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rcluster-computingdistributed-computingpbsslurm

Passing SLURM batch command line arguments to R

I'm trying to run a SLURM sbatch command with various parameters that I can read in an R script. When using PBS system, I used to write qsub -v param1=x,param2=y (+ other system parameters like the memory requirements etc and the script name to be read by PBS) and then in the R script read it with x = Sys.getenv(‘param1’).

Now I tried 

sbatch run.sh --export=basePath=‘a’

With run.sh:

#!/bin/bash

cd $SLURM_SUBMIT_DIR
echo $PWD

module load R/common/3.3.3

R CMD BATCH --quiet --no-restore --no-save runDo.R output.txt

And runDo.R:

base.path = Sys.getenv('basePath')

print(base.path)

The script is running but the argument value is not assigned to base.path variable (it prints an empty string).

Solution

  • The export parameter has to be passed to sbatch not to the run.sh script.

    It should be like this:

    sbatch --export=basePath=‘a’ run.sh