PETASCALE MOLECULAR DYNAMICS DATA PROCESSING

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 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 所产生的数据集非常大，以至于现有的工作站过于有限  在 物理内存、处理和可视化能力以及大容量存储  有效地 处理他们。常见的可视化计算，如三维 在长轨迹上的静电势场图，可能需要几分钟， 一个标准的桌面工作站。因此，研究人员的互动分析 一个大型的模拟结果被中断和减慢，以至于几乎 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的缺点， 提供了必要的硬件功能，以实现实用的交互式分析 和具有挑战性的千万亿次数据集的可视化。Petascale MDDPS是 一组紧密耦合的计算机，作为一个内聚单元运行， 千万亿次MD模拟所需的高性能数据分析能力。 该系统由协同存储、分析和可视化节点组成 通过独立的高速网络连接内部和外部资源。 虽然资源的两个软件包NAMD和VMD都经过了很好的调整， 到目前的计算机硬件，利用下一代的能力， Petascale MDDPS硬件需要额外的软件开发。

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.