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This paper provides the first comparison of performance and energy efficiency of high productivity computing systems based on FPGA (Field-Programmable Gate Array) and GPU (Graphics Processing Unit) technologies. The search for higher performance compute solutions has recently led to great interest in heterogeneous systems containing FPGA and GPU accelerators. While these accelerators can provide significant performance improvements, they can also require much more design effort than a pure software solution, reducing programmer productivity. The CUDA system has provided a high productivity approach for programming GPUs. This paper evaluates the High-Productivity Reconfigurable Computer (HPRC) approach to FPGA programming, where a commodity CPU instruction set architecture is augmented with instructions which execute on a specialised FPGA co-processor, allowing the CPU and FPGA to co-operate closely while providing a programming model similar to that of traditional software. To compare the GPU and FPGA approaches, we select a set of established benchmarks with different memory access characteristics, and compare their performance and energy efficiency on an FPGAbased Hybrid-Core system with a GPU-based system. Our results show that while GPUs excel at streaming applications, highproductivity reconfigurable computing systems outperform GPUs in applications with poor locality characteristics and low memory bandwidth requirements.

In many application domains, data are represented using large graphs involving millions of vertices and edges. Graph analysis algorithms, such as finding short paths and isomorphic subgraphs, are largely dominated by memory latency. Large cluster-based computing platforms can process graphs efficiently if the graph data can be partitioned, and on a smaller scale partitioning can be used to allocate graphs to low-latency onchip RAMs in reconfigurable devices. However, there are many graph classes, such as scale-free social networks, which lack the locality to make partitioning graph data an efficient solution to the latency problem and are far too large to fit in onchip RAMs and caches. In this paper, we present a framework for reconfigurable hardware acceleration of these large-scale graph problems that are difficult to partition and require highlatency off-chip memory storage. Our reconfigurable architecture tolerates off-chip memory latency by using a memory crossbar that connects many parallel identical processing elements to shared off-chip memory, without a traditional cached memory hierarchy. Quantitative comparison between the software and hardware performance of a graphlet counting case-study shows that our hardware implementation outperforms a quad-core software implementation by 10 times for large graphs. This speedup includes all software and IO overhead required, and reduces execution time for this common bioinformatics algorithm from about 2 hours to just 12 minutes. These results demonstrate that our methodology for accelerating graph algorithms is a promising approach for efficient parallel graph processing.

This paper proposes a highly parallel and scalable reconfigurable design for the All-Pairs Shortest-Paths (APSP) algorithm for very sparse networks. Our work is motivated by a computationally intensive bioinformatics application that employs this memory-latency bound algorithm. The proposed design methodology takes advantage of distributed on-chip memory resources of modern FPGAs to reduce accesses to high-latency off-chip memories. We develop design optimisations that yield different FPGA configurations which are selected at run time based on the input graph data. Using human brain network data, we are able to achieve performance results superior to those from multi-core CPU and GPU, while attaining linear scaling over the number of processors introduced. Our FPGA-based APSP design is over 10 times faster than a quad-core CPU implementation and 2-5 times faster than an AMD Cypress GPU implementation.

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