论文标题

从头开始将分子动力学的极限扩展到100亿原子

Extending the limit of molecular dynamics with ab initio accuracy to 10 billion atoms

论文作者

Guo, Zhuoqiang, Lu, Denghui, Yan, Yujin, Hu, Siyu, Liu, Rongrong, Tan, Guangming, Sun, Ninghui, Jiang, Wanrun, Liu, Lijun, Chen, Yixiao, Zhang, Linfeng, Chen, Mohan, Wang, Han, Jia, Weile

论文摘要

高性能计算以及从使用第一原理方法生成的数据训练的神经网络模型,在现代超级计算机上的空间和时间尺度方面,具有\ textIt {ab intio}分子动力学的应用大大提高了应用。以前的最先进的方法可以在整个Summit SuperCupter中获得1亿原子的每天1-2美元的纳秒分子动力学模拟。在本文中,我们通过算法和系统创新的全面方法大大减少了记忆足迹和计算时间。神经网络模型通过模型制表,内核融合和冗余去除压缩。然后,在GPU和ARM体系结构上实现了诸如定制内核加速度,激活函数的制表,MPI+OpenMP并行化之类的优化。铜系统的测试结果表明,优化的代码可以扩展到Fugaku和Summit的整个机器,相应的系统尺寸可以将$ 134 $扩展到前所未有的170亿原子。强劲的缩放量表的耗资13.5美元,原子铜系统表明,解决的时间可以更快7倍,每天达到$ 11.2 $纳米秒。这项工作为基于{\ IT启用}精确度的前所未有的大规模分子动力学模拟打开了大门,并且可以潜在地用于研究更现实的应用,例如金属的机械性能,半导体设备,电池等。该论文还详细介绍了对相关的优化技术详细介绍的详细信息。

High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on modern supercomputers. Previous state-of-the-art can achieve $1-2$ nanoseconds molecular dynamics simulation per day for 100-million atoms on the entire Summit supercomputer. In this paper, we have significantly reduced the memory footprint and computational time by a comprehensive approach with both algorithmic and system innovations. The neural network model is compressed by model tabulation, kernel fusion, and redundancy removal. Then optimizations such as acceleration of customized kernel, tabulation of activation function, MPI+OpenMP parallelization are implemented on GPU and ARM architectures. Testing results of the copper system show that the optimized code can scale up to the entire machine of both Fugaku and Summit, and the corresponding system size can be extended by a factor of $134$ to an unprecedented $17$ billion atoms. The strong scaling of a $13.5$-million atom copper system shows that the time-to-solution can be 7 times faster, reaching $11.2$ nanoseconds per day. This work opens the door for unprecedentedly large-scale molecular dynamics simulations based on {\it ab initio} accuracy and can be potentially utilized in studying more realistic applications such as mechanical properties of metals, semiconductor devices, batteries, etc. The optimization techniques detailed in this paper also provide insight for relevant high-performance computing applications.

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