#!/bin/bash --login
#SBATCH --job-name=mdrun_mpi_omp
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=6
#SBATCH --exclusive
#SBATCH --time=0-24:00:00
#SBATCH --mem=120G
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --account=<account>

shopt -q login_shell || exit 1
test -n "$SLURM_NODELIST" || exit 1

module load gnu
module load openmpi
module load gromacs/5.1.5-cpu

# Set OMP_NUM_THREADS to the same value as --cpus-per-task with a fallback in
# case it isn't set. SLURM_CPUS_PER_TASK is set to the value of --cpus-per-task,
# but only if --cpus-per-task is explicitly set.
if [ -n "$SLURM_CPUS_PER_TASK" ]; then
    OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
else
    if [ -n "$SLURM_NTASKS_PER_NODE" ]; then
        OMP_NUM_THREADS=$((SLURM_CPUS_ON_NODE/SLURM_NTASKS_PER_NODE))
    else
        if [ -n "$SLURM_NTASKS" ] && [ -n "$SLURM_NNODES" ]; then
            OMP_NUM_THREADS=$((SLURM_CPUS_ON_NODE/(SLURM_NTASKS/SLURM_NNODES)))
        else
            OMP_NUM_THREADS=1
        fi
    fi
fi

export OMP_NUM_THREADS

mpirun gmx mdrun -deffnm topology -pin on