Difference between revisions of "UFRC Help and Documentation"

From UFRC
Jump to navigation Jump to search
(216 intermediate revisions by 8 users not shown)
Line 1: Line 1:
[[Category:Software]]
+
[[Category:Docs]]
The following is a list of the installed software at the UF HPC Center.
+
__NOTOC__
  
List updated '''11 October 2011'''.
+
{{Note|[[:News:Latest|The latest HiPerGator News and Announcements]]|news}}
==Software==
+
 
{| border="1"
+
<!-- {{Note|Interactive Jobs in the GPU partition are limited to 6 hrs|news}} -->
! Software !! Version !! Home Website !! Category !! Notes
+
Welcome to the <span class="plainlinks">[http://www.ufl.edu/ University of Florida] Research Computing Help and Documentation site. The information here is focused on particular applications, services, and usage examples and complements more general policies and information found on our [https://www.rc.ufl.edu main web site]. It is used for information that changes more frequently and might become quickly dated or incorrect on the web site. This site is edited by individual UFRC staff members. If you find inaccuracies, errors, or omissions on this site please [https://support.rc.ufl.edu let us know].</span>
 +
 
 +
<span>[https://outlook.office365.com/owa/calendar/UFITResearchComputingSupport@uflorida.onmicrosoft.com/bookings/ Book an In-Person or Zoom support appointment.]</span>
 +
=== 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;"  
 
|-
 
|-
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html Abaqus] || Simulation||
+
| scope="col" width="150" |
 +
* [[Getting Started ]]
 +
* [[Quick Start Guide]]
 +
* [[New user training]]
 +
| scope="col" width="150" |
 +
* [[Training|Training, Events and How-To Videos]]
 +
* [[Development_and_Testing|Interactive Development and Testing]]
 +
* [[Storage|Practical Storage Use]]
 +
| scope="col" width="150" |
 +
* [[AI Help|AI Help]]
 +
* <span class="plainlinks">[https://support.rc.ufl.edu/enter_bug.cgi Submit a Support Request]</span>
 +
* [[Support|All Support Options]]</span>
 
|-
 
|-
| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org] || Modeling, math ||
+
|}
 +
 
 +
=== Interfaces and Access===
 +
{| 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.scripps.edu] || Simulation, chemistry ||
+
| scope="col" width="150" |
 +
* [[Jupyter_Notebooks| Jupyter (Python, R)]]
 +
* [[Galaxy|Galaxy Genomics Framework]]
 +
* [[GPU_Access|GPU Access]]
 +
| scope="col" width="150" |
 +
* [[GUI Programs|Running GUI Apps]]
 +
* [[Open OnDemand|OnDemand (Matlab, RStudio,...)]]
 +
| scope="col" width="150" |
 +
* [[Authentication With MFA|Multi-Factor Authentication]]
 +
* [[SSH Multiplexing]]
 +
* [[Blocked Accounts]]
 
|-
 
|-
| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS SourceForge] || Biology, Genomics ||
+
|}
 +
 
 +
=== Scheduler ===
 +
{| 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/ www.ansys.com] || Simulation, Engineering ||
+
| scope="col" width="150" |
 +
* [[SLURM_Commands|SLURM Commands]]
 +
* [[Account_and_QOS_limits_under_SLURM|Account and QOS Limits Under SLURM]]
 +
| scope="col" width="150" |
 +
* [[Large-Memory_SMP_Servers|Big Memory Partition]]
 +
* [[Available Node Features]]
 +
| scope="col" width="150" |
 +
* [[Sample_SLURM_Scripts|SLURM Job Script Examples]]
 +
* [[SLURM_Job_Arrays|SLURM Job Arrays]]
 +
|}
 +
 
 +
=== Software and Reference Data===
 +
{| 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/ http://www.antlr.org/] || Linguistics, Parser ||
+
| scope="col" width="150" |
 +
* [[Applications|Installed Applications]]
 +
* [[UFRC_environment_module|HiPerGator ufrc Tools]]
 +
| scope="col" width="150" |
 +
* [[Modules|Environment Modules System]]
 +
 
 +
| scope="col" width="150" |
 +
* [[Reference Data]]
 +
* [[AI Reference Datasets]]
 
|-
 
|-
| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational- Broadinstitute page] || Biology, Genomics ||
+
|}
 +
 
 +
=== Transfer Data ===
 +
{| 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 ||
+
| scope="col" width="150" |
 +
* [[Transfer Data]]
 +
| scope="col" width="150" |
 +
* [[Globus]]
 +
| scope="col" width="150" |
 +
* [[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 page] || Biology, Sequence alignment ||
+
|}
|-
+
 
| [[Boost]] || 1.37.0, 1.46.1 || [http://www.boost.org/ Boost.org] || C++, Library ||
+
=== Specific Research Areas ===
|-
+
{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 http://bowtie-bio.sourceforge.net/] || Biology, NGS ||
 
|-
 
| [[Charmm]] || 35b2 || [http://www.charmm.org/] || Simulation, Chemistry ||
 
|-
 
| [[Circuit]] || &nbsp; || [http://www.circuitscape.org/Circuitscape/Welcome.html circuitscape.org] || GIS ||
 
|-
 
| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ www.cpmd.org] || 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/ SF.net] || 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 www.cse.clrc.ac.uk] || Simulation, Biology, Chemistry ||
 
|-
 
| [[dock]] || 6.3, 6.4 || [http://dock.compbio.ucsf.edu/ dock.compbio.ucsf.edu] || Chemistry, ligand binding prediction ||
 
|-
 
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ emboss.sourceforge.net] || Biology, multi-tool suite ||
 
|-
 
| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ quantum-espresso.org] || Modeling, Physics ||
 
|-
 
| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website] || 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/ www.gromacs.org]||Physics, Modeling||
 
|-
 
| [[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 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools ||
 
|-
 
| [[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||
+
| scope="col" width="150" |
 +
* [[Biology|Biocomputing]]
 +
| scope="col" width="150" |
 +
| scope="col" width="150" |
 +
* [[Nlp|Natural Language Processing]]
 
|-
 
|-
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]||Statistics, Graphing||
 
|-
 
| [[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||
 
|-
 
| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS||
 
|-
 
| [[tuxedo]] || ||  || 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}}
 

Revision as of 20:27, 7 December 2021


Welcome to the University of Florida Research Computing Help and Documentation site. The information here is focused on particular applications, services, and usage examples and complements more general policies and information found on our main web site. It is used for information that changes more frequently and might become quickly dated or incorrect on the web site. This site is edited by individual UFRC staff members. If you find inaccuracies, errors, or omissions on this site please let us know.

Book an In-Person or Zoom support appointment.

Getting Started

Interfaces and Access

Scheduler

Software and Reference Data

Transfer Data

Specific Research Areas