Typical Software Installation Process
List of Current Software Projects
| Application Name
|
Installation Status
|
Estimated Start
|
Estimated Completion
|
Notes
|
| kallisto 0.44.0
|
In Progress
|
Sept 2018
|
Sept 2018
|
|
| Picard 2.18.14
|
Pending
|
Sept 2018
|
|
|
Recently Completed Software Projects
| Application Name
|
Date Completed
|
License Type
|
Notes
|
Additional Info
|
| FLINT 2.5.2
|
09/07/2018
|
Open Source
|
|
|
| MPFR 4.0.1
|
09/06/2018
|
Open Source
|
|
|
| MPIR 3.0.0
|
09/05/2018
|
Open Source
|
|
|
| YASM 1.3.0
|
09/04/2018
|
Open Source
|
|
|
| OrthoFinder 2.2.7
|
08/30/2018
|
Open Source
|
Updated to recently released 2.2.7 and integrated with 9 additional dependencies.
|
|
| Maple 2018
|
08/17/2018
|
USF Site License
|
|
|
| Mothur 1.40.5
|
07/31/2018
|
Open Source
|
|
|
| GISMO 1.1.0
|
07/26/2018
|
Open Source
|
Matlab add-on package for seismic data analysis
|
Installed and available in /apps/matlab/share/GISMO on the CIRCE cluster.
|
| Perl 5.28.0
|
07/12/2018
|
Open Source
|
Newer version of Perl programming language needed for some applications.
|
|
| SCIP 6.0.0
|
07/02/2018
|
Open Source
|
Dependency issues prevented 5.X versions from installing properly. A work-around was developed and found to be valid with the 6.0.0 version.
|
Contact rc-help@usf.edu for details regarding work-around if SCIP > 3.1.1 is needed.
|
| Ansys Electronics Desktop Suite v19.1
|
06/29/2018
|
Restricted - Authorized users only
|
|
Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
|
| Ansys Multiphysics v19.1
|
06/29/2018
|
Restricted - Authorized users only
|
|
ANSYS finite-element analysis applications
|
| Wannier90 2.1.0
|
06/29/2018
|
Open Source
|
|
|
| Quantum Espresso 6.2.1
|
06/28/2018
|
Open Source
|
|
|
| MaxQuant 1.6.2.3
|
06/15/2018
|
Academic License
|
Required an update of system tool "mono" to the specific version 5.4.1.7
|
|
| NCBI Blast 2.7.1+
|
06/07/2018
|
Open Source
|
Issues encountered and resolved when compiling on RHEL6 using Intel compilers
|
Standalone and dependency for OrthoFinder
|
| Circos 0.69-6
|
06/06/2018
|
Open Source
|
Requires additional Perl modules for full functionality and an update to Perl 5.27
|
|
| LinBox 1.5.2
|
05/22/2018
|
Open Source
|
Required updated install of 8 additional library packages
|
|
| MPlus 8
|
05/15/2018
|
Restricted - Authorized users only
|
|
|
| Matlab R2018a
|
05/14/2018
|
USF Site License
|
|
|
| Mathematica 11.3
|
05/11/2018
|
USF Site License
|
|
|
| Julia 0.6.2
|
05/03/2018
|
Open Source
|
|
|
| R 3.5.0
|
04/30/2017
|
Open Source
|
|
|
| RSEM 1.3.0
|
04/27/2018
|
Open Source
|
|
|
| Tophat 2.1.1
|
04/26/2018
|
Open Source
|
|
|
| Pear 0.9.11
|
04/20/2018
|
Open Source
|
|
|
| Bowtie 2.3.4.1
|
04/19/2018
|
Open Source
|
|
|
| Intel Parallel Studio XE 2018
|
04/18/2018
|
USF Site License
|
|
|
| Trimmomatic 0.36
|
04/12/2018
|
Open Source
|
|
|
| SIESTA 4.0.1
|
04/05/2018
|
Open Source
|
|
|
| SPAdes 3.11.1
|
03/30/2018
|
Open Source
|
|
|
| Psi4 1.1
|
03/15/2018
|
Open Source
|
|
|
| GCC 7.3.0
|
02/28/2018
|
GNU License
|
|
|
| OpenMPI 2.0.4
|
03/14/2018
|
GNU License
|
|
|
| COMSOL 5.3a
|
02/28/2018
|
USF Site License
|
|
|
| Trinity 2.6.5
|
02/26/2018
|
Open Source
|
|
|
| SageMath 7.5.1
|
02/12/2018
|
Open Source
|
|
|
| Cufflinks 2.2.1
|
02/07/2018
|
Open Source
|
|
|
| ORCA 4.0.1
|
02/05/2018
|
Open Source
|
|
|
| SPECFEM3D 3.0
|
01/30/2018
|
Open Source
|
|
|
| MEGA-CC 7.0.26-1
|
01/08/2018
|
Open Source
|
|
|
| MUSCLE 3.8.31
|
01/08/2018
|
Open Source
|
|
|
Typical Software Installation Process
- New request is submitted via email to: rc-help@usf.edu
- Please include name of software, license type, and URL to software's website.
- Application is reviewed by RC staff for compatibility with Linux and cluster resources.
- Also, is it open source or is a license required?
- Source code or installer is downloaded to cluster filesystem.
- 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.
- Once a working executable has been built, it must then be integrated with the filesystem, modules, scheduler, and other services.
- Testing and verification of compatibility with scheduler and cluster resources.
- Documentation and release.