Difference between revisions of "Apps Queue"

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|<span style="color:red">Amber16/AmberTools18</span>
|<span style="color:red">GAP 4.11</span>
|<span style="color:red">In Progress</span>  
|<span style="color:red">In Progress</span>  
|<span style="color:red">May 2019</span>
|<span style="color:red">June 2021</span>
|<span style="color:red"></span>
|<span style="color:red">July 2021</span>
|<span style="color:red">Stalled due to issues with dependent packages</span>
|<span style="color:red">Stalled due to issues with dependent packages</span>
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|<span style="color:green">VirMine for python 2.7.15</span>
|<span style="color:green">Intel OneAPI Toolkit 2021</span>
|<span style="color:green">In Progress</span>  
|<span style="color:green">In Progress</span>  
|<span style="color:green">July 2019</span>
|<span style="color:green">June 2021</span>
|<span style="color:green">Aug 2019</span>
|<span style="color:green">July 2021</span>
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|<span style="color:blue">Canu v1.8</span>
|<span style="color:green">Haddock 2.4</span>
|<span style="color:blue">Pending</span>  
|<span style="color:green">In Progress</span>  
|<span style="color:blue">Aug 2019</span>
|<span style="color:green">June 2021</span>
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|<span style="color:green">July 2021</span>
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|<span style="color:blue">Clustal Omega 1.2.4</span>
|<span style="color:blue">Amber20/AmberTools2020</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Aug 2019</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">Mothur 1.42.0</span>
|<span style="color:blue">GNUplot 5.4</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Aug 2019</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">HOOMD-Blue 2.6.0</span>
|<span style="color:blue">MuTect</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Aug 2019</span>
|<span style="color:blue">July 2021</span>
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= Recently Completed Software Projects =
{| class=wikitable
|- style="background-color:#f1edbe;"
|'''Application Name'''
|'''Date Completed'''
|'''License Type'''
|'''Notes'''
|'''Additional Info'''
|-
|-
|[[Mathematica|Mathematica 12]]
|<span style="color:blue">Mummer</span>
|07/18/2019
|<span style="color:blue">Pending</span>
|USF Site License
|<span style="color:blue">July 2021</span>
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|[[ANSYS_EDT_(formerly_HFSS)|Ansys Electronics Desktop Suite 2019r2]]
|<span style="color:blue">Psi4 1.3.2</span>
|07/15/2019
|<span style="color:blue">Pending</span>
|Restricted - Authorized users only
|<span style="color:blue">Aug 2021</span>
|
|Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
|-
|[[R_and_Rmpi|R 3.6.0]]
|07/01/2019
|Open Source
|
|GCC build for use on RHEL7 compute nodes
|-
|[[ANSYS|Ansys Multiphysics 2019r2]]
|06/28/2019
|Restricted - Authorized users only
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|ANSYS finite-element analysis applications
|-
|[[VMD|VMD 1.9.3]]
|06/12/2019
|Academic license
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|[[Matlab|Matlab R2019a]]
|05/16/2019
|USF Site License
|
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|[[Maple|Maple 2019]]
|05/09/2019
|USF Site License
|
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|-
|[[LAMMPS|LAMMPS 12Dec18]] (GPU Edition)
|04/29/2019
|Open Source
|
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|gem5 2.0
|04/25/2019
|Open Source
|
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|-
|[[ANSYS_EDT_(formerly_HFSS)|Ansys Electronics Desktop Suite 2019R1]]
|04/19/2018
|Restricted - Authorized users only
|
|Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
|-
|[[ANSYS|Ansys Multiphysics 2019R1]]
|04/18/2019
|Restricted - Authorized users only
|
|ANSYS finite-element analysis applications
|-
|[[Stacks|Stacks 2.3e]]
|04/09/2019
|Open Source
|
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|-
|SeqTK 1.0
|03/20/2019
|Open Source
|
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|-
|Deblur 1.1.0
|03/18/2019
|Open Source
|Python add-on module.
|Loads with apps/python/3.6.2
|-
|Anvio 5.4
|03/15/2019
|Open Source
|
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|-
|Prodigal 2.6.2
|03/15/2019
|Open Source
|
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|-
|Bayestraits 3.0.1
|03/14/2019
|Open Source
|
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|-
|[[R_and_Rmpi|R 3.5.2]]
|03/04/2019
|Open Source
|
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|-
|Ataqv 1.0.0
|02/27/2019
|Open Source
|
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|-
|AfterQC 0.9.7
|02/19/2019
|Open Source
|
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|-
|Tophat 2.1.1
|02/15/2019
|Open Source
|Revision
|
|-
|[[Intel_Parallel_Studio_XE|Intel Parallel Studio XE 2019]]
|02/11/2019
|USF Site License
|
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|-
|HOMER 4.10
|02/05/2019
|Open Source
|
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|-
|bcbio-nextgen 1.1.3
|01/30/2019
|Open Source
|
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|-
|Reporter 0.7.15
|01/29/2019
|Open Source
|
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|-
|DeNovoGUI 1.16.2
|01/29/2019
|Open Source
|
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|-
|PeptideShaker 1.16.37
|01/29/2019
|Open Source
|
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|-
|[[GDC-client|GDC-client 1.4.0]]
|01/28/2019
|Open Source
|Python add-on module
|Loads with apps/python/2.7.15
|-
|[[COMSOL|COMSOL 5.4]]
|01/28/2019
|USF Site License
|
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|-
|SearchGUI 3.3.12
|01/28/2019
|Open Source
|
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|-
|SICKLE 1.33
|01/28/2019
|Open Source
|
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|-
|MultiQC Version 1.7
|01/22/2019
|Open Source
|Python add-on module.
|Loads with apps/python/2.7.15
|-
|ImageMagick++ 7.0.8-23
|01/11/2019
|Open Source
|Built with Intel compiler suite 2017.
|
|-
|[[Subread|Subread 1.6.3]]
|01/11/2019
|Open Source
|
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|

Latest revision as of 17:53, 30 June 2021

Typical Software Installation Process

List of Current Software Projects

Application Name Installation Status Estimated Start Estimated Completion Notes
GAP 4.11 In Progress June 2021 July 2021 Stalled due to issues with dependent packages
Intel OneAPI Toolkit 2021 In Progress June 2021 July 2021
Haddock 2.4 In Progress June 2021 July 2021
Amber20/AmberTools2020 Pending July 2021
GNUplot 5.4 Pending July 2021
MuTect Pending July 2021
Mummer Pending July 2021
Psi4 1.3.2 Pending Aug 2021

Typical Software Installation Process

  1. New request is submitted via email to: rc-help@usf.edu
    • Please include name of software, license type, and URL to software's website.
  2. Application is reviewed by RC staff for compatibility with Linux and cluster resources.
    • Also, is it open source or is a license required?
  3. Source code or installer is downloaded to cluster filesystem.
  4. Application is built using latest Intel Cluster Studio release, if possible.
    • Compilation for cluster systems and troubleshooting can take several hours to a few days depending on the complexity of the application.
  5. Once a working executable has been built, it must then be integrated with the filesystem, modules, scheduler, and other services.
  6. Testing and verification of compatibility with scheduler and cluster resources.
  7. Documentation and release.
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