R in Palmetto

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• How to R in Palmetto

Objectives

• Learn how to run R in Palmetto

• Learn how to install package in R in Palmetto

Login to your Palmetto account Palmetto login

• Request a compute node:

  $ qsub -I -l select=1:ncpus=4:mem=32gb:interconnect=fdr,walltime=72:00:00
  

• Load R module

  $ module load r/3.6.0-gcc/8.3.1
  

• Open R and run in Interactive mode to install package

  $ R
  > install.packages("doParallel")
  

• Run R in batch mode

  $ Rscript a.R
  $ R CMD BATCH a.R # Will write separate output file
  

Key Points

• Rscript

• R CMD BATCH