Example script (hello.R):

sayHello <- function(){
  print("hello")
}
sayHello()

User can execute R scripts from the command line with the following commands:

1. R CMD BATCH script.R
2. Rscript script.R

Note: With the R CMD BATCH command the output of the R script is redirected to file instead of the screen

Next user must embed the script to the SLURM batch job file/control file (submit.sbatch):

#!/bin/bash
#SBATCH --job-name helloworld # Name for your job
#SBATCH --ntasks 1 # Number of task
#SBATCH --time 5 # Runtime in minutes.
#SBATCH --mem=2000 # Reserve 2 GB RAM for the job
#SBATCH --partition serial # Partition to submit
#SBATCH --output hello.out # Standard out goes to this file
#SBATCH --error hello.err # Standard err goes to this file
#SBATCH --mail-user username@uef.fi # this is the email you wish to be notified at
#SBATCH --mail-type ALL # ALL will alert you of job beginning, completion, failure etc

module load r # load modules

Rscript hello.R # Execute the script

sbatch

User can submit the job to the compute queue with the sbatch command. Note that the batch file (and R script and data) must be located at the /home/ disk.

sbatch submit.sbatch