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R Batch Jobs

R batch jobs

Sometimes an R script will take to long to either run via an interactive session or RStudio. In these cases we can submit the R script as a batch job.

  • Login to the HPC cluster either by Command Line or the OnDemand Website. For information on how to log into the cluster check out:

Navigate To The Cluster

  • Upload your R script to the HPC cluster

  • Go to the directory/folder which contains your R script

  • Open your favorite text editor and write a slurm submission script similar to the following one batchjob.sh (name your own)

batchjob.sh

#!/bin/bash
#SBATCH -J myRjob  #job name
#SBATCH --time=00-00:20:00 #requested time
#SBATCH -p batch  #running on "batch" partition/queue
#SBATCH -n 2  #2 cores total
#SBATCH --mem=2g #requesting 2GB of RAM total
#SBATCH --output=myRjob.%j.out #saving standard output to file
#SBATCH --error=myRjob.%j.err  #saving standard error to file
#SBATCH --mail-type=ALL  #email optitions
#SBATCH --mail-user=Your_Tufts_Email @tufts.edu
module load R/4.0.0
Rscript --no-save your_rscript_name.R
  • Submit it with: 
sbatch batchjob.sh
  • If you are submitting multiple batch jobs to run the same script on different datasets, please make sure they are saving results to different files inside of your R script.