Implementation of Hybrid Alignment Algorithm for Protein Database Search on the SW26010 Many-Core Processor

In biological research, biology sequence alignment algorithm aims to find similarities between sequences. As the size of biological database increases exponentially, the complexity of sequence alignment process also increases rapidly, which results in a large amount of computational time. The Sunway TaihuLight is the world’s first heterogeneous supercomputer with peak performance over 100 PFlops and provides a new hardware platform for database search. In this paper we present an efficient method of protein database search based on Sunway TaihuLight supercomputer. Furthermore, we also optimize protein database search on Sunway TaihuLight to give full play to the performance of the SW26010 processor. In our proposed approach, we design hybrid sequence alignment by combining the Smith-Waterman local alignment algorithm and the Needleman-Wunsch global alignment algorithm. The protein database search is paralleled by message passing interface (MPI) and accelerated thread library (Athread). Experiment results with the Swiss-Prot database show that our implementation can effectively leverage the SW26010 processor’s special hardware architecture and achieve a speedup to 15.91 times on a single node. In addition, we expand the scale to 64 nodes to test the scalability of the parallel method on the Sunway TaihuLight system, and the results show that our parallel implementation of protein database search have a good expansibility and reliability.