Passing SLURM batch command line arguments to R

Question

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).

I just know about R so forgive me if it's irrelevant, but if you're getting the output of the script you may want to try `cat` instead of `print` as the output of `print` will start with `"[1]"` and will leave escape characters in the path (`"\\"` for `"\"`). — moodymudskipper, Aug 09 '17 at 15:09

score 4 · Accepted Answer · answered Aug 09 '17 at 18:46

4

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

answered Aug 09 '17 at 18:46

Carles Fenoy

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Passing SLURM batch command line arguments to R

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