slurm_batchtools.tmpl

#!/bin/bash


## Via https://github.com/mllg/batchtools/blob/master/inst/templates/
## Job Resource Interface Definition
##
## ntasks [integer(1)]:       Number of required tasks,
##                            Set larger than 1 if you want to further parallelize
##                            with MPI within your job.
## cpus [integer(1)]:         Number of required cpus per task,
##                            Set larger than 1 if you want to further parallelize
##                            with multicore/parallel within each task.
## memory [integer(1)]:       Memory in megabytes for each cpu.
##                            Default is 7900 Mo/core
## partition [string(1)]:     Partition requested.
##                            Default is "sgg".
##
## Default resources can be set in your .batchtools.conf.R by defining the variable
## 'default.resources' as a named list.


<%
# relative paths are not handled well by Slurm
log.file = fs::path_expand(log.file)
#########################
# Set defaults if needed.

if (!"partition" %in% names(resources)) {
  resources$partition = "sgg"
}

-%>

#SBATCH --job-name=<%= job.name %>
#SBATCH --output=<%= log.file %>
#SBATCH --error=<%= log.file %>
#SBATCH --ntasks=1
#SBATCH --account=sgg
#SBATCH --partition=<%= resources$partition %>
<%= if (!is.null(resources[["cpus"]])) sprintf(paste0("#SBATCH --cpus-per-task='", resources[["cpus"]], "'")) %>
<%= if (array.jobs) sprintf("#SBATCH --array=1-%i", nrow(jobs)) else "" %>
<%= if (!is.null(resources[["memory"]])) sprintf(paste0("#SBATCH --mem-per-cpu='", resources[["memory"]], "'")) %>


## module add ...

## Run R:
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'