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Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition

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3 Author(s)
Martin C. Herbordt ; Dept. of Electr. & Comput. Eng., Boston Univ., Boston, MA, USA ; Md. Ashfaquzzaman Khan ; Tony Dean

Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretized models, enabling simulations to be advanced by event, with a resulting performance increase of several orders of magnitude. Even so, DMD is compute bound. Moreover, unlike MD, causality issues make DMD difficult to scale. Here we present a microarchitecture-inspired parallel algorithm for DMD: speculative execution enables multithreading, while in-order commitment ensures correctness. Our initial not-yet optimized implementation obtains scalability for a multicore processor when running realistic simulation models.

Published in:

2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors

Date of Conference:

7-9 July 2009