PETASCALE MOLECULAR DYNAMICS DATA PROCESSING

千万亿级分子动力学数据处理

• 批准号: 8172048
• 负责人: John H Stone
• 金额: $ 6.7万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8172048
• 关键词: Cells; Computer Hardware; Computer Retrieval of Information on Scientific Projects Database; Computer Workstations; Computer software; Computers; Coupled; Data Analyses; Data Set; Electrostatics; Funding; Grant; Imagery; Institution; Maps; Performance; Process; Research; Research Personnel; Resources; Source; Speed; Structure; System; United States National Institutes of Health; computerized data processing; computing resources; 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. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 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。这 结果数据集是如此之大，以至于现有工作站过于限制 物理记忆，处理和可视化功率以及质量存储至有效 处理它们。常见的可视化计算，例如三维 跨长轨迹的静电势场的地图，可以使用几分钟的时间使用 标准桌面工作站。结果，研究人员的互动分析 大型模拟结果被中断并减慢了 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工作站和 提供必要的硬件功能以实现实用的交互式分析 和挑战性佩斯卡尔数据集的可视化。 Petascale MDDPS是 一组紧密耦合的计算机，它们作为一个凝聚力单元提供 Petascale MD模拟所需的高性能数据分析功能。 该系统由协同存储，分析和可视化节点组成 通过单独的高速网络在内部连接到外部资源。 虽然资源的软件包NAMD和VMD都经过良好调整 到当前的计算机硬件，利用 Petascale MDDPS硬件需要额外的软件开发。