关键词: 分子动力学, 图形处理器, 多核中央处理器, AMBER力场, 计算统一设备架构, OpenMP

Abstract: On the heterogeneous architecture of multi-core Central Processing Unit (CPU) and Graphic Processing Unit (GPU), the Open Multi-Processing (OpenMP) and the programming interfaces of Compute Unified Device Architecture (CUDA) were used to implement a molecular dynamics simulation program based on AMBER force field. In order to efficiently use computer processing power, the program was divided into different parts which were processed by CPU single-thread, CPU multi-thread and GPU multi-thread respectively. The experimental results show that compared with the optimized CPU-based implementations, the heterogeneous parallel computing model based on multi-core CPU-GPU gets powerful performance advantage. Especially, the calculations of forces, which account for more than 90% of processing time, get at most 12 times faster than CPU-based implementations while being implemented on GPU.

Key words: Molecular Dynamics (MD), Graphic Processing Unit (GPU), multi-core Central Processing Unit (CPU), AMBER force field, Compute Unified Device Architecture (CUDA), Open Multi-Processing (OpenMP)