多核CPU和GPU加速分子动力学模拟

在多核中央处理器(CPU)—图形处理器(GPU)异构并行体系结构上，采用OpenMP和计算统一设备架构(CUDA)编程实现了基于AMBER力场的蛋白质分子动力学模拟程序。通过合理地将程序划分为CPU单线程、CPU多线程和GPU多线程执行部分，高效地利用了计算机的处理能力。性能测试结果表明，相对于优化后的CPU串行计算，多核CPU-GPU异构并行计算模型有强大的性能优势，特别是将占整个程序执行时间90%的作用力的计算移植到GPU上执行，获得了最高可达12倍的计算加速比。

Accelerated molecular dynamics simulation using multi-core CPU and GPU

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.