Massively parallel genomic sequence search on the Blue Gene/P architecture

Heshan Lin, Pavan Balaji, Ruth Poole, Carlos Sosa, Xiaosong Ma, Wu-chun Feng
2008 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis  
This paper presents our first experiences in mapping and optimizing genomic sequence search onto the massively parallel IBM Blue Gene/P (BG/P) platform. Specifically, we performed our work on mpiBLAST, a parallel sequence-search code that has been optimized on numerous supercomputing environments. In doing so, we identify several critical performance issues. Consequently, we propose and study different approaches for mapping sequence-search and parallel I/O tasks on such massively parallel
more » ... tectures. We demonstrate that our optimizations can deliver nearly linear scaling (93% efficiency) on up to 32,768 cores of BG/P. In addition, we show that such scalability enables us to complete a large-scale bioinformatics problem -sequence searching a microbial genome database against itself to support the discovery of missing genes in genomes -in only a few hours on BG/P. Previously, this problem was viewed as computationally intractable in practice.
doi:10.1109/sc.2008.5222005 dblp:conf/sc/LinBPSMF08 fatcat:pwjowi5w6ba5vnnbupejeejm4a