Higher global bandwidth requirement for many applications and lower network cost have motivated the use of the Dragonfly network topology for high performance computing systems. In this paper we present the architecture of the Cray Cascade system, a distributed memory system based on the Dragonfly [1] network topology. We describe the structure of the system, its Dragonfly network and the routing algorithms. We describe a set of advanced features supporting both mainstream high performance computing applications and emerging global address space programing models.We present a combination of performance results from prototype systems and simulation data for large systems. We demonstrate the value of the Dragonfly topology and the benefits obtained through extensive use of adaptive routing.

Dynamic programming for approximate string matching is a large family of different algorithms, which vary significantly in purpose, complexity, and hardware utilization. Many implementations have reported impressive speed-ups, but have typically been point solutions -highly specialized and addressing only one or a few of the many possible options. The problem to be solved is creating a hardware description that implements a broad range of behavioral options without losing efficiency due to feature bloat. We report a set of three component types that address different parts of the approximate string matching problem. This allows each application to choose the feature set required, then make maximum use of the FPGA fabric according to that application's specific resource requirements. Multiple, interchangeable implementations are available for each component type. We show that these methods allow the efficient generation of a large, if not complete, family of accelerators for this application. This flexibility was obtained while retaining high performance: We have evaluated a sample against serial reference codes and found speed-ups of from 150× to 400× over a high-end PC.

Modeling of molecule interactions often uses two or more successive models of increasing complexity. Rigid models based on correlation techniques are common as early screening passes-to detect interactions worth costlier examination-and are often at the heart of later passes as well. Even these rigid models are time-consuming when applied to large models at 10 3 − 10 5 different three-axis rotations. This paper presents an FPGA structure for performing the correlations efficiently by using a systolic array for 3-D correlation and arithmetic tailored to the application. The system includes a novel addressing technique for performing a three-axis rotation of a 3-D voxel model using modest amounts of logic and nearly no cost in time or buffer space. We compare our FPGA implementation with one on a PC using the standard transform-based method and find a speed-up of a factor of 200. We present extensions for handling implementation technologies with different performance characteristics and for handling models too large to fit on-chip.

Abstract. Modeling of molecule interactions often uses two or more successive models of increasing complexity. Rigid models based on correlation techniques are common as early screening passes-to detect interactions worth costlier examination-and are often at the heart of later passes as well. Even these rigid models are time-consuming when applied to large models at 10 3 − 10 5 different three-axis rotations. This paper presents an FPGA structure for performing the correlations efficiently by using a systolic array for 3-D correlation and arithmetic tailored to the application. The system includes a novel addressing technique for performing a three-axis rotation of a 3-D voxel model using modest amounts of logic and nearly no cost in time or buffer space. We compare our FPGA implementation with one on a PC using the standard transform-based method and find a speed-up of a factor of 200. We present extensions for handling implementation technologies with different performance characteristics and for handling models too large to fit on-chip.

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