Software Modules
The available modules for a specific software/package can be listed with the command module avail <package name> . This will list the available matches based on the keyword. Wildcard searching is also supported if you only know part of the package name.
[vega0051@ahl01 ~ ]$ module avail R/*rocky8
--------------------- /common/software/modulefiles/manual/common ---------------------------------------------------
R/4.2.0-openblas-rocky8 R/4.2.0-rocky8 R/4.3.0-openblas-rocky8 R/4.4.0-openblas-rocky8 R/4.4.2-openblas-rocky8
Loading Modules
module load <package name> will load the default version of the package into your session. If there is a specific module version that should be used instead, specify it with module load <package name>/<version>.
e.g.,
module load R/4.4.0-openblas-rocky8
After the module is loaded, it can now be called from the loaded environment. Loading modules will not automatically launch the software package.
The loaded modules can be checked anytime with module list.
Tip ml is a shorthand version of the module command and can be used to perform the same functions.
Unloading Modules
module purge will clear out all modules loaded in the current session. Individual modules can be unloaded with the command module unload <package name>.
Module Collections
Some workflows require loading in a number of modules into the session. Loaded modules can be saved into a module collection to easily retain the module set for future use.
After loading your modules, save the collection with module save <collection name>, in future sessions the modules can be restored with module restore <collection name>.
Saved collections can be listed with module savelist and individual collections can be inspected with module saveshow <collection name>.
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.
Support Tiers
Software packages are marked with a support tier: 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 packages are compiled, installed, benchmarked, and documented as a service to users. They are tested after major system upgrades, new versions are installed in a timely manner, and MSI expects 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 packages 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.
Need a Specific Package?
First, try installing it yourself in your MSI home directory following the guidelines below.
Software Installation Guide
Installing software on any Unix platform can be challenging for novice 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 many libraries and scientific applications in your own home directory.
Introductory Compiling
Building a Python interpreter from its source code is straightforward, requiring only a C compiler, and serves 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. For example, if you downloaded Python-2.7.2.tar.gz to your home directory, the appropriate commands are:
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 or other 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
mkdir -v $SHARED/$USER/software
./configure --prefix=$SHARED/$USER/software/python
make install
When the make install step completes you will have access to the binary in:
/projects/standard/<project name>/shared/<UMN InternetID>/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 the MSI help desk for support.
Include a web link to the installation documentation for the package.
Will this package be used by several groups within MSI? Submit the Software Request Form and MSI staff will consider the functionality of the package, its usage, and how well it fits into MSI’s mission.