Difference between revisions of "Gromacs Job Scripts"
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| Line 51: | Line 51: | ||
#PBS -o stdout | #PBS -o stdout | ||
#PBS -m abe | #PBS -m abe | ||
| − | #PBS -M | + | #PBS -M YOUR_MAIL_ADDRESS_HERE |
#PBS -j oe | #PBS -j oe | ||
#PBS -l nodes=1:ppn=2:gpus=1 | #PBS -l nodes=1:ppn=2:gpus=1 | ||
| Line 73: | Line 73: | ||
exit 0 | exit 0 | ||
| + | </source> | ||
| + | ==GPU Acceleration (Single GPU, Gromacs 4.6.5)== | ||
| + | <source lang=bash> | ||
| + | #!/bin/bash | ||
| + | #PBS -N gromacs | ||
| + | #PBS -o stdout | ||
| + | #PBS -m abe | ||
| + | #PBS -M YOUR_MAIL_ADDRESS_HERE | ||
| + | #PBS -j oe | ||
| + | #PBS -l nodes=1:ppn=4:gpus=2 | ||
| + | #PBS -l walltime=36:00:00 | ||
| + | #PBS -q gpu | ||
| + | |||
| + | module load intel/2013 | ||
| + | module load cuda/5.5 | ||
| + | module load gromacs/4.6.5 | ||
| + | |||
| + | myHostName=`hostname -s` | ||
| + | export PBS_GPUS=`gpus=; while read gpu ; do gpus="$gpus,$gpu"; done < $PBS_GPUFILE; echo $gpus | sed -e "s%^,%%"` | ||
| + | export OMP_NUM_THREADS=$PBS_NUM_PPN | ||
| + | export CUDA_VISIBLE_DEVICES=`echo $PBS_GPUS | sed -e "s%$myHostName-gpu%%g"` | ||
| + | echo CUDA_VISIBLE_DEVICES = $CUDA_VISIBLE_DEVICES | ||
| + | |||
| + | cd $PBS_O_WORKDIR | ||
| + | |||
| + | grompp -f prodmd.mdp -c nptsim1.pdb -t nptsim1.cpt -p topology1.top -o prodmd.tpr | ||
| + | mdrun -v -s prodmd.tpr -c prodmd.tpr -deffnm prodmd > gromacs.log 2>&1 | ||
| + | |||
| + | exit 0 | ||
</source> | </source> | ||
Revision as of 16:55, 10 February 2014
Contents
Serial
#!/bin/bash
#
#PBS -r n
#PBS -N Gromacs
#PBS -o stdout
#PBS -e stderr
#PBS -j oe
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#PBS -l nodes=1:ppn=1
#PBS -l pmem=200mb
#PBS -l walltime=01:00:00
module load intel
module load gromacs
cd $PBS_O_WORKDIR
mdrun_d < gromacs.in > gromacs.out 2>&1Parallel (MPI)
#!/bin/bash
#
#PBS -r n
#PBS -N Gromacs
#PBS -o stdout
#PBS -e stderr
#PBS -j oe
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#PBS -l nodes=2:ppn=4
#PBS -l pmem=200mb
#PBS -l walltime=01:00:00
module load intel
module load openmpi
module load gromacs
cd $PBS_O_WORKDIR
mpiexec mdrun_mpi_d < gromacs.in > gromacs.out 2>&1GPU Acceleration (Single GPU, Gromacs 4.6.5)
#!/bin/bash
#PBS -N gromacs
#PBS -o stdout
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#PBS -j oe
#PBS -l nodes=1:ppn=2:gpus=1
#PBS -l walltime=36:00:00
#PBS -q gpu
module load intel/2013
module load cuda/5.5
module load gromacs/4.6.5
myHostName=`hostname -s`
export PBS_GPUS=`gpus=; while read gpu ; do gpus="$gpus,$gpu"; done < $PBS_GPUFILE; echo $gpus | sed -e "s%^,%%"`
export OMP_NUM_THREADS=$PBS_NUM_PPN
export CUDA_VISIBLE_DEVICES=`echo $PBS_GPUS | sed -e "s%$myHostName-gpu%%g"`
echo CUDA_VISIBLE_DEVICES = $CUDA_VISIBLE_DEVICES
cd $PBS_O_WORKDIR
grompp -f prodmd.mdp -c nptsim1.pdb -t nptsim1.cpt -p topology1.top -o prodmd.tpr
mdrun -v -s prodmd.tpr -c prodmd.tpr -deffnm prodmd > gromacs.log 2>&1
exit 0GPU Acceleration (Single GPU, Gromacs 4.6.5)
#!/bin/bash
#PBS -N gromacs
#PBS -o stdout
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#PBS -j oe
#PBS -l nodes=1:ppn=4:gpus=2
#PBS -l walltime=36:00:00
#PBS -q gpu
module load intel/2013
module load cuda/5.5
module load gromacs/4.6.5
myHostName=`hostname -s`
export PBS_GPUS=`gpus=; while read gpu ; do gpus="$gpus,$gpu"; done < $PBS_GPUFILE; echo $gpus | sed -e "s%^,%%"`
export OMP_NUM_THREADS=$PBS_NUM_PPN
export CUDA_VISIBLE_DEVICES=`echo $PBS_GPUS | sed -e "s%$myHostName-gpu%%g"`
echo CUDA_VISIBLE_DEVICES = $CUDA_VISIBLE_DEVICES
cd $PBS_O_WORKDIR
grompp -f prodmd.mdp -c nptsim1.pdb -t nptsim1.cpt -p topology1.top -o prodmd.tpr
mdrun -v -s prodmd.tpr -c prodmd.tpr -deffnm prodmd > gromacs.log 2>&1
exit 0