Cluster-Based parallel simulation for large scale molecular dynamics in microscale thermophysics

Authors:
Jiwu Shu;Bing Wang;Weimin Zheng
Affiliations:
Institue of HPC, Dept. of Computer Science and Technology, Tsinghua Uni., Beijing, China;Institue of HPC, Dept. of Computer Science and Technology, Tsinghua Uni., Beijing, China;Institue of HPC, Dept. of Computer Science and Technology, Tsinghua Uni., Beijing, China
Venue:
ISPA'04 Proceedings of the Second international conference on Parallel and Distributed Processing and Applications
Year:
2004

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Abstract

A cluster-based spatial decomposition algorithm for solving large-scale Molecular Dynamics simulation of thermophysics is proposed. Firstly, three kinds of domain division strategies are provided and their efficiency and scalability are analyzed. Secondly, a method called FLNP (Fast Location of Neighboring Particles) to accelerate the location of neighboring particles is proposed, which greatly reduces the cost of calculation and communication of interaction. Additionally, a new memory management technique called AMM (Adaptive Memory Management) is applied to meet the large memory requirement. The parallel algorithm based on these above technologies was implemented on a cluster of SMPs and tested on a system of 6,912,000 particles and achieved an efficiency of 77.0%.