Software modules

Roar provides many different applications in its software stack, which consists of two parts:

preloaded software, available immediately on login;
modular software, which must be loaded to be used.

Not all software is preloaded, because conflicts inevitably arise between different versions of libraries used by different software packages. To manage these conflicts, ICDS uses the Lmod Environment Module System.

To find out if an application is available, use which:

which <appName>

which returns the path to the executable <appName>, if it exists on your $PATH. (The $PATH variable contains the set of directories where Unix looks for executables; defaults for $PATH are initialized at logon.)

If which doesn’t find the app you are looking for, it may need to be loaded via the module system. Here are the various commands to search for, get info on, list, load, and unload modules:

Module commands

Command	Description
`module avail`	List all modules
`module show <module_name>`	Show module file contents
`module spider <module_name>`	Search for a module
`module load <module_name>`	Load a module
`module load <module>/<version>`	Load a specific version
`module unload <module_name>`	Unload a module
`module list`	List all loaded modules
`module purge`	Unload all modules
`module use <path>`	Add a path to `$MODULEPATH`

What module files mainly do is set environment variables and add directories to the paths Unix searches when looking for applications. To see what a given modulefile does, use module show <moduleName>.

Batch files must include module load commands to load the modules they need. Modules you have loaded when you submit a job with sbatch are not available to the job itself.

Automatic loading

On Unix machines, settings are stored in "hidden" text files, (names start with ., so they don't show up with ls), in your home directory. Settings files are hidden to keep users from meddling with them. But one such file that you may want to alter is ~/.bashrc.

When you log in, commands in .bashrc are automatically executed. So lines may be added to .bashrc to load modules for software you use frequently.

If your .bashrc file contains module load commands, and your batch script begins with #!/bin/bash, then your .bashrc file will execute when the batch job starts, and the job will have access to the loaded modules.