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Table of Contents



Many popular software packages are installed and available as modules.  There may be several versions of a package available.

The responsibility of software management is primarily that of users since it is not practical or helpful to maintain a large library of packages with different configurations of each package.

If there is a package that you believe would be of wide enough interest to be installed as  a module, you can place a request here.

You can install software packages into your home directories with the space that is allocated to you with your HPC account.  However you cannot install software that requires root permission, or use a method like "yum install" that accesses system paths.

The Running Jobs page has examples of how to run some of the applications.


Modules Software Management


 module avail

 Display all the software and versions installed on the system

 module list

 Display the software you have loaded in your environment

 module load modulename

 Load a software module in your environment

 module purge

 Unload all the software modules from your environment

 module unload modulename

 Unload a specific software package from your environment

 module help

 Display a help menu for the module command


Example for Using Modules

First log in to the login node:

To display a list of the available packages:
module avail

To load the latest installed version of the "Trinity" software:
module load trinity

To list the software you currently have loaded: 
module list

To unload all modules if you want to start over.  Logging out will also unload modules.
module purge

Installing Your Own Software

Follow this  link for detailed information on how to install your own software


Using and Installing Python

Follow this link for more information on using Python.


There are four versions of Python available on the 1st generation cluster.

  1. Python 2.6.5 is the default if you just want to use the system version
  2. Python 2.7.3 is the version you get with "module load python"
  3. Python 2.7.9 is provided with "module load python/2.7.9"
  4. Python 3.4.1 is provided with "module load python/3.4.1"

Python 2.7.3 has the most packages installed. "pip list"  will display the packages along with the version installed.  



There are several compilers available for your use.  Remember when you run your code and you need to do a module load that you use the same version of compiler that the code was originally compiled with.

  • GCC is available by default.  gcc --version shows that it is 4.4.4  That version was installed at cluster installation and has not been updated to maintain consistency between compiling software and subsequently running it. If you also need the GNU Scientific Libraries (gsl), that is available using module load gsl which will get you version 1.15
  • The Intel 2012 compiler suite is available as a module.  module load intel will load the 2012 suite.  It is the default for the same reason as gcc. The math kernel libraries (mkl) are provided when you module load intel (any version) - no separate step is required.
  • The Intel 2013 compiler suite is also available as an optional module.  module load intel/2013.5.192 will provide that version if needed.

MPI compilers

  • intel-mpi/2012.0.032 is the default version which matches the non-mpi version.  Use module load intel-mpi
  • intel-mpi/2013.5.192 is available by specifying module load intel-mpi/2013.5.192
  • openmpi version 1.4.4 is available by specifying module load openmpi
  • mpich2 is available at version 1.4.1p1 by default or you can get version 3.1.4 wth module load  mpich2/3.1.4


The new cluster has Intel V3 Haswell processors.  A key feature of these is AVX2. Read this Intel document.

For AVX2 support, compile with the -xHOST option. Note that -xHOST alone does not enable aggressive optimization, so compilation with -O3 is also suggested. The -fast flag invokes -xHOST, but should be avoided since it also turns on interprocedural optimization (-ipo), which may cause problems in some instances.

For GNU compilers, AVX support is only available in version 4.6 or later.  For AVX support, compile with -mavx


El Gato

The principals are similar for ElGato except that the intel and intel-mpi compilers are only available for the 2013 versions.

openmpi is available both for version 1.6.5 and version 1.8.1

El Gato has a separate web site with easy to follow instructions.