serial_batch_job.sh

#!/bin/bash
#SBATCH --account=project_2015299    # Choose the project to be billed
#SBATCH --reservation=geocomputing_day2 # Only available during the course
#SBATCH --output=slurm-%j.out  # File to write the standard output to. %j is replaced by the job ID.
#SBATCH --error=slurm-%j.err  # File to write the standard error to. %j is replaced by the job ID. Defaults to slurm-%j.out if not provided. 
#SBATCH --time=0:05:00  # Maximum duration of the job. Upper limit depends on partition.
#SBATCH --partition=small  # Which queue to use. Defines maximum time, memory, tasks, nodes and local storage for job
#SBATCH --nodes=1  # Number of compute nodes. Upper limit depends on partition.
#SBATCH --ntasks=1  # Number of tasks. Upper limit depends on partition.
#SBATCH --mem-per-cpu=1000  # Minimum memory required per usable allocated CPU.  Default units are megabytes.

module load r-env

# Clean up .Renviron file in home directory
if test -f ~/.Renviron; then
    sed -i '/TMPDIR/d' ~/.Renviron
fi

# Specify a temp folder path
# echo "TMPDIR=/scratch/<project>/tmp" >> ~/.Renviron
echo "TMPDIR=$PWD/tmp" >> ~/.Renviron

srun apptainer_wrapper exec Rscript --no-save Contours_simple.R