#!/bin/bash --login
#SBATCH --job-name=mdrun_omp
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=14
#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.                                 
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK:-1}

gmx mdrun -deffnm topology -pin on