Performance metrics in a hybrid MPIOpenMP based molecular dynamics simulation with short-range interactions
We discuss computational bottlenecks in MD and discuss challenges in parallelizing. We present a hybrid algorithm using MPI with OpenMP threads for parallelizing MD scheme. The algorithm is discussed using nano-indentation of Cr films with C indenters using the EAM and Morse potentials. We study performance of our algorithm for a range of MPIthread combinations. Speed up achieved by our algorithm compares favorably with that by LAMMPS.
molecular dynamics openmp threading hybrid programming message passing parallel computing