Efficiency of dynamic load balancing based on permanent cells for parallel molecular dynamics simulation

Abstract

This paper addresses a dynamic load balancing method of domain decomposition for 3-dimensional molecular dynamics on parallel computers. In order to reduce interprocessor communication overhead, we are introducing a concept of permanent cells to the dynamic load balancing method. Molecular dynamics simulations on a parallel computer T3E prove that the proposed method using load balancing much improves the execution time. Furthermore, we analyze theoretical effective ranges of the dynamic load balancing method, and compare them with experimental effective ranges obtained by parallel molecular dynamics simulations. As a result, the theoretical upper bounds predict experimental effective ranges and are also valid on commercial parallel computers.