If you are trying to run R from the terminal, and you see this scary-looking message,
[email@example.com@sshgw00 ~]$ R -bash: R: command not found
you might wonder why R (or Python, or whatever other program you’re trying to run) isn’t found! Read on to solve this problem.
What’s a module?
As of September 2021, SESYNC’s servers now use environment modules to keep different versions of software organized on our system. This means that you can choose what version of R you want to use to run your code. Even if SESYNC has updated R to a more recent version, you can make sure your code is reproducible by always running it with the same version of R (and all the same R package versions) that you used when you originally developed the code.
The R environment module is always loaded on the RStudio server and Slurm nodes, but you will need to load it on the SSH gateway. For other software, you’ll always need to load the environment module before you run it, whether it’s on the RStudio server, the Slurm nodes, the Jupyter server, or the SSH gateway.
To get rid of the error message, just type this command in the terminal before you try to run R:
module load R
This will load the R environment module, which includes the default version of R. We’ve set the most recent stable version on our servers to be the default (as of October 2021, this is R 4.1.1). If you’d rather load a specific version of R, you will need to specify the version number. Run module avail R to see which versions are available. Then you can type module load R/4.0.5, for example, to load that version of R.
For Python, you can load the default version of Python 3.x with:
module load Python3
For more information, please see