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<font color=red> ''THIS PAGE IS UNDER CONSTRUCTION'' </font>
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<H1>Software</H1>
== Software ==
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__TOC__
We currently have many commercial and freeware packages installed on our supercomputers. Online documentation and links to the vendor's website are available to TAMU computers and to computers using TAMU's [https://tamu.service-now.com/tamu-selfservice/knowledge_detail.do?sysparm_document_key=kb_knowledge,02ce68792badc6009b4c26e405da151e VPN]. Requests to use restricted software should be emailed to the [[HPRC:Consulting |SC helpdesk]]. Please also consult our [[HPRC:Polices:EAR_ITAR | Restricted Software Policy]] for more information. The software acquisition and licensing policy for our facility is [[HPRC:Policies:SWLicensing | here]].
 
  
=== Finding Software ===
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We currently have many commercial and freeware (foss, free and open source software) packages installed on our supercomputers. Online documentation and links to the vendor's website are available to TAMU computers and to computers using TAMU's [https://u.tamu.edu/KB0010938 VPN]. Requests to use restricted software should be emailed to the [https://hprc.tamu.edu/user_services/consulting.html HPRC helpdesk]. Please also consult our [https://hprc.tamu.edu/policies/software.html Software Policy page] for more information about acquiring and using restricted (EAR and ITAR) and licensed software on our clusters.
 +
 
 +
== Finding Software ==
 
On our clusters, the software is available through the [[SW:Modules | module system]].  Available software can be queried with:
 
On our clusters, the software is available through the [[SW:Modules | module system]].  Available software can be queried with:
* '''module avail''' or  
+
* '''module avail'''
* '''module spider'''.
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or
 +
* '''module spider'''
 +
or  
 +
* '''fml'''
 +
 
 +
fml command is a fast alternative to module spider. However, for the most up-to-date module information, please use ''module spider''
 +
 
 +
To search for available Python module,
 +
 
 +
fml Python
 +
 
 +
To query information about a particular module
 +
 
 +
fml Python/3.8.2-GCCcore-9.3.0
 +
 
 +
 
 +
A complete module listing for each cluster can be found here:
 +
* [https://hprc.tamu.edu/software/faster/ FASTER Module List]
 +
* [https://hprc.tamu.edu/software/grace/ Grace Module List]
 +
* [https://hprc.tamu.edu/software/terra/ Terra Module List]
  
 
On our Linux workstations, a list of available packages can be queried with:  
 
On our Linux workstations, a list of available packages can be queried with:  
* '''rpm -qa | sort '''.
+
* '''rpm -qa | sort '''
  
=== Available Packages ===
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{{:SW:Temporary_Files}}
We maintain a number of pages documenting the use of some of the available packages including:
 
  
 +
== Available Packages and Software Collections==
 +
We maintain a number of pages documenting the use of some of the available software packages, including: <!-- COMMENTING OUT PAGES THAT DO NOT YET EXIST -->
 +
 +
<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
 
* [[SW:ABAQUS | ABAQUS]]
 
* [[SW:ABAQUS | ABAQUS]]
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* [[SW:AlphaFold | AlphaFold]]
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* Altair
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** [[SW:Hyperworks | Hyperworks]]
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** [[SW:Hyperworks:Optistruct | Optistruct]]
 +
* [[SW:Anaconda | ANACONDA]]
 
* [[SW:ANSYS | ANSYS]]
 
* [[SW:ANSYS | ANSYS]]
 
