Accelerating BLAST Computation on an FPGA-enhanced PC Cluster

Abstract

This paper introduces an FPGA-based scheme to accelerate mpiBLAST, which is a parallel sequence alignment algorithm for computational biology. Recent rapidly growing biological databases for sequence alignment require high-throughput storage and network rather than computing speed. Our scheme utilizes a specialized hardware configured on an FPGA-board which connects flash storage and other FPGA-boards directly. The specialized hardware configured on the FPGAs, we call a Data Stream Processing Engine (DSPE), take a role for preprocessing to adjust data for high-performance multi- and many- core processors simultaneously with offloading system-calls for storage access and networking. DSPE along the datapath achieves in-datapath computing which applies operations for data streams passing through the FPGA. Two functions in mpiBLAST are implemented using DSPE to offload operations along the datapath. The first function is database partitioning, which distributes the biological database to multiple computing nodes before commencing the BLAST processes. Using DSPE, we observe a 20-fold improvement in computation time for the database partitioning operation. The second function is an early part of the BLAST process that determines the positions of sequences for more detailed computations. We implement IDP-BLAST (In-datapath BLAST), which annotates positions in data streams from solid-state drives. We show that IDP-BLAST accelerates the computation time of the preprocess of BLAST by a factor of three hundred by offloading heavy operations to the introduced special hardware.