NDLI: Parallel Algorithms for Approximate String Matching with k Mismatches on CUDA

Content Provider	IEEE Xplore Digital Library
Author	Yu Liu Longjiang Guo Jinbao Li Meirui Ren Keqin Li
Copyright Year	2012
Abstract	Approximate string matching using the k-mismatch technique has been widely applied to many fields such as virus detection and computational biology. The traditional parallel algorithms are all based on multiple processors, which have high costs of computing and communication. GPU has high parallel processing capability, low cost of computing, and less time of communication. To the best of our knowledge, there is no any parallel algorithm for approximate string matching with k mismatches on GPU. With a new parallel programming model based on CUDA, we present three parallel algorithms and their implementations on GPU, namely, the thread parallel algorithm, the block-thread parallel algorithm, and the OPT-block-thread parallel algorithm. The OPT-block thread parallel algorithm can take full advantage of the powerful parallel capability of GPU. Furthermore, it balances the load among the threads and optimizes the execution time with the memory model of GPU. Experimental results show that compared with the traditional sequential algorithm on CPU, our best parallel algorithm on GPU in this paper achieves speedup of 40¨C80.
Starting Page	2414
Ending Page	2422
File Size	505571
Page Count	9
File Format	PDF
ISBN	9781467309745
DOI	10.1109/IPDPSW.2012.298
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-05-21
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	CUDA Parallel algorithm Hamming distance Instruction sets Approximate string matching Complexity theory Parallel algorithms Kernel GPU Graphics processing unit
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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