** [[SW:ANSYS:CFX | CFX]]
 
** [[SW:ANSYS:CFX | CFX]]
 +
** [[SW:ANSYS:Ensight | Ensight]]
 
** [[SW:ANSYS:Fluent | Fluent]]
 
** [[SW:ANSYS:Fluent | Fluent]]
 
** [[SW:ANSYS:ICEM | ICEM CFD]]
 
** [[SW:ANSYS:ICEM | ICEM CFD]]
 
** [[SW:ANSYS:Turbogrid | TurboGrid]]
 
** [[SW:ANSYS:Turbogrid | TurboGrid]]
* [[SW:CHARMM | CHARMM]]
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** [[SW:ANSYS:Workbench | Workbench]]
* [[SW:Comsol | Comsol]]
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* [[SW:Avogadro | Avogadro]]
* [[SW:Gaussian | Gaussian]]
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* [[Bioinformatics | Bioinformatics Software Collection]]
* [[SW:Globus | Globus Connect]]
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* [[SW:Caffe | Caffe]]
 +
* [[SW:cctools | cctools/parrot]] access CVMFS
 +
* [[SW:Dalton | Dalton]]  
 +
* [[SW:Faster-RCNN | Faster-RCNN]]
 +
* [[SW:Galaxy | Galaxy]]  
 +
* [[SW:GlobusConnect | Globus Connect]]
 +
* <!-- [[SW:GCC | GNU Compiler Collection]] --> GNU Compiler Collection
 +
* [[SW:GROMACS | GROMACS]]
 
* Intel Cluster Suite
 
* Intel Cluster Suite
** [[SW:Intel:Compilers | compilers]]
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** <!-- [[SW:Intel:Compilers | Compilers]] --> Compilers
** [[SW:Intel:MPI | MPI]]
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** <!-- [[SW:Intel:MPI | MPI]] --> MPI
** [[SW:Intel:MKL | Math Kernel Library]]
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** [[SW:MKL | Math Kernel Library]]
** [[SW:Intel:VTune | VTune Amplifier performance profiler]]
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** <!-- [[SW:Intel:VTune | VTune Amplifier performance profiler]] --> VTune
 +
* [[SW:Julia | Julia]]
 +
* [[SW:Keras | Keras ]]
 +
* [[SW:Knitro | Knitro]]
 +
* [[SW:LAMMPS | LAMMPS]]
 
* Livermore Software Technology
 
* Livermore Software Technology
 
** [[SW:LSDYNA | LS-DYNA]]
 
** [[SW:LSDYNA | LS-DYNA]]
** [[SW:LSOPT | LS-OPT]]
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** [[SW:LS-OPT | LS-OPT]]
* [[SW:Mathematica | Mathematica]]
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** [[SW:LS-PREPOST | LS-PREPOST]]
 +
* [[SW:Machine_Learning | Machine Learning]]
 
* [[SW:Matlab | Matlab]]
 
* [[SW:Matlab | Matlab]]
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* [[SW:moose | moose]]
 
* [[SW:myhadoop | myHadoop]]
 
* [[SW:myhadoop | myHadoop]]
* [[SW:NCL | NCAR Command Language (NCL)]]
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* [[SW:NAMD | NAMD]]
* [[SW:netCDF | netCDF]]
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* <!-- [[SW:NCL | NCAR Command Language (NCL)]] --> NCAR Command Language (NCL)
 +
* <!-- [[SW:netCDF | netCDF]] --> netCDF
 +
* [[SW:NWChem | NWChem]]
 +
* [[SW:OpenFOAM | OpenFOAM]]
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* [[SW:pigz | pigz]] (parallel gzip)
 +
* [[SW:Portal | Portal]]
 +
* [[SW:PostgreSQL | PostgreSQL]]
 +
* [[SW:Psi4 | Psi4]]
 +
* [[SW:Python | Python]]
 +
* [[SW:PyTorch | PyTorch]]
 +
* [[SW:QuantumESPRESSO | QuantumESPRESSO]]
 
* [[SW:R | R]]
 
* [[SW:R | R]]
 +
* [[SW:R_tamu | R_tamu]]
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* [[SW:rclone | rclone]] (cloud backup)
 +
* [[SW:RCS | RCS]] (Revision Control System)
 +
* SAS
 +
* [[SW:Scikit_Learn | Scikit_Learn]]
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* [[SW:Singularity | Singularity]]
 
* [[SW:Starccm | STAR-CCM+]]
 
