基于国产申威众核架构的二维材料分子动力学模拟算法优化

Optimization of molecular dynamics simulation algorithm for two-dimensional material on Sunway

分子动力学(Molecular Dynamics,MD)模拟是探索微观世界的重要工具,在多个领域中得到广泛应用。二维材料是MD在材料科学领域的一个重要研究方向,其中层间作用力的计算是耗时最多的部分。高性能计算是能够提升二维材料模拟效率的关键技术,利用新一代神威超级计算机的强大计算能力,来提高二维材料体系的MD模拟效率。针对层间力场的计算,采用消除冗余计算、多核心融合和设置缓冲区等多种算法优化策略;采用软件Cache累加受力、从核通信累加能量和从核C++特性等技术实现线程级并行;采用软硬件Cache协同策略提升访存效率。实验结果表明:优化后的整体性能提升155倍,模拟效率可达2 ns/day,弱扩展并行效率达到92.7%。

Molecular dynamics(MD)simulation is an important tool to explore the microcosmic world,which is widely used in many fields.Two-dimensional materials is an important research direction of MD in the field of materials science,in which the calculation of interlayer interactions is the most time-consuming part.High performance computing is a key technology to im-prove the simulation efficiency of two-dimensional materials.In this work,the powerful computing power of a new generation of Sunway supercomputer is utilized to improve the MD simulation efficiency of two-dimensional materials.For the interlayer force field,multiple algorithm optimization strategies such as eliminating redundant calculation,multi-core fusion and setting buffer are adopted.It implements thread-level parallelism by software Cache accumulation force,communication between computation pro-cessing elements accumulation energy and C++feature.The hardware and software Cache coordination policy is adopted to im-prove storage access efficiency.The experimental results show that the overall performance is improved by 155 times,the simula-tion efficiency is about 2 ns/day,and the weak extension parallel efficiency reaches 92.7%.