Parallel FPGA-based all pairs shortest paths for sparse networks: A human brain connectome case study

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.