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 '''07 October 2011'''.
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==Software==
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{| border="1"
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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 || || Simulation||
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|-
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| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org] || Modeling, math ||
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|-
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| [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ amber.scripps.edu] || 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 SourceForge] || Biology, Genomics ||
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|-
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| [[Ansys]] || 10.0 || [http://www.ansys.com/ www.ansys.com] || Simulation, Engineering ||
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|-
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| [[antlr]] || 3.1.3 || [http://www.antlr.org/ http://www.antlr.org/] || 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- Broadinstitute page] || 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 page] || Biology, Sequence alignment ||
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|-
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| [[Boost]] || 1.37.0, 1.46.1 || [http://www.boost.org/ Boost.org] || C++, Library ||
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|-
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| [[tuxedo|Bowtie]] || 0.12.7 || [http://bowtie-bio.sourceforge.net/index.shtml http://bowtie-bio.sourceforge.net/] || Biology, NGS ||
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|-
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| [[Charmm]] || 35b2 || [http://www.charmm.org/] || Simulation, Chemistry ||
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|-
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| [[Circuit]] || &nbsp; || [http://www.circuitscape.org/Circuitscape/Welcome.html circuitscape.org] || GIS ||
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|-
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| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ www.cpmd.org] || 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/ http://cufflinks.cbcb.umd.edu/] || Biology, NGS ||
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|-
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| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ SF.net] || Backup ||
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|-
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| [[Newbler|denovo]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
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|-
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| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html 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 www.cse.clrc.ac.uk]  || Simulation, Biology, Chemistry ||
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|-
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| [[dock]] || 6.3, 6.4 || [http://dock.compbio.ucsf.edu/ dock.compbio.ucsf.edu] || Chemistry, ligand binding prediction ||
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|-
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| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ emboss.sourceforge.net] || 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/ quantum-espresso.org]
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|-
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| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website]
 
|-
 
|-
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|
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| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ www.gaussian.com]
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* [[Getting Started]]
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|-
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* [[Getting Help]]
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| [[fluent]] || 6.3.26 ||
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* [[Policies]]
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|-
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||
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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 website]
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* [[Frequently Asked Questions]]
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|-
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* [[Password | Changing your Password]]
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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ www.msg.ameslab.gov/gamess]
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* [[Samba Access]]
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|-
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| [[gaussian]] || 03,09 || [http://www.gaussian.com/ www.gaussian.com]
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|-
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| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ www.gromacs.org]
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|-
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| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html Lawrence Livermore National Labs]
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|-
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| [[Inelastica]] || 1.1 ||
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|-
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| [[IE3D]] || 15.1 ||
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|-
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| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS Home Page]
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|-
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| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS Home Page]
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|-
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| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT Home Page]
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|-
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| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS Home Page]
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|-
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| [[Matlab]] || 2009b || [http://www.mathworks.com www.mathworks.com]
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|-
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| [[meep]] || 0.10.0, 0.20.3 ||
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|-
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| [[meme]] || 3.0.13, 4.3.0 ||
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|-
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| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis glaros.dtc.umn.edu]
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|-
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| [[mira]] || 3.2.0 ||
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|-
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| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ mrbayes.scs.fsu.edu]
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|-
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| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ www.ks.uiuc.edu]
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|-
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| [[netcdf]] || 3.6.3, 4.1.2 ||
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|-
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| [[Newbler]] || 2.5.3, 2.6 ||
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|-
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| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page http://www.nwchem-sw.org]
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|-
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| [[OpenFOAM]] || 1.7.1 ||
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|-
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| [[papi]] || 4.1.2.1 ||
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|-
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| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html Upstream sofware page]
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|-
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| [[pdt]] || 3.16 ||
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|-
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| [[petsc]] || 2.3.3-p8, 3.0.0-p12 ||
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|-
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| [[pqs]] || 3.3-19 ||
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|-
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| [[pyopencl]] || 0.92 ||
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|-
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| [[python]] || 2.5.1, 2.6.4, 2.6.5 ||
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|-
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| [[RAxML]] || 7.3.0 || [http://wwwkramer.in.tum.de/exelixis/software.html RAxML]
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|-
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| [[RAxML-Light]] || 1.0.5 || [http://wwwkramer.in.tum.de/exelixis/software.html RAxML]
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|-
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| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]
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|-
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| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ www.rosettacommons.org]
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|-
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| [[rsm]] || 2961 ||
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|-
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| [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ http://samtools.sourceforge.net/]  
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|-
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| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]
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|-
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| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ www.uam.es]
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|-
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| [[Stata]] || 10 || [http://www.stata.com/ Stata]
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|-
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| [[tau]] || 2.20.1 ||
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|-
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| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html Tandem Repeats Finder]
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|-
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| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ http://tophat.cbcb.umd.edu/]
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|-
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| [[tuxedo]] ||  || 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/ cms.mpi.univie.ac.at]
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|-
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| [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ www.ebi.ac.uk/~zerbino/velvet/]
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|-
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| [[vmd]] || 1.9 ||
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|-
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| [[weka]] || 3.6.2 ||
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|-
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| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast] [[WUBLAST|WU-BLAST Readme file]]
 
|}
 
|}
  
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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 15:21, 11 October 2011

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

List updated 07 October 2011.

