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] Research Computing Help and Documentation site. General information, announcements, and purchase request forms are on our [https://www.rc.ufl.edu main web site]. The information here is focused on particular applications, services, and usage examples. [https://support.rc.ufl.edu Provide Feedback].</span>
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The following is a list of the installed software at the UF HPC Center.
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{| cellspacing="20" cellpadding="0" width="100%"
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| width="50%" |
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Setup.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">FOR NEW USERS</h1>
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Guides to get you started with HPG, and best practices!
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Getting Started ]]''' | [[Training|Training, Events, Videos]] | [[New user training]] | [[Development_and_Testing|Interactive Development and Testing]] | [[Storage|Practical Storage Use]] </span>
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|}
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Access.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">ACCESS</h1>
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How to connect to HPG with Duo, authenticate multiple connections, or check account.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Authentication With MFA|Multi-Factor Authentication]]''' | [[SSH Multiplexing]] | [[Blocked Accounts]]</span>
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|}
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Question.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">HELP</h1>
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Resources to ask questions, get support, or communicate directly.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Get_Help|How To Get Help]]''' | <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span> | [[AI Help|AI Help]] | [[FAQ]]</span>
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|}
  
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List updated '''07 October 2011'''.
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==Software==
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{| width="100%"
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{| border="1"
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| style="width: 7%; vertical-align: top" | [[Image:Inter.png|frameless|upright=0.2]]
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! Software !! Version !! Home Website !! Category !! Notes
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">INTERFACES</h1>
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|-
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Guides for GUI/web interfaces you can run on HPG.
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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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<hr style="margin: 4px 0" />
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|-
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<span style="font-size: 12pt"> '''[[Jupyter_Notebooks| Jupyter (Python, R)]]''' | [[Galaxy|Galaxy Genomics Framework]] | [[Open OnDemand|OnDemand (Matlab, RStudio,...)]] | [[Managing Python environments and Jupyter_kernels | Conda and Jupyter Kernels ]] | [[GUI Programs|Running GUI Apps]] </span>
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| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org] || Modeling, math ||
 
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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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| [[antlr]] || 3.1.3 || [http://www.antlr.org/ http://www.antlr.org/] || Linguistics, Parser ||
 
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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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| [[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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| [[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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| [[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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| [[Charmm]] || 35b2 || [http://www.charmm.org/] || Simulation, Chemistry ||
 
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| [[Circuit]] || &nbsp; || [http://www.circuitscape.org/Circuitscape/Welcome.html circuitscape.org] || GIS ||
 
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| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ www.cpmd.org] || Simulation, Chemistry ||
 
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| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30
 
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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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| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ SF.net] || Backup ||
 
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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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| [[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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| [[dock]] || 6.3, 6.4 || [http://dock.compbio.ucsf.edu/ dock.compbio.ucsf.edu] || Chemistry, ligand binding prediction ||
 
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| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ emboss.sourceforge.net] || Biology, multi-tool suite ||
 
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| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ quantum-espresso.org] || Modeling, Physics ||
 
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|-
 
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| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website] || Biology, NGS ||
 
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| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ FFTW Gaussian] || Math, Library, C++ ||
 
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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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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ www.msg.ameslab.gov/gamess GAMESS]|| Quantum Chemistry||
 
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| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
 
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| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ www.gromacs.org]||Physics, Modeling||
 
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| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics||
 
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| [[Inelastica]] || 1.1 || [http://sourceforge.net/projects/inelastica/ Inelastica]||Quantum Chemistry||
 
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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 Home Page]||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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|-
 
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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 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF|| Data exchange, Tools ||
 
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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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| [[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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| [[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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| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]
 
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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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| [[tuxedo]] ||  || The "tuxedo suite," Bowtie, Tophat, and Cufflinks
 
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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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| [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ www.ebi.ac.uk/~zerbino/velvet/]
 
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| [[vmd]] || 1.9 ||
 
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| [[weka]] || 3.6.2 ||
 
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| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast] [[WUBLAST|WU-BLAST Readme file]]
 
 
|}
 
|}
  
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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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{{App Add Page}}
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||
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Scheduler.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SCHEDULER</h1>
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How to schedule and manage jobs and resources on HPG and more SLURM info.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[SLURM_Commands|SLURM Commands]]''' | [[Account_and_QOS_limits_under_SLURM|Account/QOS Limits Under SLURM]] | [[Large-Memory_SMP_Servers|Big Memory Partition]] | [[Available Node Features]] | [[Sample_SLURM_Scripts|SLURM Job Script Examples]] | [[SLURM_Job_Arrays|SLURM Job Arrays]] | [[GPU_Access|GPU Access]] </span>
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|}
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||
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Software.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SOFTWARE AND REFERENCE DATA</h1>
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View installed programs and tools, how to utilize them, and reference data that they can run.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Applications|Installed Applications]]''' | [[UFRC_environment_module|HiPerGator ufrc Tools]] | [[Modules|Environment Modules System]] | [[Reference Data]] | [[AI Reference Datasets]]</span>
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|}
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|- valign="top"
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Transfer.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">TRANSFER DATA</h1>
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How to move different sizes of data to and from HPG.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Transfer Data]]''' | [[Globus]] | [[Samba Access]]</span>
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|}
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||
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{| width="100%"
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| style="width: 7%; vertical-align: top" | [[Image:Areas.png|frameless|upright=0.2]]
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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">SPECIFIC RESEARCH AREAS</h1>
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Highlighted areas of specialization commonly seen with HPG.
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<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Biology|Biology]]''' | [[Nlp|Natural Language Processing]]</span>
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|}
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|}
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__NOTOC__
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__NOEDITSECTION__

Revision as of 17:14, 22 July 2022

Welcome to the University of Florida Research Computing Help and Documentation site. General information, announcements, and purchase request forms are on our main web site. The information here is focused on particular applications, services, and usage examples. Provide Feedback.

Setup.png

FOR NEW USERS

Guides to get you started with HPG, and best practices!

Getting Started | Training, Events, Videos | New user training | Interactive Development and Testing | Practical Storage Use

Access.png

ACCESS

How to connect to HPG with Duo, authenticate multiple connections, or check account.

Multi-Factor Authentication | SSH Multiplexing | Blocked Accounts

Question.png

HELP

Resources to ask questions, get support, or communicate directly.

How To Get Help | Submit a Support Request | AI Help | FAQ

Inter.png

INTERFACES

Guides for GUI/web interfaces you can run on HPG.

Jupyter (Python, R) | Galaxy Genomics Framework | OnDemand (Matlab, RStudio,...) | Conda and Jupyter Kernels | Running GUI Apps

Scheduler.png

SCHEDULER

How to schedule and manage jobs and resources on HPG and more SLURM info.

SLURM Commands | Account/QOS Limits Under SLURM | Big Memory Partition | Available Node Features | SLURM Job Script Examples | SLURM Job Arrays | GPU Access

Software.png

SOFTWARE AND REFERENCE DATA

View installed programs and tools, how to utilize them, and reference data that they can run.

Installed Applications | HiPerGator ufrc Tools | Environment Modules System | Reference Data | AI Reference Datasets

Transfer.png

TRANSFER DATA

How to move different sizes of data to and from HPG.

Transfer Data | Globus | Samba Access

Areas.png

SPECIFIC RESEARCH AREAS

Highlighted areas of specialization commonly seen with HPG.

Biology | Natural Language Processing


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