#!/bin/bash --login
#SBATCH --job-name=mdrun_omp_cuda
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --gres=gpu:1
#SBATCH --time=0-24:00:00
#SBATCH --mem=16G
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --account=<account>

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

module load gnu
module load openmpi
module load gromacs/2016.6-gpu

# 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 -dlb auto -plumed plumed.dat