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] [https://it.ufl.edu/ UFIT] [https://www.rc.ufl.edu 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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<br>
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<!-- {{Note|Submit a support request at [https://support.rc.ufl.edu https://support.rc.ufl.edu]|warn}} -->
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<!-- {{Note|See an important message about EL7->EL8 migration on HiPerGator at [[Rolling Upgrade from RHEL7 to RHEL8]]|warn}} -->
  
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List updated '''11 October 2011'''.
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==Software==
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|- valign="top"
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{| border="1"
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| width="50%" |
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! Software !! Version !! Home Website !! Category !! Notes
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{| width="100%"
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|-
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| style="width: 7%; vertical-align: top" | [[Image:Setup.png|frameless|upright=0.2]]
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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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| style="padding-left: 10px" | <h1 style="border: 0; margin: 0 0 3px 0; padding: 0">FOR NEW USERS</h1>
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|-
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Guides to get you started with HPG, and best practices!
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| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org] || Modeling, math ||
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<hr style="margin: 4px 0" />
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|-
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<span style="font-size: 12pt">'''[[Getting Started ]]''' | [[Training Videos]] | [[Training|Trainings & Events]] | [[Development_and_Testing|Interactive Development and Testing]] | [[Storage|Practical Storage Use]] </span>
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| [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ amber.scripps.edu] || Simulation, chemistry ||
 
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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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| [[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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|-
 
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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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|-
 
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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/ Cufflinks] || 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 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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|-
 
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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] || 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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|-
 
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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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| [[gamess]] || 11-Aug11 || [http://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]||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 || [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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|-
 
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| [[pdt]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php PDT]||Programming, Profiler||
 
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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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| [[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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| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
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| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
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| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]||Biology, Genomics||
 
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| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ Rosetta]||Biology, Structural, Modeling||
 
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| [[rsm]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm RSM]||Math, Modeling, Geometry||
 
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| [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ Samtools]||Biology, NGS||
 
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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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| [[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]] || ||  || 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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| [[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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||
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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]] | [[Using SSH Keys To Access HPG | SSH Keys]] | [[Blocked Accounts]] | [[Federated_Account_Request|Federated Access]] and [[Federated_login|Login]] </span>
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|}
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|- valign="top"
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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.
 +
<hr style="margin: 4px 0" />
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<span style="font-size: 12pt">'''[[Get_Help|How To Get Help]]'''  | [[AI Help]] | [[FAQ]] | <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request] | [[HiPerGator Metrics]] | [[Remote Support]]</span></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:Inter.png|frameless|upright=0.2]]
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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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Guides for GUI/web interfaces you can run on HPG.
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<hr style="margin: 4px 0" />
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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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|}
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|- valign="top"
  
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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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||
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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|Commands]]''' | [[Account_and_QOS_limits_under_SLURM|Account/QOS Limits]] | [[Available Node Features]] | [[Sample_SLURM_Scripts|Job Script Examples]] | [[SLURM_Job_Arrays|Job Arrays]] | [[GPU_Access|GPU Access]] | [[SLURM_Job_States|Job States]] | [[SLURM Partition Limits|Time Limits]]</span>
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|}
  
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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: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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||
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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]] | [[Sharing Within A Cluster]] | [[Rsync]] </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]]''' | '''[[Computer Vision]]''' </span>
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|}
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|- valign="top"
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|}
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__NOTOC__
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__NOEDITSECTION__

Latest revision as of 17:20, 22 July 2024

Welcome to the University of Florida UFIT 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 Videos | Trainings & Events | 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 | SSH Keys | Blocked Accounts | Federated Access and Login

Question.png

HELP

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

How To Get Help | AI Help | FAQ | Submit a Support Request | HiPerGator Metrics | Remote Support

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.

Commands | Account/QOS Limits | Available Node Features | Job Script Examples | Job Arrays | GPU Access | Job States | Time Limits

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 | Sharing Within A Cluster | Rsync

Areas.png

SPECIFIC RESEARCH AREAS

Highlighted areas of specialization commonly seen with HPG.

Biology | Natural Language Processing | Computer Vision


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