使用OpenMP的DeepMD-Kit并行化策略：提高基于机器学习的分子模拟效率

IF 3.8 2区计算机科学 Q2 COMPUTER SCIENCE, HARDWARE & ARCHITECTURE

IEEE Transactions on Computers Pub Date : 2025-08-04 DOI:10.1109/TC.2025.3595078

Qi Du;Feng Wang;Chengkun Wu

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引用次数: 0

摘要

DeepMD-kit支持基于深度学习的分子动力学（MD）模拟，这些模拟需要高效的并行化来利用现代HPC架构。在这项工作中，我们使用先进的OpenMP策略优化DeepMD-kit，以提高基于ARMv8处理器的服务器上的可扩展性和计算效率。我们的优化包括神经网络推理的数据并行性、力计算加速、numa感知内存管理和同步减少，与基线实现相比，加速高达4.1美元，内存带宽效率提高82%。强大的缩放分析证明了在中等核心数量下的超线性加速，改进了工作负载平衡和矢量化计算。然而，由于同步开销的增加，在超大规模上仍然存在挑战。

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Parallelization Strategies for DeepMD-Kit Using OpenMP: Enhancing Efficiency in Machine Learning-Based Molecular Simulations

DeepMD-kit enables deep learning-based molecular dynamics (MD) simulations that require efficient parallelization to leverage modern HPC architectures. In this work, we optimize DeepMD-kit using advanced OpenMP strategies to improve scalability and computational efficiency on an ARMv8 processor-based server. Our optimizations include data parallelism for neural network inference, force calculation acceleration, NUMA-aware memory management, and synchronization reductions, leading to up to

$4.1\boldsymbol{\times}$

speedup and 82% higher memory bandwidth efficiency compared to the baseline implementation. Strong scaling analysis demonstrates superlinear speedup at mid-range core counts, with improved workload balancing and vectorized computations. However, challenges remain at ultra-large scales due to increasing synchronization overhead.

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来源期刊

IEEE Transactions on Computers 工程技术-工程：电子与电气

CiteScore

6.60

自引率

5.40%

发文量

199

审稿时长

6.0 months

期刊介绍： The IEEE Transactions on Computers is a monthly publication with a wide distribution to researchers, developers, technical managers, and educators in the computer field. It publishes papers on research in areas of current interest to the readers. These areas include, but are not limited to, the following: a) computer organizations and architectures; b) operating systems, software systems, and communication protocols; c) real-time systems and embedded systems; d) digital devices, computer components, and interconnection networks; e) specification, design, prototyping, and testing methods and tools; f) performance, fault tolerance, reliability, security, and testability; g) case studies and experimental and theoretical evaluations; and h) new and important applications and trends.