Hybrid decomposition method in parallel molecular dynamics simulation based on SMP cluster architecture

Bing Wang, Jiwu Shu, Weimin Zheng, Jinzhao Wang, Min Chen
2005 Tsinghua Science and Technology  
A hybrid decomposition method for molecular dynamics simulations was presented, using simultaneously spatial decomposition and force decomposition to fit the architecture of a cluster of symmetric multi-processor (SMP) nodes. The method distributes particles between nodes based on the spatial decomposition strategy to reduce inter-node communication costs. The method also partitions particle pairs within each node using the force decomposition strategy to improve the load balance for each node.
more » ... Simulation results for a nucleation process with 4 000 000 particles show that the hybrid method achieves better parallel performance than either spatial or force decomposition alone, especially when applied to a large scale particle system with non-uniform spatial density.
doi:10.1016/s1007-0214(05)70052-3 fatcat:otysyljfjnh6pem6yp3adiqn3y