NDLI: Thread-cooperative, bit-parallel computation of levenshtein distance on GPU

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Thread-cooperative, bit-parallel computation of levenshtein distance on GPU

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Thread-cooperative, bit-parallel computation of levenshtein distance on GPU

Content Provider	ACM Digital Library
Author	Moure, Juan Carlos Marco-Sola, Santiago Espinosa, Antonio Chacón, Alejandro Ribeca, Paolo
Abstract	Approximate string matching is a very important problem in computational biology; it requires the fast computation of string distance as one of its essential components. Myers' bit-parallel algorithm improves the classical dynamic programming approach to Levenshtein distance computation, and offers competitive performance on CPUs. The main challenge when designing an efficient GPU implementation is to expose enough SIMD parallelism while at the same time keeping a relatively small working set for each thread. In this work we implement and optimise a CUDA version of Myers' algorithm suitable to be used as a building block for DNA sequence alignment. We achieve high efficiency by means of a cooperative parallelisation strategy for (1) very-long integer addition and shift operations, and (2) several simultaneous pattern matching tasks. In addition, we explore the performance impact obtained when using features specific to the Kepler architecture. Our results show an overall performance of the order of tera cells updates per second using a single high-end Nvidia GPU, and factor speedups in excess of 20x with respect to a sixteen-core, non-vectorised CPU implementation.
Starting Page	103
Ending Page	112
Page Count	10
File Format	PDF
ISBN	9781450326421
DOI	10.1145/2597652.2597677
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-06-10
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Simd Gpu Myer's algorithm Cuda
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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