slurm_batchtools.tmpl

#!/bin/bash
<%
if (!is.null(resources$log.file))
  log.file = resources$log.file
# relative paths are not handled well by Slurm
log.file = fs::path_expand(log.file)

if (is.null(resources$walltime))
  resources$walltime = 24 * 3600
-%>

#SBATCH --job-name=<%= job.name %>
#SBATCH --output=<%= log.file %>
#SBATCH --error=<%= log.file %>
<%= if (!is.null(resources$partition)) sprintf("#SBATCH --partition='%s'", resources$partition) %>
#SBATCH --ntasks=1
<%= if (!is.null(resources$ncpu)) sprintf("#SBATCH --cpus-per-task=%d", resources$ncpu) %>
<%= if (!is.null(resources$mcpu)) sprintf("#SBATCH --mem-per-cpu=%d", resources$mcpu) %>
#SBATCH --mail-type=ALL
#SBATCH --mail-user=gibbs@uni-greifswald.de
#SBATCH --time=<%= ceiling(resources$walltime / 60) %>

MODULESPATH="/usr/share/[Mm]odules/init/bash"
. ${MODULESPATH}
module load r
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'