R in Palmetto

R in Palmetto#

Learning objectives

  • Questions:

    • How to run R scripts in Palmetto

  • Objectives:

    • Learn how to run R in Palmetto

    • Learn how to install R packages in Palmetto

  • Keypoints:

    • Rscript

Palmetto access

  • If you need to process a large amount of data and you think your laptop/desktop is not fast enough, you can utilize the power of the Palmetto supercomputing cluster. If you have an account on Palmetto, you can log in as described in our manual.

  • Let’s request a compute node:

qsub -I -l select=1:ncpus=4:mem=32gb:interconnect=fdr,walltime=2:00:00

  • In order to run R, you will first need to load the R module. We have several versions of R installed on Palmetto, most recent being 4.0.3:

module load r/4.0.5-gcc/9.5.0

  • We can now open R in interactive mode (text-only console). Let’s install a package doParallel:

R
> install.packages("doParallel")

  • To quit the R console, type quit(). Let’s create a simple script and run it. We can use the text editor called nano:

nano randmatrix.r

  • This will open a text editor. Let’s paste these lines which create a random 4x4 matrix (to paste, Mac users can use Cmd+V, and PC users can use Shift+Ins):

M <- matrix(rnorm(16), nrow=4)
M

  • Let’s save it by pressing Ctrl+O, then Enter, then Ctrl+X. We can run this script with the RScript command:

Rscript randmatrix.r

  • If you want to use RStudio on Palmetto, you can use OpenOnDemand interface – please see our manual.