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HPCC has an extensive list of software installed. To use a piece of software, an appropriate module must be loaded.This page reviews how to use modules before providing a list of installed software.

Modules

A module manages environment variables needed to load a particular piece of software. The login process loads a few modules by default for HPCC users. The default loaded modules include the GNU compilers, the OpenMPI communication library, MATLAB and R.

  • To see a list of modules that are currently loaded, type "module list"

    [username@dev-intel07 ~]$ module list
    Currently Loaded Modulefiles:
      1) GNU/4.4.5(default)       5) Boost/1.47.0(default)    9) R/2.13.2(default)
      2) OpenMPI/1.4.3(default)   6) CMake/2.8.5(default)    10) Stata/12.0(default)
      3) TBB/4.1.0(default)       7) Python/2.7.2(default)
      4) MKL/10.3(default)        8) MATLAB/R2011b(default)
    
  • To see a list of modules that are available to be loaded, type "module avail"
  • To see what environment variables would be set/changed if you load a specific module, type "module show <module_name>"
  • To load a module, type "module load <module_name>"
  • To unload a module, type "module unload <module_name>"

A video tutorial of how to use the modules can be found here: Video Tutorial - Modules

List of installed software

The following is a list of installed software, sorted by application area. If you require a software title that is not installed, you may install it locally to your home directory. Alternatively, if the software will benefit other users at HPCC, a request can be submitted to http://www.hpcc.msu.edu/contact to request a more global installation by HPCC staff.

Bioinformatics Software


 

 

Biology Software

Module Name

Version

Brief Description

SEEDS

1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6, 1.0.7, 1.0.8, 1.0.9, 1.0.10, 1.0.11, 1.0.12, 1.0.13

Stochastic Cellular Artificial Life Simulator

avida

2011.09.05

Program for studying biological evolution.

NetworkX

1.1,1.6,1.9

Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Chemistry Software

Engineering Software

Geography Software

Mathematics Software and Libraries

Molecular Dynamics Software

Profiling and Debugging Tools

Programming

Python related modules

Utilities

Visualization

Software Specific Tutorials

Various software specific tutorials are available .

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