GROMACS

Ready for users on athena

Replace X where X is the number of processors

#!/bin/csh
#PBS -q para -l select=1:ncpus=1:athena=True:mpiprocs=1
source /apps/gromacs/bin/GMXRC
cd /user/m747g263/gromacs
grompp -f 6data_spceh2o-nve.mdp -po 7data_spceh2o-nve.mdp -c 5eq_spceh2o.gro -n box-spceh2o.ndx -p spceh2o.top -o 6data_spceh2o-nve.tpr

Followed by

#!/bin/csh
#PBS -q special -l select=1:ncpus=
X:athena=True:mpiprocs=X
source /apps/gromacs/bin/GMXRC
cd /user/m747g263/gromacs
cp * $TMPDIR
cd $TMPDIR
mdrun -s 6data_spceh2o-nve.tpr -deffnm 6data-spceh2o-nve -cpo 6data-spceh2o-nve.cpt - nt X
cp * /user/m747g263/gromacs
cd
rm -rf $TMPDIR



GPGPU Specific GPU Example

Run GPGPU-status command on cronus to determine host and GPU number

#PBS -l select=1:ncpus=4:host=compute-7-5:mpiprocs=4
cd /user/m747g263/gromacs
source /apps/gromacs/gpgpu/bin/GMXRC
cp * $TMPDIR
cd $TMPDIR
export CC=gcc; export CXX=g++
mdrun -deffnm -gpu_id 1
cp * /user/m747g263/gromacs
cd
rm -rf $TMPDIR