Environment Modules

The bash shell  

In order to provide multiple versions of software compiled with different and varying libraries, we use modules. Modules allow us to add and remove software from our $PATH using a simple module command.

Common Usage  

• module avail [name] – View all the modules on the HPC system filtered by name.
• module list – View currently loaded modules
• module load moduleName– Load the module denoted by moduleName
• module purge – Unload all loaded modulefiles

Loading the R module  

First we want to take a look at what R modules are available. To do that issue:

module avail R [john@discovery ~]$ module avail R --------------------- /dartfs-hpc/admin/opt/modules/el7 ---------------------- R/4.0 R/4.0.4(default) R/4.1.2

As you can see from this output there are multiple versions of R available. The one with (default) next to it is the default module and will be picked unless you specify the full path. For example, if I wanted R/4.1.2 I would issue:

module load R/4.1.2

If I did not care about what version I recieved then I can just issue module load R.

module load R

Once you have loaded the module you would like you can issue module list to see what you have currently loaded.

module list [john@discovery ~]$ module load R [john@discovery ~]$ module list Currently Loaded Modulefiles: 1) R/4.0.4

Since I did not specify a version, the module command pulled in the (default) version of R, which happens to be R/4.0.4