PETASCALE MOLECULAR DYNAMICS DATA PROCESSING

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 与生物医学相关的细胞尺度过程发生在由以下物质组成的分子组件中 几百万到几亿个原子。原子分子动力学模拟 提供了对它们的功能机制的洞察；这样的模拟 都是极其苛刻的，并且需要千万亿级的计算资源。这些数据集 结果是如此之大，以至于现有工作站的物理内存太有限， 处理和可视化能力，以及高效处理它们的海量存储。普普通通 可视化计算，例如静电势场的三维地图 在漫长的轨迹中，使用标准台式机工作站可能需要几分钟时间。结果, 研究人员对大型模拟结果的交互分析被中断并因此减慢 几乎是不可能的；Petascale分子动力学数据处理 MDDPS系统是为克服台式计算机的缺点而设计的 工作站，并提供必要的硬件功能，以实现实用的交互 具有挑战性的PB级数据集的分析和可视化。Petascale MDDPS是一个星系团 作为一个聚合单元运行的紧密耦合的计算机，以提供高性能 Petascale MD模拟所需的数据分析能力。该系统由以下部分组成 内部和外部连接的协同存储、分析和可视化节点 通过单独的高速网络提供资源。虽然资源的两个软件 NAMD和VMD包针对当前的计算机硬件进行了很好的调整，利用 Petascale MDDPS硬件的下一代功能需要额外的软件 发展。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Biomedically-relevant cell-scale processes take place in molecular assemblies made of millions to hundreds of millions of atoms. Atomistic molecular dynamics simulation of these structures provides insight into their functional mechanisms; such simulations are extremely demanding and require petascale computational resources. The datasets that result are so large that existing workstations are too limited  in physical memory, processing and visualization power, and mass storage  to efficiently handle them. Common visualization calculations, such as three-dimensional maps of electrostatic potential fields across a long trajectory, can take minutes using a standard desktop workstation. As a result, a researcher's interactive analysis of a large simulation result is interrupted and slowed so much as to be virtually impossible; the Petascale Molecular Dynamics Data Processing System (MDDPS) is designed to overcome the shortcomings of desktop computer workstations and provides the necessary hardware features to enable practical interactive analysis and visualization of challenging petascale datasets. The Petascale MDDPS is a cluster of tightly coupled computers that operate as a cohesive unit to provide high-performance data analysis capabilities required by petascale MD simulations. The system is composed of synergistic storage, analysis, and visualization nodes connected internally and to external resources by separate high-speed networks. While both of the Resource's software packages, NAMD and VMD, are well-tuned to current computer hardware, harnessing the next-generation capabilities of the Petascale MDDPS hardware requires additional software development.