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

T. MattheyContact Information and J. P. HansenContact Information

(6)  Department of Informatics, University of Bergen, Høyteknologisenteret i Bergen, N-5020 Bergen, Norway
(7)  Institute of Physics, University of Bergen, Allégaten 55, N-5007 Bergen, Norway
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 in- creasing 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.

Contact Information T. Matthey
Email: Thierry.Matthey@ii.uib.no

Contact Information J. P. Hansen
Email: JanPetter.Hansen@fi.uib.no
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