slurm_clustermq.tmpl

#!/bin/sh
# From https://github.com/mschubert/clustermq/wiki/SLURM
#SBATCH --job-name={{ job_name }}           # job name
#SBATCH --partition=hpg2-compute                 # partition
#SBATCH --output={{ log_file | logs/workers/dat_pipeline%j_%a.out }} # you can add .%a for array index
#SBATCH --error={{ log_file | logs/workers/dat_pipeline%j_%a.err}}  # log file
#SBATCH --mem-per-cpu={{ memory | 6144 }}   # memory
#SBATCH --array=1-{{ n_jobs }}              # job array
#SBATCH --time={{ time | 1440 }}

source /etc/profile

ulimit -v $(( 1024 * {{ memory | 6144 }} ))
module load R              # Uncomment if R is an environment module.
CMQ_AUTH={{ auth }} Rscript -e 'clustermq:::worker("{{ master }}")'