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arXiv 2104.08245physics.comp-phcs.DC
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面向数亿原子规模的基于电子结构的从头算分子动力学模拟

Towards Electronic Structure-Based Ab-Initio Molecular Dynamics Simulations with Hundreds of Millions of Atoms

Paderborn University(帕德博恩大学);ETH Zürich(苏黎世联邦理工学院);HPE Switzerland GmbH(惠普企业瑞士有限公司);Nextmol (Bytelab Solutions SL)(Nextmol(ByteLab Solutions SL));Barcelona Supercomputing Center (BSC)(巴塞罗那超级计算中心);University of Zurich(苏黎世大学)

Robert Schade, Tobias Kenter, Hossam Elgabarty, Michael Lass, Ole Schütt, Alfio Lazzaro, Hans Pabst, Stephan Mohr, Jürg Hutter, Thomas D. Kühne, Christian Plessl

AI总结:

本研究结合线性标度AIMD、稀疏线性代数、GPU混合精度计算及误差补偿方案,提出非正交化局部子矩阵方法NOLSM,将基于电子结构的从头算分子动力学模拟规模突破至1亿原子以上,在1536块A100上实现67.7%效率的324 PFLOP/s持续性能。

摘要:

我们将基于电子结构的从头算分子动力学(AIMD)的模拟规模突破至1亿原子以上,这一规模原本就连经典力场方法、新型神经网络与机器学习势函数都几乎难以达到。我们通过结合线性标度AIMD的创新、高效近似稀疏线性代数、GPU上的低精度与混合精度浮点计算,以及针对数值近似引入误差的补偿方案,实现了这一突破。本研究的核心是非正交化局部子矩阵方法(NOLSM),该方法对大规模并行计算系统具有极佳的扩展性,可将大型稀疏矩阵运算转化为高度并行的稠密矩阵运算,完美适配硬件加速器。我们验证了作为每个AIMD步骤核心的NOLSM方法:在1536块NVIDIA A100 GPU上运行时,其混合FP16/FP32精度下的持续性能可达324 PFLOP/s,对应效率为67.7%。

英文摘要:

We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine learning potentials. We achieve this breakthrough by combining innovations in linear-scaling AIMD, efficient and approximate sparse linear algebra, low and mixed-precision floating-point computation on GPUs, and a compensation scheme for the errors introduced by numerical approximations. The core of our work is the non-orthogonalized local submatrix method (NOLSM), which scales very favorably to massively parallel computing systems and translates large sparse matrix operations into highly parallel, dense matrix operations that are ideally suited to hardware accelerators. We demonstrate that the NOLSM method, which is at the center point of each AIMD step, is able to achieve a sustained performance of 324 PFLOP/s in mixed FP16/FP32 precision corresponding to an efficiency of 67.7% when running on 1536 NVIDIA A100 GPUs.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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