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

现在，计算机模拟与理论和实验一起构成了第三支柱。科学探究，使研究人员能够建立和测试无法在实验室复制的复杂现象的模型。分子动力学模拟的方法尤其关键：应用范围从药物设计等实际应用到了解疾病过程的基础研究。总体目标是为分子动力学用户社区提供计算能力，通过由现成组件构建的可扩展、经济高效、高性能的通用系统来进行变革性研究。这项研究的目标是弥合最大电流模拟和潜在物理系统之间的许多数量级的差距。限制性能的三个基本问题是(I)每芯片面积的计算效率，(Ii)即将达到经济冷却方法的极限的功率密度，以及(Iii)处理和通信设备之间的瓶颈。使用现场可编程门阵列(FGA)的大规模可重构计算解决了所有这三个问题。现场可编程门阵列是一种商用集成电路，其电路可以现场配置或编程。其可重新配置的体系结构使其能够获得特定应用的最大效率，同时消耗的功率不到传统处理设备的四分之一。由于现场可编程门阵列是互联网路由器的核心组件，因此它们是为处理灵活的高吞吐量通信而构建的。这一规划奖是为了研究使用相同的现场可编程门阵列进行通信和计算的新颖系统设计。这种方法有几个优点。首先，它缓解了多个设备之间的功能分离所造成的关键瓶颈。其次，基于现场可编程门阵列的通信提供了灵活性，既可以使用标准协议，也可以使用创新的应用感知型路由，从而实现快速傅立叶变换等重要模式的无拥塞路由。最后，现场可编程门阵列非常适合分子动力学计算，允许通过创新的路由、负载平衡和算术来处理分层数据移动。

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.