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cd /sw/gromacs/5.1.2/src/gromacs-5.1.2/build

module load fftw/3.3.4
module load cmake/3.5.0
module load boost/1.60.0

cmake  -DCMAKE_INSTALL_PREFIX=/sw/gromacs/5.1.2/5.1.2-gcc-mpi-gpu --with-fft=mkl --enable-mpi  -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON .. 2>&1 | tee configure-mpi.log

make 2>&1 | tee makelog.txt

make install 2>&1 | tee makeInstall.txt

Usage: module load gromacs/5.1.2-gcc-mpi-gpu


>>>Sample pbs script>>>>>>>>
#!/bin/bash
#PBS -N GromacsCuda
#PBS -m abe
#PBS -M YourEmail@griffith.edu.au
#PBS -l select=1:ncpus=2:mem=4g:mpiprocs=2:ngpus=1,walltime=100:00:00
####PBS -l select=1:ncpus=2:mem=4g:mpiprocs=2:ngpus=1:host=n020,walltime=100:00:00
#####PBS -l select=1:ncpus=1:mem=12gb,walltime=100:00:00
#PBS -l walltime=1:00:00
###Comment group_list if not in the group named gpu. This feature is for accounting only and not currently used on gowonda.
###PBS -W group_list=gpu
#PBS -q gpu
source $HOME/.bashrc
## The number of chunks is given by the select =<NUM > above

###$PBS_NODEFILE is a node-list file created with select and mpiprocs options by PBS
###### The number of MPI processes available is mpiprocs * chunks (=NPROCS)
NPROCS=2

echo "Starting job"
echo Running on host `hostname`
echo Directory is `pwd`
module load gromacs/5.1.2-gcc-mpi-gpumodule load mpi/mpt/2.02
module list
nvcc --version
echo `cat $PBS_NODEFILE`
mpirun $NPROCS  "/sw/mpi/mpt/pingpong_mpt"
#
echo "Done with job"

>>>>>>>Another Sample >>>>>
#!/bin/bash
#PBS -N GromacsCuda
#PBS -m abe
#PBS -e 5md_s10v.err
#PBS -o 5md_s10v.log
#PBS -M YourEmail@griffith.edu.au
#PBS -l select=1:ncpus=2:mem=4g:mpiprocs=2:ngpus=1:host=n020,walltime=100:00:00
#PBS -l walltime=1:00:00
#PBS -q gpu
source $HOME/.bashrc
## The number of chunks is given by the select =<NUM > above

###$PBS_NODEFILE is a node-list file created with select and mpiprocs options by PBS
###### The number of MPI processes available is mpiprocs * chunks (=NPROCS)
NPROCS=2

cd $PBS_O_WORKDIR
echo "Starting job"
echo Running on host `hostname`
echo Directory is `pwd`
module load gromacs/5.1.2-gcc-mpi-gpu
module load mpi/mpt/2.02
module list
nvcc --version
echo `cat $PBS_NODEFILE`

mpirun $NPROCS gmx mdrun -cpo s10v100hydrap01.cpt -s /sw/gromacs/5.1.2/5.1.2-gcc-mpi-gpu/examples/md100.tpr -o s10v100hydra.trr -c s10v100hydra.gro -g s10v100hydra.log -e s10v100hydra.edr -noappend -maxh 1

echo "Done with job"
>>>>>>>>>>>