecular Dynamics||
 
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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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| [[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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| [[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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| [[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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| [[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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|-
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* [[Getting Started]]
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| [[Stata]] || 10 || [http://www.stata.com/ Stata]||Statistics, Data analysis||
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* [[Getting Help]]
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|-
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* [[Policies]]
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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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* [[Frequently Asked Questions]]
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| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics||
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* [[Password | Changing your Password]]
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|-
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* [[Samba Access]]
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| [[Trinity]] || r20110519, r20110820 || [http://trinityrnaseq.sourceforge.net/ Trinity RNA-Seq]||
 
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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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| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast]||Biology, Sequence Alignment||
 
 
|}
 
|}
  
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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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=== System Information ===
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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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{{App Add Page}}
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=== Specific Research Areas ===
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* [[Biology|Biological Research Computing]]

Revision as of 20:39, 17 October 2011

Welcome to the University of Florida 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 Support System or send email to HPC support.

Getting Started

System Information

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.

Software and Libraries

Specific Research Areas

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=UFRC_Help_and_Documentation&oldid=5308"