Accessing Software Resources

Software packages will be marked with a support tier -- either Primary, Secondary, or Minimal. Primary support is given to mature, popular scientific software important to a large fraction of the user base and generally receives the highest level of support. These software are compiled, installed, benchmarked, and documented as a service to you. They are tested after major system upgrades, new versions are installed in a timely manner, and we expect to be able to offer advice to assist with the majority of inquiries. Conversely, Secondary or Minimally supported software are only useful to a very small number of users. These software may not be actively maintained, regularly updated, or tested after system updates. They may be removed without notice if usage is found to be too low to continue support.

HPC and Interactive HPC Systems

To access software on Linux systems, use the ‘module’ command to load the software into your environment. You can find the module name to load on the MSI software page for a package. For example, if you want to use the 2014b version of MATLAB, you would type in your job script or at the command line:

% module load matlab/R2014b
% matlab 

To find out what software modules and versions are available, consult the MSI software page or use the ‘module avail’ command to search by name.

To see all software modules available on our system, type:

% module avail 

For example, to find out what versions of Python are available, type:

​% module avail python 

Windows Software

Windows-only software can be accessed and run via the Windows Virtual Environment (Citrix). Once a Windows session is started you access software applications in the same manner as if you were using a physical Windows computer. 
 

First, try and install it yourself in your MSI home directory following the guidelines below:

Software Installation Guide

Installing software on any Unix platform can be challenging for inexperienced and veteran users alike.

While it is impossible to cover every issue you may experience, the following steps will allow you to compile and install in your own home directory many of the libraries and scientific applications that you will come across.

Introductory Compiling

Building a Python interpreter from its source code is straightforward, requiring only a C compiler, and will serve as an instructive example.
Installation materials are most commonly distributed as compressed tar files with the extension .tar.gz or .tar.bz.
These files can be untarred and unzipped with the tar -xzf and tar -xjf commands, respectively.
We have downloaded the file Python-2.7.2.tar.gz from www.python.org to our home directory, so the appropriate command is:

tar -xzf Python-2.7.2.tar.gz 
cd Python-2.7.2 

Your next step should always be to review the distributed files for a README file, which can be viewed in a text editor, or some other file that is named to indicate it contains installation instructions.

In many cases, and as is the case with Python, a configure script is included. In the simplest case, all that is necessary to compile the code is to run the configure script, then make.

By default many codes will try to install to system directories you cannot access. The recommended installation method is to create a directory in your home directory for software installation.

pwd (It will display a result such as /home/xe2/nlabello/Python-2.7.2)
mkdir /home/xe2/nlabello/software/python
./configure --prefix=/home/xe2/nlabello/software/python/ make install 

When the make install step completes you will have access to binary in /home/xe2/nlabello/software/python/bin.

Advanced Compiling

In many cases, it is necessary to use specific compilers and MPI libraries to build a working binary. See the quick start guides for details about the configuration of each HPC system.

• Can't get the install to work? Contact our help desk for support. 
• Will this package be used by several groups within MSI?  Submit our Software Request Form and MSI staff will consider the functionality of the package, its usage and how well it fits into MSI's mission.