#!/bin/bash --login
#SBATCH --job-name=amber20gpu
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --gres=gpu:1
#SBATCH --time=0-01:00:00
#SBATCH --mem=16G
#SBATCH --partition=gpu
#SBATCH --account=<account>

shopt -q login_shell || exit 1

module load apptainer/1.0

container='/hpc/share/applications/amber/20/amber-20-gpu'

bind="${GROUP:+$GROUP,}${ARCHIVE:+$ARCHIVE,}${SCRATCH:+$SCRATCH,}$(test -d /node && echo /node)"
bind="${bind:+$bind,}/opt/hpc/system/nvidia/driver:/usr/local/nvidia/lib,/opt/hpc/system/nvidia/driver:/usr/local/nvidia/bin"

apptainer exec ${bind:+--bind $bind} "$container.sif" \
pmemd.cuda -i min.in -o test-min.out -p test.prmtop -c test.inpcrd -r test-min.rst -ref test.inpcrd -e test-min.en -inf test-min.mdinfo -O

apptainer exec ${bind:+--bind $bind} "$container.sif" \
pmemd.cuda -i test_amber_MD.in -o test-MD.out -p test.prmtop -c test-min.rst -r test-MD.rst -x test-MD.nc -e test-MD.en -inf test-MD.mdinfo -O