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Parallel discrete molecular dynamics simulation with speculation and in-order commitment
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DOI：10.1016/j.jcp.2011.05.001.png)
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Abstract
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Discrete molecular dynamics simulation (DMD) uses simplified and discretized models enabling simulations to advance by event rather than by timestep. DMD is an instance of discrete event simulation and so is difficult to scale: even in this multi-core era, all reported DMD codes are serial. In this paper we discuss the inherent difficulties of scaling DMD and present our method of parallelizing DMD through event-based decomposition. Our method is microarchitecture inspired: speculative processing of events exposes parallelism, while in-order commitment ensures correctness. We analyze the potential of this parallelization method for shared-memory multiprocessors. Achieving scalability required extensive experimentation with scheduling and synchronization methods to mitigate serialization. The speed-up achieved for a variety of system sizes and complexities is nearly 6x on an 8-core and over 9x on a 12-core processor. We present and verify analytical models that account for the achieved performance as a function of available concurrency and architectural limitations. (C) 2011 Elsevier Inc. All rights reserved.
Keywords:
Parallel discrete molecular dynamics
Parallel discrete event simulation
Parallel processing
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