A Multi GPU Read Alignment Algorithm with Model-based Performance Optimization

Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka
Tokyo Institute of Technology, 2-12-1-W8-33, Ookayama, Meguro-ku, Tokyo, 152-8552, Japan
Lecture Notes in Computer Science Volume 7851, pp 270-277, 2013


   title={A Multi GPU Read Alignment Algorithm with Model-based Performance Optimization},

   author={Drozd, Aleksandr and Maruyama, Naoya and Matsuoka, Satoshi},

   journal={Book name Springer’s Lecture Notes in Computer Science},





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This paper describes a performance model for read alignment problem, one of the most computationally intensive tasks in bioinformatics. We adapted Burrows Wheeler transform based index to be used with GPUs to reduce overall memory footprint. A mathematical model of computation and communication costs was developed to find optimal memory partitioning for index and queries. Last we explored the possibility of using multiple GPUs to reduce data transfers and achieved super-linear speedup. Performance evaluation of experimental implementation supports our claims and shows more than 10fold performance gain per device.
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