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Evaluation of MPI’s One-Sided Communication Mechanism for Short-Range Molecular Dynamics on the Origin2000
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Evaluation of MPI’s One-Sided Communication Mechanism for Short-Range Molecular Dynamics on the Origin2000
T. Matthey6 and J. P. Hansen7 
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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.
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