Modules: Managing software on SSRDE
Computational projects often require specialized software, and/or certain versions of various tools to function correctly. SSRDE uses a system called modules to assist with this. Modules allow different researchers to select their preferred tools from a list of available software. For instance, modules let Alice use Matlab 2017a so that she can run code from a specific paper she needs to reproduce, while allowing Bob to use 2019b so that he can take advantage of the latest and greatest features.
The command to list the modules you can use is module avail:
We can see a few different versions of R in this list; as well as other tools like different versions of CUDA (a toolkit for GPU computing), and more specific utilities like GATK (which is used for analyzing genetic data). Having these programs available as modules allow us to set up our environment exactly as we need it to be.
The default version of R on SSRDE is 3.4.4, as we can see when we run the R command:
If we want to take advantage of a newer version of R, we'll run the command module load and provide the name of the module we want. In this case, the command will be module load R/3.6.1 to get the latest available version of R. We'll see that once this is done, the version of R we want is what we get when we launch R again:
You can keep track of which modules you have loaded using the command module list. If you want to unload all of your modules, you can run module clear:
Modules loaded this way are only available to you in the context of your command line session. To take advantage of them during jobs you'll need to load them in your job submission scripts as well:
SSCF representatives are not programmers and will not be able to provide substantial help with your code itself, but we can assist with the transfer and organization of files, navigating the server, and using the job submission program Slurm.
If you need additional help setting up your environment, please don't hesitate to contact SSCF at firstname.lastname@example.org (or reach out to your department SSCF representative, ex. email@example.com) and we'll be happy to assist!