Difference between revisions of "UFRC Help and Documentation"

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[[Category:Software]]
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[[Category:Docs]]
The following is a list of the installed software at the UF HPC Center.
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__NOTOC__
  
List updated '''12 October 2011'''.
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<!-- {{Note|Interactive Jobs in the GPU partition are limited to 6 hrs|news}} -->
==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, policies, 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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{{Note|[[https://lists.ufl.edu/cgi-bin/wa?A0=HPC-ANNOUNCE-L HiPerGator News and Announcements]] |news}}
! Software !! Version !! Home Website !! Category !! Notes
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=== For New Users ===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #FF4A00; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"  
 
|-
 
|-
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html Abaqus] || Simulation||
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| scope="col" width="150" |
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* '''[[Getting Started ]]'''
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* '''[[Training|Training, Events, Videos]]'''
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* [[New user training]]
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| scope="col" width="150" |
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* [[Development_and_Testing|Interactive Development and Testing]]
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* [[Storage|Practical Storage Use]]
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| scope="col" width="150" |
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* '''[[Get_Help|How To Get Help]]'''</span>
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* <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span>
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* [[AI Help|AI Help]]
 
|-
 
|-
| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ ADMB] || Modeling, math ||
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|}
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=== Interfaces and Access===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #0021A5; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
 
|-
 
|-
| [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ Amber] || Simulation, chemistry ||
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| scope="col" width="150" |
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* [[Jupyter_Notebooks| Jupyter (Python, R)]]
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* [[Galaxy|Galaxy Genomics Framework]]
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* [[Open OnDemand|OnDemand (Matlab, RStudio,...)]]
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| scope="col" width="150" |
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* [[Managing Python environments and Jupyter_kernels | Conda and Jupyter Kernels ]]
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* [[GUI Programs|Running GUI Apps]]
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* [[GPU_Access|GPU Access]]
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| scope="col" width="150" |
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* [[Authentication With MFA|Multi-Factor Authentication]]
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* [[SSH Multiplexing]]
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* [[Blocked Accounts]]
 
|-
 
|-
| [[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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=== Scheduler ===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #FF4A00; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
 
|-
 
|-
| [[Ansys]] || 10.0 || [http://www.ansys.com/ Ansys] || Simulation, Engineering ||
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| scope="col" width="150" |
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* [[SLURM_Commands|SLURM Commands]]
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* [[Account_and_QOS_limits_under_SLURM|Account and QOS Limits Under SLURM]]
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| scope="col" width="150" |
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* [[Large-Memory_SMP_Servers|Big Memory Partition]]
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* [[Available Node Features]]
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| scope="col" width="150" |
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* [[Sample_SLURM_Scripts|SLURM Job Script Examples]]
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* [[SLURM_Job_Arrays|SLURM Job Arrays]]
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|}
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 +
=== Software and Reference Data===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #0021A5; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
 
|-
 
|-
| [[antlr]] || 3.1.3 || [http://www.antlr.org/ Antlr] || Linguistics, Parser ||
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| scope="col" width="150" |
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* [[Applications|Installed Applications]]
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* [[UFRC_environment_module|HiPerGator ufrc Tools]]
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| scope="col" width="150" |
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* [[Modules|Environment Modules System]]
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| scope="col" width="150" |
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* [[Reference Data]]
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* [[AI Reference Datasets]]
 
|-
 
|-
| [[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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=== Transfer Data ===
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{| cellpadding=10 width="100%" style="background-color: #FFF; border-color: #FF4A00; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
 
|-
 
|-
| [[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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| scope="col" width="150" |
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* [[Transfer Data]]
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| scope="col" width="150" |
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* [[Globus]]
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| scope="col" width="150" |
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* [[Samba Access]]
 
|-
 
|-
| [[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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=== Specific Research Areas ===
|-
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{cellpadding=10 width="100%" style="background-color: #FFF; border-color: #0021A5; border-style: solid; border-width: 3px 3px 3px 3px; color: #444444; vertical-align:top;"
| [[tuxedo|Bowtie]] || 0.12.7 || [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] || Biology, NGS ||
 
|-
 
| [[Charmm]] || 35b2 || [http://www.charmm.org/ Charmm] || Simulation, Chemistry ||
 
|-
 
| [[Circuit]] || &nbsp; || [http://www.circuitscape.org/Circuitscape/Welcome.html Circuitscape] || GIS ||
 
|-
 
| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ CPMD] || Simulation, Chemistry ||
 
|-
 
| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30
 
|-
 
| [[tuxedo|Cufflinks]] || 1.0.3 || [http://cufflinks.cbcb.umd.edu/ Cufflinks] || Biology, NGS ||
 
|-
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ Dar] || Backup ||
 
|-
 
| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html Desmond] || Simulation, Biology, Chemistry ||
 
|-
 
| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml DL_POLY] || Simulation, Biology, Chemistry ||
 
