摘要
Silicon-Crystal应用运用分子动力学方法对晶体热传导性进行模拟,采用Tersoff势模拟硅晶体的运动轨迹.本文利用神威Athread在神威太湖之光上成功移植了Silicon-Crystal应用,针对SW26010异构众核处理器带来的内存受限问题,提出5种主要优化方式:1)将计算所需参数预取到LDM(Local Data Memory);2)通过DMA(Direct Memory Access)方式对中心原子数据进行传输;3)合理设计软件cache,利用软件cache实现邻居原子数据的读取;4)在从核定制超越函数,避免从核访问超越函数时的离散访存;5)利用寄存器通信实现从核间任务分步流水优化.经过优化,单核组较主核串行取得了12.89倍的加速,较Intel Xeon E5-2620 v4处理器取得了8.7倍的加速.本文还对Silicon-Crystal应用进行了可扩展性测试及分析,实验结果证明Silicon-Crystal应用在神威太湖之光平台上具有良好的可扩展性.
Silicon-Crystal application uses molecular dynamics(MD)to simulate the thermal conductivity of crystals and uses Tersoff potential function to simulate silicon crystals growth.we successfully ported the Silicon-Crystal application on the Sunway TaihuLight using the Sunway Athread,and proposed five main optimizations for the problem caused by the memory constraints of SW26010 heterogeneous many-core processor:1)Prefetch the parameters required for the calculation to LDM;2)Transfer central particle data by DMA;3)Design the software cache reasonably and use the software cache to read the neighbor particle data;4)Customize the transcendental functions in CPE(Computing Processing Element)to avoid the discrete access when the CPE calls the transcendental functions;5)Use register level communication to realize step-to-step pipeline and double buffering between CPEs.After implementing these optimizations,the single-core group has achieved 12.89 times speed-up than the serial version in MPE(Management Processing Element),and 8.7 times speed-up than the serial version in the Intel Xeon E5-2620 v4 processor.This paper also conducted the scalability tests and analysis on the Silicon-Crystal application.Experimental results show that the Silicon-Crystal application has good scalability on the Sunway TaihuLight.
作者
朱文强
傅游
梁建国
郭强
花嵘
ZHU Wen-qiang;FU You;LIANG Jian-guo;GUO Qiang;HUA Rong(College of Computer Science and Engineering,Shandong University of Science and Technology,Qingdao 266590,China;Shandong Computer Science Center(National Supercomputing Center in Jinan),Jinan 250101,China)
出处
《小型微型计算机系统》
CSCD
北大核心
2021年第6期1313-1320,共8页
Journal of Chinese Computer Systems
基金
国家重点研发计划项目(2017YFB0202002)资助
山东省重点研发计划项目(2019GGX101066)资助.
