Sourcing an R script within another script executed through SLURM

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I am executing an R script on a cluster, using the following sbatch file:

#!/bin/bash

#SBATCH --job-name=ReconstructScans
#SBATCH --mem=4g
#SBATCH --account=XXXXXX
#SBATCH --array=1-1013%5

module load StdEnv/2020
module load gcc/9.3.0
module load r/4.0.2

srun Rscript ReconstructScans.R

ReconstructScans.R calls another R script, using

source("path_to_script.R", local=FALSE)

However, for some reason, the variables declared within path_to_script.R are not accessible to ReconstructScans.R. I get the object 'DataPath' not found error.

Why might this be happening? When I open an interactive R shell and source ReconstructScans.R, everything works fine. It's when ReconstructScans.R is executed through sbatch that the problem arises.

Is it a problem with how I'm executing it using: srun Rscript ReconstructScans.R?

Thank you,

Mrinmayi

0 Answers
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