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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© 2001 Springer-Verlag Berlin Heidelberg
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Matthey, T., Hansen, J.P. (2001). Evaluation of MPI’s One-Sided Communication Mechanism for Short-Range Molecular Dynamics on the Origin2000. In: Sørevik, T., Manne, F., Gebremedhin, A.H., Moe, R. (eds) Applied Parallel Computing. New Paradigms for HPC in Industry and Academia. PARA 2000. Lecture Notes in Computer Science, vol 1947. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-70734-4_42
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DOI: https://doi.org/10.1007/3-540-70734-4_42
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Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-41729-3
Online ISBN: 978-3-540-70734-9
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