55 lines
1.3 KiB
Bash
Executable File
55 lines
1.3 KiB
Bash
Executable File
#!/bin/bash -l
|
|
|
|
#SBATCH --partition=normal
|
|
#SBATCH --ntasks=1
|
|
#SBATCH --cpus-per-task=8
|
|
#SBATCH --gres=gpu:1
|
|
##SBATCH --exclude=linux-05,linux-06,linux-07,linux-08
|
|
|
|
#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2023.3* ] ; then
|
|
# echo "Version loaded is not 2023.3! Exiting!"
|
|
# exit 1
|
|
#fi
|
|
|
|
PHYS_CORES=$(lscpu | awk -F: '/Core\(s\) per socket/ {print $2+0}')
|
|
if [ -n "$SLURM_CPUS_PER_TASK" ]; then
|
|
NT="-nt $SLURM_CPUS_PER_TASK"
|
|
elif [ "$PHYS_CORES" -lt 9 ] ; then
|
|
NT="-nt $PHYS_CORES"
|
|
else
|
|
NT="-nt 8"
|
|
fi
|
|
|
|
WORKDIR="$(dirname $(readlink -f "$0"))"
|
|
if [ "${WORKDIR%/*}" = "/var/lib/slurm/slurmd" ] ; then
|
|
WORKDIR="$(pwd)"
|
|
fi
|
|
|
|
mkdir -p "$WORKDIR/out"
|
|
|
|
export GMX_MAXCONSTRWARN=-1;
|
|
gmx -nobackup grompp \
|
|
-f $WORKDIR/mdp_parameters.mdp \
|
|
-o $WORKDIR/out/tpr_run.tpr \
|
|
-c $WORKDIR/gro_start.gro \
|
|
-r $WORKDIR/gro_start.gro \
|
|
-p $WORKDIR/topology.top \
|
|
-po $WORKDIR/out/mdp_mdout.mdp \
|
|
-maxwarn 6
|
|
|
|
if [ $? != 0 ] ; then
|
|
echo "grompp failed, exiting"
|
|
exit 1
|
|
fi
|
|
|
|
gmx mdrun \
|
|
-s $WORKDIR/out/tpr_run.tpr \
|
|
-o $WORKDIR/out/trr_traj.trr \
|
|
-c $WORKDIR/out/out.gro \
|
|
-x $WORKDIR/out/xtc_traj.xtc \
|
|
-e $WORKDIR/out/edr_energy.edr \
|
|
-g $WORKDIR/out/log.log \
|
|
-cpo $WORKDIR/out/state.cpt \
|
|
-cpi $WORKDIR/out/state.cpt \
|
|
-cpt 1 -notunepme -v $NT
|