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%.
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Shu, J., Wang, B., Zheng, W. (2004). Cluster-Based Parallel Simulation for Large Scale Molecular Dynamics in Microscale Thermophysics. In: Cao, J., Yang, L.T., Guo, M., Lau, F. (eds) Parallel and Distributed Processing and Applications. ISPA 2004. Lecture Notes in Computer Science, vol 3358. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30566-8_25
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DOI: https://doi.org/10.1007/978-3-540-30566-8_25
Publisher Name: Springer, Berlin, Heidelberg
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