Computational Techniques for Life Sciences

Modules

Environment variables are finicky, prone to typos, and a lot of work to edit manually. Modules make dynamically changing environment variables a lot easier and safer. Modules contain all the necessary environment variables for running a particular application or providing access to a particular library. In addition:

• They are a convenient way to dynamically change the user’s environment
• They help avoid conflicts between program versions, compilers, libraries, etc.

Different clusters have different implementations of modules. More info on the TACC implementation of modules can be found here

To list all of your currently loaded modules:

$ module list

To list modules that are available for you to load, do:

$ module avail

There are quite a few! Modules are organized both by version, and by compiler dependencies (more on this later). To filter, search for modules either by the name of the application, or a keyword. For example:

$ module avail blast
$ module spider blast
$ module key genomics

Each module, when loaded, will modify your environment variables so that you can run the desired application. To see what the effect of loading a module is, do:

$ module show blast/2.2.31

Once you have identified the module you are interested in, you can load it to put it in your PATH, and unload it to remove it from your PATH:

$ module list
$ module load blast/2.2.31
$ module list
$ module unload blast/2.2.31
$ module list
$ ml blast/2.2.31               # ml is a shortcut for module load

Finally, find more help on using module commands by doing:

$ module help

Exercise

1. Search the module system for any application(s) that you need for your research.
2. Figure out if any dependencies are required to load the module.
3. Load the module and determine what effect it has on your environment.
4. Make sure the desired executables (and correct version) are in your PATH.

Click here for solution

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