IEEE/ACM Trans Comput Biol Bioinform. 2020 May-Jun;17(3):804-816. doi: 10.1109/TCBB.2018.2805709. Epub 2018 Feb 13.
Molecular dynamics (MD) is a computer simulation method of studying physical movements of atoms and molecules that provide detailed microscopic sampling on molecular scale. With the continuous efforts and improvements, MD simulation gained popularity in materials science, biochemistry and biophysics with various application areas and expanding data scale. Assisted Model Building with Energy Refinement (AMBER) is one of the most widely used software packages for conducting MD simulations. However, the speed of AMBER MD simulations for system with millions of atoms in microsecond scale still need to be improved. In this paper, we propose a parallel acceleration strategy for AMBER on the Tianhe-2 supercomputer. The parallel optimization of AMBER is carried out on three different levels: fine grained OpenMP parallel on a single CPU, single node CPU/MIC parallel optimization and multi-node multi-MIC collaborated parallel acceleration. By the three levels of parallel acceleration strategy above, we achieved the highest speedup of 25-33 times compared with the original program.
分子动力学（MD）是一种研究原子和分子物理运动的计算机模拟方法，它在分子尺度上提供了详细的微观采样。随着不断的努力和改进，MD 模拟在材料科学、生物化学和生物物理学中得到了广泛的应用，应用领域不断扩大，数据规模不断扩大。辅助模型构建与能量精炼（AMBER）是进行 MD 模拟最广泛使用的软件包之一。然而，对于百万个原子的系统，在微秒尺度上进行 AMBER MD 模拟的速度仍需要提高。在本文中，我们提出了一种在天河-2 超级计算机上的 AMBER 并行加速策略。在三个不同层次上对 AMBER 进行了并行优化：在单个 CPU 上进行细粒度的 OpenMP 并行，单个节点 CPU/MIC 并行优化，以及多节点多-MIC 协作并行加速。通过以上三个层次的并行加速策略，与原始程序相比，我们实现了最高 25-33 倍的加速。
