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首页> 外文期刊>Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological >Parallelization of CPPTRAJ Enables Large Scale Analysis of Molecular Dynamics Trajectory Data
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Parallelization of CPPTRAJ Enables Large Scale Analysis of Molecular Dynamics Trajectory Data

机译：CPPTRAJ的并行化能够对分子动力学轨迹数据进行大规模分析

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摘要

Advances in biomolecular simulation methods and access to large scale computer resources have led to a massive increase in the amount of data generated. The key enablers have been optimization and parallelization of the simulation codes. However, much of the software used to analyze trajectory data from these simulations is still run in serial, or in some cases many threads via shared memory. Here, we describe the addition of multiple levels of parallel trajectory processing to the molecular dynamics simulation analysis software CPPTRAJ. In addition to the existing OpenMP shared-memory parallelism, CPPTRAJ now has two additional levels of message passing (MPI) parallelism involving both across-trajectory processing and across-ensemble processing. All three levels of parallelism can be simultaneously active, leading to significant speed ups in data analysis of large datasets on the NCSA Blue Waters supercomputer by better leveraging the many available nodes and its parallel file system. (C) 2018 Wiley Periodicals, Inc.
机译：生物分子仿真方法的进步和对大规模计算机资源的访问导致产生的数据量大幅增加。关键推动者一直是仿真代码的优化和并行化。但是，用于分析来自这些模拟的轨迹数据的大部分软件仍然是串行运行，或者在某些情况下通过共享内存进行许多线程。在这里，我们描述了对分子动力学模拟分析软件CPPTRAJ的多级并行轨迹处理。除了现有的OpenMP共享 - 内存并行性之外，CPPTRAJ现在还具有两个额外的消息传递（MPI）并行性，涉及跨轨迹处理和跨整体处理。所有三个级别的并行性都可以同时活动，导致NCSA蓝色Waters超级计算机上的大型数据集的数据分析中的显着增速，通过更好地利用许多可用节点及其并行文件系统。 （c）2018 Wiley期刊，Inc。

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