摘要
AMBER是一款主流的分子动力学模拟软件,用于研究分子体系内的微观运动状态。为利用神威太湖之光的海量计算资源加速AMBER软件模拟分子体系的运动过程,将AMBER软件移植到SW26010处理器的主核上建立主从加速模型,实现AMBER软件的从核并行化设计。在从核并行化的基础上提出主从异步流水化方案,利用SW26010处理器从核的局部数据缓存和直接内存存取通道技术,解决从核访存速度过低及并行访存带宽受限的问题,并通过SIMD指令将部分从核代码向量化,进一步提升AMBER软件在神威太湖之光平台上的计算性能。测试结果表明,AMBER热点函数的计算性能较优化前约提升15倍,单核组的整体性能较Intel Xeon Platinum 8163约提升4.6倍。
As the mainstream Molecular Dynamics(MD)simulation software,AMBER is widely used for researches in the microscopic movements in molecular systems.In order to use the massive computing resources of Sunway TaihuLight to accelerate the AMBER-based simulation of the movement process of molecular systems,AMBER is migrated to the master core of the SW26010 processor to build a master-slave acceleration model,so as to realize AMBER’s parallelization design for slave core.On this basis the master-slave asynchronous pipelining scheme is proposed.The local data cache Local Data Memory(LDM)and Direct Memory Access(DMA)channel techniques of slave core of SW26010 are used to address the low memory access speed and limited parallel memory access bandwidth of slave core.Also,part of slave core codes is vectorized through the SIMD command to further improve the computational performance of AMBER on Sunway TaihuLight.Test results show that the computational performance of the optimized AMBER hotspot functions is improved by 15 times,and the overall performance of the single-core group is improved by 4.6 times compared with the Intel Xeon Platinum 8163.
作者
彭龙
陈俊仕
安虹
PENG Long;CHEN Junshi;AN Hong(School of Computer Science and Technology,University of Science and Technology of China,Hefei 230031,China)
出处
《计算机工程》
CAS
CSCD
北大核心
2020年第12期12-20,共9页
Computer Engineering
基金
国家重点研发计划(2018YFB0204102)。
关键词
分子动力学模拟
神威太湖之光
异构众核处理器
并行优化
异步流水化
Molecular Dynamics(MD)simulation
Sunway TaihuLight
heterogeneous many-core processor
parallel optimization
asynchronous pipelining
