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#!/bin/bash
## 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.
## ncpus [integer(1)]: Number of required cpus per task,
## Set larger than 1 if you want to further parallelize
## with multicore/parallel within each task.
## walltime [integer(1)]: Walltime for this job, in seconds.
## Must be at least 60 seconds for Slurm to work properly.
## memory [integer(1)]: Memory in megabytes for each cpu.
## Must be at least 100 (when I tried lower values my
## jobs did not start at all).
##
## 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)
-%>
#SBATCH --job-name=<%= job.name %>
#SBATCH --output=<%= log.file %>
#SBATCH --error=<%= log.file %>
#SBATCH --time=<%= ceiling(resources$walltime / 60) %>
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=<%= resources$ncpus %>
#SBATCH --mem-per-cpu=<%= resources$memory %>
<%= if (!is.null(resources$partition)) sprintf(paste0("#SBATCH --partition='", paste(resources$partition, collapse = ","), "'")) %>
<%= if (array.jobs) sprintf("#SBATCH --array=1-%i", nrow(jobs)) else "" %>
## Initialize work environment like
## source /etc/profile
## module add ...
## Export value of DEBUGME environemnt var to slave
export DEBUGME=<%= Sys.getenv("DEBUGME") %>
<%= sprintf("export OMP_NUM_THREADS=%i", resources$omp.threads) -%>
<%= sprintf("export OPENBLAS_NUM_THREADS=%i", resources$blas.threads) -%>
<%= sprintf("export MKL_NUM_THREADS=%i", resources$blas.threads) -%>
## Run R:
## we merge R output with stdout from SLURM, which gets then logged via --output option
singularity exec /home/mpib/peikert/a-future-for-tardis_latest.sif Rscript -e 'batchtools::doJobCollection("<%= uri %>")'