MSPA-MCS: Data-Driven Parallelization of Time in Molecular Dynamics Simulations

传统的并行化策略不能很好地扩展时，计算工作量来自于需要模拟到长的时间跨度，而不是从大的状态空间。分子动力学模拟是一个重要的应用领域，但这也是一个瓶颈.该模拟器开发了一种新的方法来并行化分子动力学，这是基于观察，模拟通常发生在一个背景下，丰富的数据从其他相关的模拟。他们使用这些数据来并行化时域，这产生了一个更可扩展的算法。这种方法是基于观察，长的时间跨度往往在模拟多个时间尺度。精细尺度是负责大的计算工作。然而，细尺度的重要贡献往往是它们对粗尺度的影响。研究人员使用降阶建模来识别重要的粗尺度效应，使用聚类和机器学习来动态确定正在执行的模拟与先验数据之间的关系。他们使用ODE和控制理论进行稳定性分析，不确定性估计和系统识别。研究人员使用各种实际应用在纳米和生物纳米材料中验证他们的技术。选择的应用程序的重要性源于这样一个事实，即材料在历史上曾在人类进步中发挥了关键作用。它们的重要性体现在这样一个事实上，即人类进步的时代，如铁器时代和青铜时代，都是以促进这种进步的材料命名的。纳米和生物纳米材料是基于对原子尺度的基本理解而设计的，它预示着另一场革命，将导致诸如节能汽车、抗灾结构和治疗疾病的新方法等产品的出现。研究人员的技术消除了这种发展的一个重要障碍。此外，参与研究的学生获得了跨学科研究的培训。在HBCU联合任命一名合作者，确保了代表性不足的学生也能从这项工作中受益。

Conventional parallelization strategies do not scalewell when the computational effort arises from theneed to simulate to long time spans, rather than fromlarge state space. Molecular Dynamics simulationsconstitute an important class of applications wherethis proves to be a bottleneck. The investigatorsdevelop a new approach to parallelization of MolecularDynamics, which is based on the observation thatsimulations typically occur in a context rich in datafrom other related simulations. They use such data toparallelize the time domain, which yields a morescalable algorithm. This approach is based on theobservation that long time-spans are often encounteredin simulations with multiple time scales. The finescales are responsible for the large computationaleffort. However, the important contribution of thefine-scales is often to the effect they have on thecoarse scale. The investigators use reduced ordermodeling to identify important coarse scale effects.They use clustering and machine learning todynamically determine the relationship between thesimulation being performed and prior data. They useODE and controls theory for stability analysis,uncertainty estimation, and system identification.The investigators validate their techniques using avariety of realistic applications in nano and bio-nanomaterials. The importance of the applications chosenarises from the fact that materials have historicallyplayed a pivotal role in human progress. An indicationof their importance lies in the fact that eras ofhuman progress, such as the iron age and the bronzeage, are named after the materials that contributed tosuch progress. Nano and bio-nano materials, designedbased on fundamental understanding at the atomicscale, promise yet another revolution, leading toproducts such as fuel efficient cars, disasterresistant structures, and new ways of treatingdiseases. The investigators' techniques remove animportant impediment to such developments.Furthermore, the students involved obtain training ininterdisciplinary research. Inclusion of acollaborator with a joint appointment at an HBCUensures that under-represented students too benefitfrom this work.