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

—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.

• Type: Conference
• Year: 2009
• Where: ASAP
• Authors: Martin C. Herbordt, Md. Ashfaquzzaman Khan, Tony Dean
• Keywords: ASAP 2009, Computer Science, Discrete Event Simulation, DMD Difficult, Realistic Simulation Models