Difference between revisions of "UFRC Help and Documentation"

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[[Category:Software]]
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[[Category:Docs]]
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The following is a list of the installed software at the UF HPC Center.
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__NOTOC__
  
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List updated '''07 October 2011'''.
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<!-- {{Note|Interactive Jobs in the GPU partition are limited to 6 hrs|news}} -->
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==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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{| border="1"
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{{Note|[[https://lists.ufl.edu/cgi-bin/wa?A0=HPC-ANNOUNCE-L HiPerGator News and Announcements]] |news}}
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! Software !! Version !! Home Website !! Category !! Notes
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=== Getting Started ===
 +
{| 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;"  
 
|-
 
|-
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| [[Abaqus]] || 6.6-1, 6.9-2 || || Simulation||
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| scope="col" width="150" |
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* '''[[Getting Started ]]'''
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* [[Quick Start Guide]]
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* [[New user training]]
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| scope="col" width="150" |
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* '''[[Training|Training, Events, Videos]]'''
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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]]
 
|-
 
|-
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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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=== 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;"
 
|-
 
|-
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| [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ amber.scripps.edu] || 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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* [[GPU_Access|GPU Access]]
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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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* [[Open OnDemand|OnDemand (Matlab, RStudio,...)]]
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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]]
 
|-
 
|-
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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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=== 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;"
 
|-
 
|-
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| [[Ansys]] || 10.0 || [http://www.ansys.com/ www.ansys.com] || 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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|}
 +
 
 +
=== 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;"
 
|-
 
|-
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| [[antlr]] || 3.1.3 || [http://www.antlr.org/ http://www.antlr.org/] || 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]]
 
|-
 
|-
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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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=== 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;"
 
|-
 
|-
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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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| 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]]
 
|-
 
|-
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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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|-
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| [[Boost]] || 1.37.0, 1.46.1 || [http://www.boost.org/ Boost.org] || C++, Library ||
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=== Specific Research Areas ===
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|-
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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;"
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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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| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website]
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| scope="col" width="150" |
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* [[Biology|Biocomputing]]
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| scope="col" width="150" |
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| scope="col" width="150" |
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* [[Nlp|Natural Language Processing]]
 
|-
 
|-
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| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ www.gaussian.com]
 
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|-
 
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| [[fluent]] || 6.3.26 ||
 
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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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|-
 
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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ www.msg.ameslab.gov/gamess]
 
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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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* 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}}
 

Revision as of 16:57, 24 May 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.

[HiPerGator News and Announcements]

Getting Started

Interfaces and Access

Scheduler

Software and Reference Data

Transfer Data

Specific Research Areas

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=UFRC_Help_and_Documentation&oldid=22549"