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guides:slurm:using-r

Using R with Slurm

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 into the SLURM batch job file/control file (e.g. scriptR.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

The last step is to 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 local file system of login node, e.g. /home/users/ disk.

sbatch scriptR.sbatch
guides/slurm/using-r.txt · Last modified: 29.10.2019 15:10 (external edit)