* [[SW:Starccm | STAR-CCM+]]
 +
* [[SW:SWAN | SWAN]]
 +
* [[SW:tamulauncher | tamulauncher ]]
 +
* [[SW:VMD | VMD]]
 +
* [[SW:TensorFlow | TensorFlow]]
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* [[SW:WebProxy | Web Proxy]] (internet access from compute nodes)
 +
* [[SW:WRF | WRF]]
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* [[SW:Zebulon | Zebulon]]
 +
</div>
 +
 +
=== License-Restricted Packages ===
 +
These packages are restricted by license. Individuals or groups have purchased licenses for these packages and manage the list of users that may access them.
 +
 +
'''Note:''' These packages are not the same as ''Export-Controlled Software'', as mentioned in the [https://hprc.tamu.edu/policies/software.html Software Policy].
 +
 +
<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
 +
* [[SW:Amber | Amber]]
 +
* <!-- [[SW:CHARMM | CHARMM]] --> CHARMM
 +
* [[SW:Comsol | Comsol]]
 +
* GAMS
 +
* [[SW:Gaussian | Gaussian]]
 +
* [[SW:IDL  | IDL]]
 +
* [[SW:ORCA | ORCA]]
 +
* [[SW:Schrodinger | Schrödinger]]
 +
* Stata
 
* [[SW:VASP | VASP]]
 
* [[SW:VASP | VASP]]
* [[SW:WRF | WRF]]
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* [[SW:Cadence | Cadence]]
 +
 
 +
</div>
 +
=== Toolchains for Compiling Software ===
 +
Information on the available toolchains for compiling software can be found on our [[ SW:Toolchains | Toolchains ]] page.
 +
 
 +
== Useful Tools ==
 +
The following is a list of the most frequently requested / needed tools on our clusters.
 +
 +
<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
 +
*[[SW:dos2unix | dos2unix]]
 +
*[[SW:gedit | gedit]]
 +
*[[SW:tamulauncher | tamulauncher]]
 +
<!-- *[[SW:Ada_Batch_Builder | Ada Batch Job Builder]] -->
 +
*[[HPRC:AMS:UI#Ada | Ada Project Allocation Tool]]
 +
*[[SW:License_Checker | License Checker Tool]]
 +
*[[SW:Misc | Other Useful Utilities & Tips]]
 +
</div>
 +
 
 +
[[Category:Software]]

Latest revision as of 22:50, 7 July 2022

Software

We currently have many commercial and freeware (foss, free and open source software) packages installed on our supercomputers. Online documentation and links to the vendor's website are available to TAMU computers and to computers using TAMU's VPN. Requests to use restricted software should be emailed to the HPRC helpdesk. Please also consult our Software Policy page for more information about acquiring and using restricted (EAR and ITAR) and licensed software on our clusters.

Finding Software

On our clusters, the software is available through the module system. Available software can be queried with:

  • module avail

or

  • module spider

or

  • fml

fml command is a fast alternative to module spider. However, for the most up-to-date module information, please use module spider

To search for available Python module,

fml Python

To query information about a particular module

fml Python/3.8.2-GCCcore-9.3.0


A complete module listing for each cluster can be found here:

On our Linux workstations, a list of available packages can be queried with:

  • rpm -qa | sort

Temporary Files and Using the Home Directory

Many software packages create and manipulate temporary files during the execution of the program. These temporary files are commonly placed within your Home directory by default. You must remain aware of how much quota space is left within your Home directory at all times. If your Home directory is filled, attempts to write or modify temporary files will fail.

This may cause your jobs to terminate (be killed) or hang (do nothing, waste SUs).

The easiest way to avoid this issue is to store your files within your Scratch directory. Use cd $SCRATCH to navigate to your Scratch directory.

showquota will allow you to view your quota limits.

Available Packages and Software Collections

We maintain a number of pages documenting the use of some of the available software packages, including:

License-Restricted Packages

These packages are restricted by license. Individuals or groups have purchased licenses for these packages and manage the list of users that may access them.

Note: These packages are not the same as Export-Controlled Software, as mentioned in the Software Policy.

Toolchains for Compiling Software

Information on the available toolchains for compiling software can be found on our Toolchains page.

Useful Tools

The following is a list of the most frequently requested / needed tools on our clusters.