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

Authors:
T. Matthey;J. P. Hansen
Affiliations:
-;-
Venue:
PARA '00 Proceedings of the 5th International Workshop on Applied Parallel Computing, New Paradigms for HPC in Industry and Academia
Year:
2000

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Abstract

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 asynchronous message-passing multi-cell approach using MPI as message-passing layer and the Leap-Frog/Verlet algorithm for the time integration. We compare one-sided with two different two-sided communication approaches for typical production runs (105 - 109 atoms) where we discuss the communication vs. computation time for increasing number of processes. We also show how the partitioning of the problem affects the different communication approaches. Using one-sided communication we achieved 10-70% better performance over two-sided.