  We discuss the computational bottlenecks in molecular dynamics (MD) and
describe the challenges in parallelizing the computation intensive tasks. We
present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP
threads for parallelizing a generalized MD computation scheme for systems with
short range interatomic interactions. The algorithm is discussed in the context
of nanoindentation of Chromium films with carbon indenters using the Embedded
Atom Method potential for Cr Cr interaction and the Morse potential for Cr C
interactions. We study the performance of our algorithm for a range of
MPIthread combinations and find the performance to depend strongly on the
computational task and load sharing in the multicore processor. The algorithm
scaled poorly with MPI and our hybrid schemes were observed to outperform the
pure message passing scheme, despite utilizing the same number of processors or
cores in the cluster. Speed-up achieved by our algorithm compared favourably
with that achieved by standard MD packages.
