Accessing RStudio through OnDemand


  • Start an RStudio session from OnDemand
  • Access the command line of the node your process is running on through the RStudio terminal or SSH into the host OnDemand provides you.

Managing R package installation and environment


  • The .libPaths() function shows you where R looks for and installs packages
  • Use the .Renviron file to set environment variables you’d like to use for your project
  • Add functions and set options in the .Rprofile file to customize your R session
  • Start R from your project directory and use relative paths

Parallelizing your R code with future


  • Setup code you want to parallelize as “mapping” a function over an array
  • Setup a future backend to distribute each of these function applications over cores, nodes, or both
  • Use the batchtools_slurm backend to have future submit SLURM jobs for you
  • Use a future adapter to link your code to the backend

Using R on the command line


  • Use module spider R/<version> to learn how to load a version of R on the HPCC
  • Run R from the command line to start an interactive R console
  • Use the --vanilla option to ignore extra configuration files
  • Run Rscript to run an R script
  • Use commandArgs to parse command line arguments in an R script
  • Use pdf() to capture plotting into a PDF file

Submitting R code to SLURM


  • A SLURM script requests resources
  • Generally, the only code you need in a SLURM script is loading the R module, changing to the right directory and running your R code with Rscript
  • Check the status of your jobs with squeue --me