摘要
A hybrid decomposition method for molecular dynamics simulations was presented, using simul- taneously 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 decom- position 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. Simulation results for a nucleation process with 4 000 000 particles show that the hybrid method achieves better paral- lel performance than either spatial or force decomposition alone, especially when applied to a large scale particle system with non-uniform spatial density.
A hybrid decomposition method for molecular dynamics simulations was presented, using simul- taneously 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 decom- position 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. Simulation results for a nucleation process with 4 000 000 particles show that the hybrid method achieves better paral- lel performance than either spatial or force decomposition alone, especially when applied to a large scale particle system with non-uniform spatial density.
基金
Supported by the "985" Basic Research Foundation of Tsinghua University of China (No. JC2001024)
