Title :
Parallel implementation of the treecode Ewald method
Author :
Liu, Dongqing ; Duan, Zhong-Hui ; Krasny, Robert ; Zhu, Jianping
Author_Institution :
Dept. of Comput. Sci., Akron Univ., OH, USA
Abstract :
Summary form only given. Here, we discuss an efficient parallel implementation of the treecode Ewald method for fast evaluation of long-range Coulomb interactions in a periodic system for molecular dynamics simulations. The parallelization is based on an adaptive decomposition scheme using the Morton order of the particles. This decomposition scheme takes advantage of the data locality and involves minimum changes to the original sequential code. The message passing interface (MPI) is used for interprocessor communications, making the code portable to a variety of parallel computing platforms. We also discuss communication and performance models for our parallel algorithm. The predicted communication time and parallel performance from these models match the measured results well. Timing results obtained using a system of water molecules on the IA32 Cluster at the Ohio Supercomputer Center demonstrate high speedup and efficiency of the parallel treecode Ewald method.
Keywords :
message passing; molecular dynamics method; parallel algorithms; sequential codes; tree codes; Coulomb interaction; IA32 Cluster; MPI; Morton order; Ohio Supercomputer Center; adaptive decomposition scheme; code portability; data locality; interprocessor communication; message passing interface; molecular dynamics simulation; parallel algorithm; parallel computing platform; parallel treecode Ewald method; Biological information theory; Biological system modeling; Biology computing; Clustering algorithms; Computational efficiency; Computational modeling; Computer science; Computer simulation; Costs; Mathematics;
Conference_Titel :
Parallel and Distributed Processing Symposium, 2004. Proceedings. 18th International
Print_ISBN :
0-7695-2132-0
DOI :
10.1109/IPDPS.2004.1303285