54 lines
1.2 KiB
Bash
Executable File
54 lines
1.2 KiB
Bash
Executable File
#!/bin/bash -l
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#SBATCH --partition=normal
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=8
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#SBATCH --gres=gpu:1
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#SBATCH --exclude=linux-05,linux-08,linux-02,linux-03,linux-04,linux-07
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#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2025.2* ] ; then
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# echo "Version loaded is not 2025.2! Exiting!"
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# exit 1
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#fi
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if [ -n "$SLURM_CPUS_PER_TASK" ]; then
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NT="-nt $SLURM_CPUS_PER_TASK"
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elif [ $(nproc) -lt 9 ] ; then
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NT="-nt $(nproc)"
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else
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NT="-nt 8"
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fi
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WORKDIR="$(dirname $(readlink -f "$0"))"
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if [ "${WORKDIR%/*}" = "/var/lib/slurm/slurmd" ] ; then
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WORKDIR="$(pwd)"
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fi
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mkdir -p "$WORKDIR/out"
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export GMX_MAXCONSTRWARN=-1;
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gmx -nobackup grompp \
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-f $WORKDIR/mdp_parameters.mdp \
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-o $WORKDIR/tpr_run.tpr \
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-c $WORKDIR/gro_start.gro \
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-r $WORKDIR/gro_start.gro \
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-p $WORKDIR/topology.top \
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-po $WORKDIR/out/mdp_mdout.mdp \
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-maxwarn 6
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if [ $? != 0 ] ; then
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echo "grompp failed, exiting"
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exit 1
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fi
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gmx mdrun \
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-s $WORKDIR/tpr_run.tpr \
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-o $WORKDIR/out/trr_traj.trr \
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-c $WORKDIR/out/out.gro \
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-x $WORKDIR/out/xtc_traj.xtc \
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-e $WORKDIR/out/edr_energy.edr \
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-g $WORKDIR/out/log.log \
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-cpo $WORKDIR/out/state.cpt \
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-cpi $WORKDIR/out/state.cpt \
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-cpt 1 -notunepme -v $NT
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