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Environment Modules (New cluster)

Enabling optional software packages using the Environment Modules system

Introduction

Environment modules are a method for configuring your terminal such that it can use different software packages (and potentially specific versions of a software package). By using these modules you can ensure that only the correct software and dependent libraries are accessed, potentially speeding up loading and reducing the likelihood of bad interactions between software packages.

The module Command​​

The ​module command is used to manage environment modules, and has many options, the most useful of which are detailed below.​ For all the available commands see the Lmod user guide.

​Ava​​ilable mod​​ules

​To see a list of available software packages use:

$ module avail
...
---------------- /cvmfs/fsl.fmrib.ox.ac.uk/el9/modules ----------------
   fsl/4.1.9          fsl_sub/2.8.3        (L)
   fsl/5.0.9          fsl_sub_config/1.0.0
   fsl/5.0.11         fsl_sub_config/1.0.1
   fsl/6.0.7.3 (D)    fsl_sub_config/1.0.2 (L,D)

---------------- /cvmfs/matlab.fmrib.ox.ac.uk/modules -----------------
   MATLAB/R2012a        MATLAB_MCR/R2012a    MATLAB_MCR/R2019b
   MATLAB/R2014b        MATLAB_MCR/R2012b    MATLAB_MCR/R2023a
   MATLAB/R2023b (D)    MATLAB_MCR/R2014b    MATLAB_MCR/R2023b (D)
...

The example above is truncated, so you will typically see much more than this. Software packages are groups into broad categories, based on their file system location, so you can see above, the FSL modules and MATLAB modules are grouped together.

To get a terse list try:

module overview

This only displays the software name (with the number of versions in parenthesis).

Loadi​ng​​​​ modules

To configure your shell for a particular software pack​age simply load the module (add is a synonym for load):

$ module load freesurfer

At this point your shell should be able to find and run any of the packages programs/tools.

Loading a specific version of a package

Where multiple versions of a package exist, these will usually appear as package/version. Loading using just the package name will always result in the version with the '(D)' next to it being loaded. To load a specific version simply use it's full name, e.g.:

$ module load MATLAB/2023b

To select the 2023b version of MATLAB.

If you would like a module to always be loaded when you login to the cluster then see the Lmod login modules instructions.

Unloadi​​ng modules 

​To remove a package from your environment (perhaps because it conflicts with another package) you ​​​use unload (or the synonym rm):

​​module unload freesurfer/7.4.0

To unlo​ad all loaded modules use

$ module purge​​

Listing current​​​ly loaded modules

To display ​​a list of currently loaded modules use:

$ module list

Switching versions​ 

If ​​you wish to switch the version of a particular package then a switch command is provided: 

$ module switch freesurfer/6.0.0 freesurfer/7.4.0