Module System

A large number of popular software packages are installed on Palmetto and can be used without any setup or configuration. These include:

Compilers (such as gcc, Intel)
Libraries (such as OpenMPI, HDF5, Boost)
Programming languages (such as Python, MATLAB, R)
Scientific applications (such as LAMMPS, ANSYS)
Others (e.g., Git, )

These packages are available as modules on Palmetto. The following commands can be used to inspect, activate and deactivate modules:

Command	Purpose
`module avail`	List all packages available (on current system)
`module spider package`	List all packages with `package` in the name
`module load package/version`	Add a package to your current shell environment
`module list`	List packages you have loaded
`module rm package/version`	Remove a currently loaded package
`module purge`	Remove all currently loaded packages

For example, to see what versions of Matlab are installed, you can use the command:

$ module spider matlab

------------------------------------
  matlab:
------------------------------------
     Versions:
        matlab/2022a
        matlab/2023a
        matlab/2023b

To load the GCC (v12.3.0) and OpenMPI (v4.1.6) modules, you can use the command:

module load gcc/12.3.0 openmpi/4.1.6

Then, check the version of gcc:

$ gcc --version

gcc (GCC) 12.3.0
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

To view all the modules you have loaded:

$ module list

Currently Loaded Modules:
  1) gcc/12.3.0   2) openmpi/4.1.6

Some modules when loaded, implicitly load other modules as well. If you use some modules to compile/install some software, then you will probably have to load them when running that software as well, otherwise you may see errors about missing libraries/headers. Modules do not remain loaded when you log out and log back in, i.e., they are active only for the current session - so you will need to load them for every session.

As an exercise, examine the environment variables PATH, LIBRARY_PATH, etc., before and after loading some module:

echo $PATH
module add anaconda3/2023.09-0
echo $PATH

You can also look at the module files in /software/ModuleFiles to understand what happens when you add a module.