Updated 2021-05-27

Run R in Batch Mode on the Cluster

Overview

  • R is a very powerful tool for statistics and data science
  • R can be run in two ways:
    • Interactively
    • Batch mode, where the program is submitted and runs without interaction
  • This guide will focus on how to run R scripts in batch mode

Tips

  • To run the R Script, you have to specify two things in your PBS script:
    • load the R module with module load <R version>
    • run the R script in batch mode with R CMD BATCH <scriptname.R?>
  • Submit with qsub <jobName.pbs>
  • Output will show up in a .Rout file in the same dir where the PBS script was submitted from.

Walkthrough: Run an R Script in Batch Mode

  • This walkthrough will use a simple R script that defines a function called add(x,y), which adds two numbers
  • The output will print 2, which is the result of add(1 + 1)

Here is the example R script, which you can save as add.R in the same directory as the PBS script. 

# Add two integers

add <- function(x,y) {
return(x + y)
}

print(add(1,1))

Part 1: The PBS Script

#PBS -N R_test
#PBS -A [Account]
#PBS -l nodes=1:ppn=2
#PBS -l pmem=2gb
#PBS -l walltime=1:00
#PBS -q inferno
#PBS -j oe
#PBS -o addR.out

cd $PBS_O_WORKDIR
module load r
R CMD BATCH add.R
  • The #PBS directives are standard, requesting just 1 minute of walltime and 1 node with 2 cores. More on #PBS directives can be found in the PBS guide
  • $PBS_O_WORKDIR is a variable that represents the directory you submit the PBS script from. Make sure the R script you want to run (in this case, add.R) is in the same directory you put the PBS script.
  • Output Files will also show up in this dir as well
  • module load R/3.4.3 loads the 3.4.3 version of R. To see what R versions are available, run module avail R, and load the one you want
  • R CMD BATCH add.R tells the cluster to run the add.R R script in batch mode. It will print the output to an .Rout file.

Part 2: Submit Job and Check Status

  • Make sure you're in the dir that contains the PBS Script
  • Submit as normal, with qsub <pbs script name>. In this case qsub addR.pbs
  • Check job status with qstat -t 22182721, replacing the number with the job id returned after running qsub
  • You can delete the job with qdel 22182721 , again replacing the number with the jobid returned after running qsub

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see a add.Rout and addR.out files. The addR.Rout file has the results of the jobs. Use cat addR.Rout or open the file in a text editor to take a look.
  • add.Rout should look like:
> # Add two integers
>
> add <- function(x,y) {
+ return(x + y)
+ }
>
> print(add(1,1))
[1] 2
>
> proc.time()
   user  system elapsed
  0.348   0.061   0.566
  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran an R script in batch mode.