Nanoscale molecular dynamics (NAMD) is an open source free molecular dynamics simulation software based on the Charm+ + parallel programming model,which can quickly simulate millions of atomic-level macromolecules in large-scale parallel computer system.SunwayTaihuLight System is a supercomputer developed independently by China,which has a theoretical peak performance of 125.4 Pflop/s with 10 million cores,and the LINPACK efficiency is no less than 70％.The NAMD partitions the atoms in the space,divides the force in the calculation,fully exposes the parallelism of the singlestep simulation,and controls the load balance through the CHARM+ +.In response to the characteristics of NAMD simulation calculation,we port and optimize NAMD calculation code,allowing it to run better on the supercomputer SunwayTaihuLight System.After optimization,the performance is improved by nearly 20 times,and the performance of the single core group is 3 times higher than Intel XeonE5-2650V2.Scalability at present parallel degree reaches about 3.25 millions of cores,which makes a breakthrough of a million of cores.%纳米级粒度分子动力学NAMD是基于Charm++并行编程模型的开源免费分子动力学模拟软件,能够在大规模并行计算机上快速模拟百万原子级别的大分子体系.太湖之光是中国自主研发的超级计算机,峰值性能为125.4 Pflop/s,共有1 000多万个核心,整机Linpack效率不低于70％.NAMD在空间上对原子进行划分,在计算上对力进行划分,充分曝露出单步模拟的并行度,并通过CHARM++对负载平衡进行调控.针对NAMD进行模拟计算时的特点,移植并优化了NAMD的核心计算代码,让其能够更好地运行在超级计算机神威太湖之光上,优化后性能提高了近20倍,单个核组的性能较IntelXeonE5-2650 v2提高3倍.扩展性方面目前至多可达到325万核的并行度,突破百万核大关.
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