Extending the limit of LR-TDDFT on two different approaches: Numerical algorithms and new Sunway heterogeneous supercomputer

IF 2 4区 计算机科学 Q2 COMPUTER SCIENCE, THEORY & METHODS Parallel Computing Pub Date : 2024-05-04 DOI:10.1016/j.parco.2024.103085
Qingcai Jiang , Zhenwei Cao , Xinhui Cui , Lingyun Wan , Xinming Qin , Huanqi Cao , Hong An , Junshi Chen , Jie Liu , Wei Hu , Jinlong Yang
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Abstract

First-principles time-dependent density functional theory (TDDFT) is a powerful tool to accurately describe the excited-state properties of molecules and solids in condensed matter physics, computational chemistry, and materials science. However, a perceived drawback in TDDFT calculations is its ultrahigh computational cost O(N5N6) and large memory usage O(N4) especially for plane-wave basis set, confining its applications to large systems containing thousands of atoms. Here, we present a massively parallel implementation of linear-response TDDFT (LR-TDDFT) and accelerate LR-TDDFT in two different aspects: (1) numerical algorithms on the X86 supercomputer and (2) optimizations on the heterogeneous architecture of the new Sunway supercomputer. Furthermore, we carefully design the parallel data and task distribution schemes to accommodate the physical nature of different computation steps. By utilizing these two different methods, our implementation can gain an overall speedup of 10x and 80x and efficiently scales to large systems up to 4096 and 2744 atoms within dozens of seconds.

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用两种不同方法扩展 LR-TDDFT 的极限:数值算法和新型 Sunway 异构超级计算机
第一原理时变密度泛函理论(TDDFT)是精确描述凝聚态物理、计算化学和材料科学中分子和固体激发态性质的有力工具。然而,TDDFT 计算的一个明显缺点是超高的计算成本 O(N5∼N6)和超大的内存占用 O(N4),特别是对于平面波基集,这使得它只能应用于包含成千上万原子的大型系统。在这里,我们提出了线性响应 TDDFT(LR-TDDFT)的大规模并行实现,并从两个不同方面加速了 LR-TDDFT:(1)X86 超级计算机上的数值算法;(2)新的 Sunway 超级计算机异构架构上的优化。此外,我们还精心设计了并行数据和任务分配方案,以适应不同计算步骤的物理特性。通过利用这两种不同的方法,我们的实现可以获得 10 倍和 80 倍的整体加速,并在数十秒内高效扩展到高达 4096 和 2744 个原子的大型系统。
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来源期刊
Parallel Computing
Parallel Computing 工程技术-计算机:理论方法
CiteScore
3.50
自引率
7.10%
发文量
49
审稿时长
4.5 months
期刊介绍: Parallel Computing is an international journal presenting the practical use of parallel computer systems, including high performance architecture, system software, programming systems and tools, and applications. Within this context the journal covers all aspects of high-end parallel computing from single homogeneous or heterogenous computing nodes to large-scale multi-node systems. Parallel Computing features original research work and review articles as well as novel or illustrative accounts of application experience with (and techniques for) the use of parallel computers. We also welcome studies reproducing prior publications that either confirm or disprove prior published results. Particular technical areas of interest include, but are not limited to: -System software for parallel computer systems including programming languages (new languages as well as compilation techniques), operating systems (including middleware), and resource management (scheduling and load-balancing). -Enabling software including debuggers, performance tools, and system and numeric libraries. -General hardware (architecture) concepts, new technologies enabling the realization of such new concepts, and details of commercially available systems -Software engineering and productivity as it relates to parallel computing -Applications (including scientific computing, deep learning, machine learning) or tool case studies demonstrating novel ways to achieve parallelism -Performance measurement results on state-of-the-art systems -Approaches to effectively utilize large-scale parallel computing including new algorithms or algorithm analysis with demonstrated relevance to real applications using existing or next generation parallel computer architectures. -Parallel I/O systems both hardware and software -Networking technology for support of high-speed computing demonstrating the impact of high-speed computation on parallel applications
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