基于SMP集群的激光化学反应模拟效率分析

摘要

This paper designed a parallel simulation system of photochemical reactions and realized based on SMP cluster.Implemented photochemical reactions simulation by using atomic decomposition algorithm and parallel matrix multiplication.Investigated the parallel efficiency by using fine-grained method with 8 threads and 16 threads on the condition of using fixed number of processors.Tested on SMP cluster, tested the simulation of the molecular with 500 carbon atoms by using 128-core processor.The parallel efficiency was over 70％.The results also strongly suggest that fine-grained play a greater role on improving the efficiency.The system could simulate photochemical reactions of moleculer system including hundreds of atoms.%基于半经典分子动力学模型,在SMP集群中实现激光化学反应双层并行模拟系统.结合粗粒度的原子分解算法和细粒度的矩阵并行乘法实现激光化学反应模拟中力计算部分的并行化,分析粒度划分对半经典分子动力学模拟并行效率的影响.在SMP集群中测试表明,采用128个处理器模拟由500个C原子构成的分子体系,并行效率可达70%.在CPU数量固定的情况下,SMP节点内的细粒度的并行对提高半经典分子动力学模拟并行效率影响较大.该系统能够模拟大分子体系的激光化学反应,在提高加速比的同时保证计算资源的利用效率,满足激光化学反应模拟需求.