|-
 
| [[dock]] || 6.3, 6.4 || [http://dock.compbio.ucsf.edu/ Dock] || Chemistry, ligand binding prediction ||
 
|-
 
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ Emboss] || Biology, multi-tool suite ||
 
|-
 
| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ Espresso] || Modeling, Physics ||
 
|-
 
| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC] || Biology, NGS ||
 
|-
 
| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ FFTW Gaussian] || Math, Library, C++ ||
 
|-
 
| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT ANSYS FLUENT] || Simulation ||
 
|-
 
| [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets] || Software Development ||
 
|-
 
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ GAMESS]|| Quantum Chemistry||
 
|-
 
| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
 
|-
 
| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ Gromacs]||Physics, Modeling||
 
|-
 
| [[HDF5]] || 1.8.7 || [http://www.hdfgroup.org/HDF5/ HDF5]||Library, Data||
 
|-
 
| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics||
 
|-
 
| [[Inelastica]] || 1.1 || [http://sourceforge.net/projects/inelastica/ Inelastica]||Quantum Chemistry||
 
|-
 
| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/ IE3D]||Simulation, Design||
 
|-
 
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
 
|-
 
| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS]||Math, DIff. Equation solving||
 
|-
 
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
 
|-
 
| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS]||Biology, ChIP-Seq||
 
|-
 
| [[Matlab]] || 2009b || [http://www.mathworks.com 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 || [http://meme.nbcr.net/meme/intro.html MEME]||Biology, Motifs, Sequence analysis||
 
|-
 
| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis Metis]||Math, Graph partitioning||
 
|-
 
| [[mira]] || 3.2.0 || [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_intro_whatismira MIRA Guide]||Biology, NGS||
 
|-
 
| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ MrBayes]||Biology, Phylogenetics||
 
|-
 
| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
 
|-
 
| [[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
 
|-
 
| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
 
|-
 
| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page NWChem]||Simulation, Chemistry||
 
|-
 
| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/ OpenFoam]||Molecular Dynamics||
 
|-
 
| [[papi]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html PAPI]||CPU API||
 
|-
 
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
 
|-
 
| [[pdt]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php PDT]||Programming, Profiler||
 
|-
 
| [[petsc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/ PETSc]||MPI toolkit||
 
|-
 
| [[pqs]] || 3.3-19 ||[http://www.pqs-chem.com/software.php PQS]||Modeling, Chemistry||
 
|-
 
| [[pyopencl]] || 0.92 || [http://mathema.tician.de/software/pyopencl PyOpenCL]||python, parallel programming||
 
|-
 
| [[python]] || 2.5.1, 2.6.4, 2.6.5 || [http://python.org Python]||Programming, scripting, language||
 
|-
 
| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
|-
 
| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
|-
 
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]||Biology, Genomics||
 
|-
 
| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ Rosetta]||Biology, Structural, Modeling||
 
|-
 
| [[rsm]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm RSM]||Math, Modeling, Geometry||
 
|-
 
| [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ Samtools]||Biology, NGS||
 
 
|-
 
|-
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]||Statistics, Graphing||
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| scope="col" width="150" |
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* [[Biology|Biology]]
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| scope="col" width="150" |
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| scope="col" width="150" |
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* [[Nlp|Natural Language Processing]]
 
|-
 
|-
| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.icmab.es/siesta/ Siesta]||Simulation, physics, ab-initio||
 
|-
 
| [[Stata]] || 10 || [http://www.stata.com/ Stata]||Statistics, Data analysis||
 
|-
 
| [[tau]] || 2.20.1 ||[http://www.cs.uoregon.edu/Research/tau/home.php TAU]||Profiling, Tracing, Programming, Toolkit||
 
|-
 
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics||
 
|-
 
| [[Trinity]] || r20110519, r20110820 || [http://trinityrnaseq.sourceforge.net/ Trinity RNA-Seq]||
 
|-
 
| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS||
 
|-
 
| [[tuxedo]] ||colspan="3"|The "tuxedo suite," Bowtie, Tophat, and Cufflinks||
 
|-
 
| [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ VASP]||Quantum Chemistry, ab initio||
 
|-
 
| [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet]||Biology, NGS||
 
|-
 
| [[vmd]] || 1.9 ||[http://ftp.ks.uiuc.edu/Research/vmd/ VMD]||Biology, Visualization||
 
|-
 
| [[weka]] || 3.6.2 ||[http://www.cs.waikato.ac.nz/ml/weka/ WEKA]||Data mining algorithms||
 
|-
 
| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast]||Biology, Sequence Alignment||
 
 
|}
 
|}
 
* 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>.
 
 
{{App Add Page}}
 

Latest revision as of 14:09, 10 June 2022


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

For New Users

Interfaces and Access

Scheduler

Software and Reference Data

Transfer Data

Specific Research Areas