example_module

RStudio Server + Singularity Module

This is an example Lmod module that sets up the environment necessary to launch RStudio Server. It assumes a Singularity module already exists or that it is installed on the machine.

Lmod modules are typically used at most high-performance computing (HPC) centers.

Setup

1. Modify the modulefiles/x.y.z.lua to your specification.

2. Download the corresponding Singularity image under x.y.z/singularity-rstudio.simg:

   $ mkdir x.y.z
   $ cd x.y.z
   $ singularity pull --name singularity-rstudio.simg shub://nickjer/singularity-rstudio:x.y.z
   $ cd ..

The downloaded Singularity image nickjer/singularity-rstudio is entirely optional. You are welcome to create and maintain your own images using the above image as an example.

Install Libraries

Users may request that you install R packages. I am not entirely sure if installed packages work across major (x) or minor (x.y) version numbers. So to err on the side of caution I treat packages separate within minor versions of R (feel free to inform me otherwise).

1. Create a library for the corresponding R minor version if one doesn't already exist:

   $ mkdir library-x.y

2. Confirm you have permissions to write to this directory.

3. Confirm the corresponding module files modulesfiles/x.y.z.lua point to this library.

4. Load any one of the corresponding module files and launch R:

   $ module load rstudio_singularity/x.y.z
   $ R

5. Install requested packages:

   install.packages("my_package", lib="/library")

   and be sure it is writing to the path /library.

Locally Install Libraries

Although it should be noted that users can install their own R packages under the R_LIBS_USER directory specified in the module file.

1. Load any one of the corresponding module files and launch R:

   $ module load rstudio_singularity/x.y.z
   $ R

2. Install requested packages:

   install.packages("my_package")