Benchmarking: Gromacs-4.6

Requirements

cmake 2.8 (for building)
CUDA 5.0

Download

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz

Build

module load cmake/2.8.10.2
module load cuda/5.0

cmake ../gromacs-4.6 -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON \
     -DCUDA_TOOLKIT_ROOT_DIR=/shared/apps/cuda/cuda-5.0 \
     -DLIB_INSTALL_DIR=/shared/apps/cuda/gromacs/4.6/lib \
     -DCMAKE_INSTALL_PREFIX=/shared/apps/cuda/gromacs/4.6

make -j 24

Modulefiles

File location: /shared/modulefiles
File name: gpu/gromacs/4.6

#%Module 1.0
#
prereq  cuda/5.0
system "source /shared/apps/cuda/gromacs/4.6/bin/GMXRC.bash"
prepend-path  PATH      /shared/apps/cuda/gromacs/4.6/bin
prepend-path  LD_LIBRARY_PATH /shared/apps/cuda/gromacs/4.6/lib

Run

module load gpu/gromacs/4.6
mdrun -s <input file>