PETASCALE MOLECULAR DYNAMICS DATA PROCESSING

千万亿级分子动力学数据处理

• 批准号: 8363662
• 负责人: John H Stone
• 金额: $ 6.63万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2012-09-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363662
• 关键词: Bioinformatics; Cells; Computer Hardware; Computer Workstations; Computer software; Computers; Coupled; Data Analyses; Data Set; Electrostatics; Funding; Grant; Imagery; Maps; Modeling; National Center for Research Resources; Performance; Principal Investigator; Process; Research; Research Infrastructure; Research Personnel; Resources; Source; Speed; Structure; System; United States National Institutes of Health; computerized data processing; computing resources; cost; design; insight; memory process; molecular assembly/self assembly; molecular dynamics; next generation; simulation; software development

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.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 生物医学相关的细胞规模的过程发生在分子组装， 数百万到数亿个原子。原子分子动力学模拟 这些结构提供了深入了解其功能机制;这种模拟 要求极高，需要千万亿次的计算资源。的数据集 结果是如此之大，以至于现有的工作站太有限  在物理存储器中， 处理和可视化能力，以及大容量存储  有效地处理它们。共同 可视化计算，例如静电势场的三维图 使用标准桌面工作站，可能需要几分钟的时间。因此，在本发明中， 研究人员对大型模拟结果的交互式分析被中断和减慢， 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，使实际的互动 具有挑战性的千万亿次数据集的分析和可视化。Petascale MDDPS是一个群集 紧密耦合的计算机，作为一个内聚单元运行，以提供高性能 千万亿次MD模拟所需的数据分析能力。 该系统包括 内部连接和外部连接的协同存储、分析和可视化节点 通过独立的高速网络提供资源。 虽然资源的软件 NAMD和VMD包已针对当前计算机硬件进行了良好调整，利用 Petascale MDDPS硬件的下一代功能需要额外的软件 发展