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; 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.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 与生物医学相关的细胞尺度过程发生在由 数百万到数亿原子。原子分子动力学模拟 这些结构中有深入的洞察力。这样的模拟 极高要求，需要佩斯卡尔计算资源。数据集 结果是如此之大，以至于现有工作站的物理记忆过于限制， 处理和可视化功率以及质量存储以有效处理它们。常见的 可视化计算，例如静电势场的三维图 跨越长长的轨迹，可以使用标准桌面工作站花费几分钟。因此， 研究人员对大型模拟结果的互动分析被中断和减慢，因此 几乎是不可能的； Petascale分子动力学数据处理 系统（MDDPS）旨在克服台式计算机的缺点 工作站并提供必要的硬件功能，以实现实用的交互式 挑战性佩斯卡尔数据集的分析和可视化。 Petascale MDDPS是一个集群 用作凝聚力单元以提供高性能的紧密耦合计算机的紧密耦合计算机 Petascale MD模拟所需的数据分析功能。 该系统由 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进行资源。 而两个资源的软件 包裹NAMD和VMD对当前的计算机硬件进行了充分的调整，并利用 Petascale MDDPS硬件的下一代功能需要其他软件 发展。