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The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis

机译:异构计算对生物分子模拟和分析工作流程的影响

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The field of biomolecular simulation has matured to where detailed, accurate, and functionally relevant information that complements experimental data about the structure, dynamics, and interactions of biomolecules can now be routinely discovered. This has been enabled by access to large-scale and heterogeneous high-performance computing resources, including special-purpose hardware. The improved performance of modern simulation methods coupled with hardware advances is shifting the rate-limiting steps of common biomolecular simulations of small to moderately sized systems from the generation of data (for example, via production molecular dynamics simulations that used to take weeks or even months) to the pre- and postprocessing phases of the workflow, namely, simulation setup and data processing, management, and analysis. Because the computational resources that are optimal for generating data aren't necessarily the same as for processing that data, access to heterogeneous computational resources enables a broader exploration of biomolecular structure and dynamics by facilitating distinct aspects of typical biomolecular simulation workflows, which might not be as efficient on a one-size-fits-all computational platform.
机译:生物分子模拟领域已经发展成熟,现在可以常规地发现详细,准确和功能相关的信息,以补充有关生物分子的结构,动力学和相互作用的实验数据。通过访问大规模和异构的高性能计算资源(包括专用硬件)可以实现这一点。现代仿真方法的性能提高以及硬件的进步,正将数据生成过程从小型到中型系统的常见生物分子仿真的限速步骤从数据生成(例如,通过过去数周甚至数月的生产分子动力学仿真)转变为)到工作流程的前处理和后处理阶段,即模拟设置和数据处理,管理和分析。由于最适合用于生成数据的计算资源不一定与用于处理该数据的计算资源相同,因此,通过支持典型的生物分子模拟工作流程的不同方面,对异构计算资源的访问可以对生物分子的结构和动力学进行更广泛的探索。在适合所有人的计算平台上效率很高。

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