Communication Protocols and Message Formats for BLAST Parallelization on Cluster Systems

With the widespread use of BLAST, many parallel versions of BLAST on cluster systems are announced, but little work has been done for the parallel execution in the search for individual query sequence on BLAST on cluster systems. Since we can improve not only throughput but also response time, the techniques for parallel execution of BLAST on cluster systems in the search for individual query sequence deserve to be developed. This paper develops communication protocols and message formats to reduce the communication overheads for the parallel execution of BLAST in the search for individual query sequence on cluster systems. The developed communication protocols and message formats are implemented on a new version of BLAST on cluster systems. The new version of BLAST is named Hyper-BLAST in this paper. In this paper, we also measured the throughput and response time of Hyper-BLAST on various cluster systems. It turned out that considerable performance improvement of BLAST on cluster systems can be achieved through parallel execution in the search for individual query sequence on small or middle-sized cluster systems. On 1-way 64-node system, Hyper-BLAST achieved scalable speedup up to 63 processors for 1000-5000 length query size.