Parallelizing Exact and Approximate String Matching via Inclusive Scan on a GPU

Yasuaki Mitani, Fumihiko Ino, Kenichi Hagihara
Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
Osaka University, 2017


   title={Parallelizing Exact and Approximate String Matching via Inclusive Scan on a GPU},

   author={Mitani, Yasuaki and Ino, Fumihiko and Hagihara, Kenichi},

   journal={IEEE Transactions on Parallel and Distributed Systems},




In this study, to substantially improve the runtimes of exact and approximate string matching algorithms, we propose a tribrid parallel method for bit-parallel algorithms such as the Shift-Or and Wu-Manber algorithms. Our underlying idea is to interpret bit-parallel algorithms as inclusive-scan operations, which allow these bit-parallel algorithms to run efficiently on a graphics processing unit (GPU); we achieve this speed-up here because inclusive-scan operations not only eliminate duplicate searches between threads but also realize a GPU-friendly memory access pattern that maximizes memory read/write throughput. To realize our ideas, we first define two binary operators and then present a proof regarding the associativity of these operators, which is necessary for the parallelization of the inclusive-scan operations. Finally, we integrate the inclusive-scan scheme into a previous segmentation-based scheme to maximize search throughput, identifying the best tradeoff point between synchronization cost and duplicate work. Through our experiments, we compared our proposed method with previous segmentation-based methods and indexing-based sequence aligners. For online string matching, our proposed method performed 6.7-16.7 times faster than previous methods, achieving a search throughput of up to 1.88 terabits per second (Tbps) on a GeForce GTX TITAN X GPU. We therefore conclude that our proposed method is quite effective for decreasing the runtimes of online string matching of short patterns.
Rating: 2.1/5. From 5 votes.
Please wait...

* * *

* * *

Featured events

Hida Takayama, Japan

The Third International Workshop on GPU Computing and AI (GCA), 2018

Nagoya University, Japan

The 5th International Conference on Power and Energy Systems Engineering (CPESE), 2018

MediaCityUK, Salford Quays, Greater Manchester, England

The 10th International Conference on Information Management and Engineering (ICIME), 2018

No. 1037, Luoyu Road, Hongshan District, Wuhan, China

The 4th International Conference on Control Science and Systems Engineering (ICCSSE), 2018

Nanyang Executive Centre in Nanyang Technological University, Singapore

The 2018 International Conference on Cloud Computing and Internet of Things (CCIOT’18), 2018

HGPU group © 2010-2018 hgpu.org

All rights belong to the respective authors

Contact us: