OM_MSY.pbs

#!/bin/sh
## job name
#PBS -N MSY_ple
## maximum runtime
#PBS -l walltime=06:00:00
## select number of nodes, cpus (per node) and memory (per node)
#PBS -l select=1:ncpus=24:mem=100gb
## standard output standard error
#PBS -o reports
#PBS -e reports
STOCK_ID="'"'ple.27.7e'"'"
OM="'"'baseline'"'"
X_LABEL="'"'F'"'"

### print details about job
echo ""
echo "This is job $PBS_JOBID index $PBS_ARRAY_INDEX"
echo "The following ressources have been allocated"
cat $PBS_NODEFILE
echo ""

### set working directory
cd $HOME/git/MSE_ple.27.7e/

## load modules
## anaconda includes R and OpenMPI
module purge
module load mpi/intel-2018.1.163 anaconda3/personal
### activate MPI environment
source activate R4_202109

echo "starting the simulations..."
### run job
R CMD BATCH --no-save --no-restore "--args n_workers=20 stock_id=$STOCK_ID OM=$OM yr_start=2021 n_iter=1000 vals_ini=seq(0,1,0.1) lower=0 upper=0.7 tol=0.001 plot=TRUE x_label=$X_LABEL save=TRUE" $HOME/git/MSE_ple.27.7e/OM_MSY.R $HOME/reports/$PBS_JOBID.$PBS_ARRAY_INDEX.Rout
## $PBS_ARRAY_INDEX

echo ""
echo "R job finished!"
echo ""

## print details about job
echo "job details from PBS:"
echo "==============================================================================="
qstat -f
echo "==============================================================================="
qstat -t
echo "==============================================================================="