面向国产超算平台的反应分子动力学(ReaxFF MD)模拟移植与优化

REACTIVE MOLECULAR DYNAMICS (REAXFF MD) SIMULATION PORTING AND OPTIMIZATION FOR DOMESTIC SUPERCOMPUTING PLATFORMS

  • 摘要: PuReMD软件是基于ReaxFF反应力场的高效、开源的实现,但现有的PuReMD在"嵩山"超级计算机平台上的实现无法利用DCU加速卡设备,模拟效率低。为了充分利用"嵩山"超级计算机平台的加速器资源,提升PuReMD的运行效率,利用gprof对PuReMD程序进行热点分析,将计算密集且具有良好并行性的热点函数根据HIP-C重写为设备函数,并设计主机端与设备端的数据传输,实现了PuReMD-DCU版本。实验结果表明,PuReMD-DCU相对于串行版本的PuReMD在 H2O 和 Al2O3 原子系统上分别取得了45.92和9.74的加速比。PuReMD-DCU可以为约瑟夫森结在"嵩山"超级计算机平台上的模拟提供支持,并且能够为分子动力学模拟的其他力场面向"嵩山"平台的移植与优化奠定研究基础。

     

    Abstract: The PuReMD software is an efficient and open- source implementation based on the ReaxFF force field. However, the existing PuReMD implementation on the "Songshan" supercomputer platform cannot utilize the DCU accelerator devices, resulting in low simulation efficiency. To fully leverage the accelerator resources on the "Songshan" supercomputer platform and improve the operational efficiency of PuReMD, a PuReMD- DCU version was developed. This involved utilizing gprof for hotspot analysis of the PuReMD program, rewriting computationally intensive and parallelizable hotspot functions in HIP- C as device functions, and designing data transfers between the host and device sides. Experimental results demonstrate that PuReMD- DCU achieved acceleration ratios of 45.92 and 9.74 on H2O and Al2O3 atomic systems, respectively, compared with the serial version of PuReMD. PuReMD- DCU provides support for simulating Josephson junctions on the "Songshan" supercomputer platform and establishes a research foundation for the porting and optimization of other force fields for molecular dynamics simulations targeting the "Songshan" platform.

     

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