CI-P: Collaborative Research: Large-Scale FPGA-Centric Computing with Molecular Dynamics

CI-P：协作研究：以 FPGA 为中心的大规模分子动力学计算

• 批准号: 1205593
• 负责人: Martin Herbordt
• 金额: $ 5.24万
• 依托单位: Trustees of Boston University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-01 至 2014-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1205593&HistoricalAwards=false
• 关键词: CI; Collaborative; Research; Large; Scale

Together with theory and experimentation, computer simulation now constitutes the ?third pillar? of scientific inquiry, enabling researchers to build and test models of complex phenomena that cannot be replicated in the laboratory. The method of Molecular Dynamics simulation in particular is critical: applications range from the practical, e.g., drug design, to basic research in understanding disease processes. The overall goal is to give the Molecular Dynamics user community the compute capability to conduct transformative research via scalable, cost-effective, high-performance, general-purpose systems built from off-the-shelf components. The objective of this research is to bridge the many orders-of-magnitude gap between the largest current simulations and the potential physical systems to be studied.Three fundamental issues limiting performance are (i) computational efficiency per chip area, (ii) power density, which is reaching the limit of economical cooling methods, and (iii) the bottleneck between processing and communication devices. All three are addressed by Large-Scale Reconfigurable Computing using Field Programmable Gate Arrays (FPGAs). FPGAs are commodity integrated circuits whose circuitry can be configured, or programmed, in the field. Their reconfigurable architecture gives them the ability to obtain maximum efficiency for a particular application while at the same time drawing less than a quarter the power of a conventional processing device. And because FPGAs are the core components in internet routers, they are built to handle flexible high-throughput communication. This planning award is to investigate the novel system design to use the same FPGAs for communication and for computation. This approach has several advantages. First, it mitigates the critical bottleneck caused by the separation of functions among multiple devices. Second, FPGA-based communication gives the flexibility either to use standard protocols, or to use innovative application-aware routing that enables important patterns, such as the Fast Fourier Transform, to be routed congestion-free. Finally, FPGAs are well-suited for Molecular Dynamics computation allowing the hierarchical data-movement to be addressed through innovative routing, load-balancing, and arithmetic.

与理论和实验一起，计算机模拟现在构成了第三个支柱？在科学探究中，使研究人员能够在实验室中建立和测试复杂现象的模型。 分子动力学仿真的方法至关重要：应用范围从实用，例如药物设计到理解疾病过程的基础研究。 总体目标是使分子动力学用户社区通过可扩展，成本效益，高性能，通用系统进行转换性研究的计算能力，从而由现成的组件构建。 这项研究的目的是弥合当前最大模拟与要研究的潜在物理系统之间的许多魔力差距。第三个基本问题限制性能是（i）每个芯片区域的计算效率，（ii）功率密度，即功率密度，即经济冷却方法的极限，以及（iii）在加工和通信设备之间进行瓶颈。 使用字段可编程阵列（FPGA）通过大规模重新配置计算来解决这三个方面。 FPGA是商品集成电路，其电路可以在现场配置或编程。 它们的可重构体系结构使他们能够获得特定应用程序的最大效率，而同时绘制的绘制小于四分之一的传统处理设备的功率。 而且，由于FPGA是Internet路由器中的核心组件，因此它们的构建是为了处理灵活的高通量通信。 该计划奖是要调查新型系统设计，以使用相同的FPGA进行通信和计算。 这种方法具有几个优势。 首先，它减轻了由多个设备之间功能分离引起的临界瓶颈。 其次，基于FPGA的通信使灵活性要么使用标准协议，要么使用创新的应用程序感知的路由，从而使重要模式（例如快速的傅立叶变换）无路由拥堵。 最后，FPGA非常适合分子动力学计算，从而可以通过创新的路由，负载平衡和算术来解决层次数据移动。