神威太湖之光上分子动力学模拟的性能优化

"神威·太湖之光"国产超级计算机的特点是适用于高通量计算系统,此类系统往往存储器访问延迟,网络延迟较长.在实际应用中,有一大类问题是时间演化的模拟问题,往往需要高频状态迭代,每次迭代需要通信.此类应用问题的典型代表是分子动力学模拟,分子的性质依赖于时间演化,导致状态相关的时间尺度上难以并行化.实际应用中,全原子模型需要...

Performance Optimization of Molecular Dynamics Simulation on Sunway TaihuLight System

Sunway TaihuLight supercomputer is suitable for high-throughput computing systems, which tend to have memory access latency and network latency. There is a large class of problems namely time-to-solution, which requires high frequency iterations. The typical application of time-to-solution problems is molecular dynamics simulation. Computations in molecular dynamics simulation depend on the time. Therefore, the iterative computations are difficult to be parallelized. Time scale usually exceeds microsecond, which means that the number of steps is more than 10¹². It is impossible to finish effective simulation in a limited time on long latency system. Therefore, the main performance bottleneck on long latency Sunway system is how to increase the iterative frequency. This study proposes a series of optimization strategies to improve the iterative frequency:(1) Reducing communication overhead and network competition costs through single-core communication combined with on-chip synchronization; (2) Optimizating the speed of synchronization between cores through waiting the shared memory variable and synchronizing the computing processing elements; (3) Reducing the data dependencies by changing the computation patterns; (4) Covering up the memory access latency by overlapping computation and communication; (5) Regulating the data structure to improve accessibility.