Software

Software Version Home Website Category Notes
Abaqus 6.6-1, 6.9-2 Simulation
ADMB 9.1, 10.0 admb-project.org Modeling, math
Amber 10,11.old, 11 amber.scripps.edu Simulation, chemistry
Amos 3.0.0 AMOS SourceForge Biology, Genomics
Ansys 10.0 www.ansys.com Simulation, Engineering
antlr 3.1.3 http://www.antlr.org/ Linguistics, Parser
arachne 37618 Broadinstitute page Biology, Genomics
bioscope 1.0.1, 1.2.1 ABI BioScope Biology, NGS
Blast 2.2.24, 2.2.25 NCBI page Biology, Sequence alignment
Boost 1.37.0, 1.46.1 Boost.org C++, Library
Bowtie 0.12.7 http://bowtie-bio.sourceforge.net/ Biology, NGS
Charmm 35b2 [1] Simulation, Chemistry
Circuit   circuitscape.org GIS
CPMD 3.11.1 www.cpmd.org Simulation, Chemistry
Crystal 1.0.2 Will be removed on 2011-10-30
Cufflinks 1.0.3 http://cufflinks.cbcb.umd.edu/ Biology, NGS
dar 2.3.9 SF.net Backup
denovo 2.5.3, 2.6 Newbler Biology, NGS
Desmond 2.4.2.1 www.deshawresearch.com/resources_desmond.html Desmond Simulation, Biology, Chemistry
dlpoly 3.0.9 www.cse.clrc.ac.uk Simulation, Biology, Chemistry
dock 6.3, 6.4 dock.compbio.ucsf.edu Chemistry, ligand binding prediction
emboss 6.4.0 emboss.sourceforge.net Biology, multi-tool suite
espresso 3.0, 3.2.2, 4.0.4 quantum-espresso.org
fastqc 0.10.0 FastQC website
fftw 2.1.5, 3.1.2 www.gaussian.com
fluent 6.3.26
gadget 2.0.4, 2.0.5 Atlassian Gadgets website
gamess 11-Aug11 www.msg.ameslab.gov/gamess
gaussian 03,09 www.gaussian.com
Gromacs 4.0.4, 4.0.7 www.gromacs.org
hypre 2.0.0 Lawrence Livermore National Labs
Inelastica 1.1
IE3D 15.1
lammps 17-Sept11 LAMPPS Home Page
madness 0.9 MADNESS Home Page
mafft 6.859 MAFFT Home Page
MACS 1.4.1 MACS Home Page
Matlab 2009b www.mathworks.com
meep 0.10.0, 0.20.3
meme 3.0.13, 4.3.0
metis 4.0 glaros.dtc.umn.edu
mira 3.2.0
MrBayes 3.1.2 mrbayes.scs.fsu.edu
NAMD 2.7b2 www.ks.uiuc.edu
netcdf 3.6.3, 4.1.2
Newbler 2.5.3, 2.6
NWChem 6.0 http://www.nwchem-sw.org
OpenFOAM 1.7.1
papi 4.1.2.1
PeakSplitter 1.0 Upstream sofware page
pdt 3.16
petsc 2.3.3-p8, 3.0.0-p12
pqs 3.3-19
pyopencl 0.92
python 2.5.1, 2.6.4, 2.6.5
RAxML 7.3.0 RAxML
RAxML-Light 1.0.5 RAxML
RepeatMasker 3.3.0 Repeat Masker
Rosetta 2.1.1, 2.1.2 www.rosettacommons.org
rsm 2961
samtools 0.1.16 http://samtools.sourceforge.net/
SAS 9.2, 9.3 SAS
Siesta 2.0, 2.0.2, 3.0b www.uam.es
Stata 10 Stata
tau 2.20.1
TRF 4.04 Tandem Repeats Finder
Tophat 1.3.0 http://tophat.cbcb.umd.edu/
tuxedo The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP 4.6.34,5.2.0 cms.mpi.univie.ac.at
velvet 1.1.05 www.ebi.ac.uk/~zerbino/velvet/
vmd 1.9
weka 3.6.2
wublast 2.0 WU-Blast WU-BLAST Readme file
  • 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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