Software modularization
Tip
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Software on Secretariat are accessed via a module system. Most of the software are not accessible unless loaded; To access the software, this must be done for each user’s environment.
To see what modules are available, run module avail from the command line. This command returns a list of loadable software in the form [software_name]/[version_number].
Load / unload
To load software, run the following from the command line:
module load [software_name]/[version_number]
Including the [version_number] portion ensures that you are loading the exact software that you would like. This is especially important if there is more than one version of the software available.
To unload software, run the following from the command line:
module unload [software_name]/[version_number]
Attention
Do not include the brackets (“[” and “]”) when substituting your software_name and version_number.
To see which software are currently loaded, run module list from the command line. This command returns a list of software that are currently loaded in the user’s environment.
For more information about additional sub-commands, run module help from the command line. This will return a help message with detailed information about more use-cases of module. To learn more about this module system, read the Lmod documentation.
Within scripts
Attention
Software must be loaded within scripts, regardless of whether the software is currently loaded in a user’s environment.
Consider these lines from the example script from the Batch jobs page:
13# Load software
14module load fastp/0.21.0
The pertinent software must be loaded in this manner before it / they can be used. A good place to do this is immediately after the #SBATCH header. Please refer to the full example to see software loading in context.