Evaluation of MPI's One-Sided Communication Mechanism for Short-Range Molecular Dynamics on the Origin2000

In this paper we evaluate the possibilities of one-sided communication, a new feature of the MPI-2 standard, on the Origin2000 for relatively short-range molecular dynamics (MD) simulations. Our algorithm is based on an asynchrony message-passing multi-cell approach using MPI as message-passing layer and the Leap-Frog/ Verlet algorithm for the time integration. We compare an one-sided with two different two-sided communication approaches for typical production runs (10 atoms, dens distribution) where we discuss the time spent for communication vs. computation for a range of different number of processes. We also show how the partitioning of the problem does affect the different communication approaches.