Performance analysis of general-purpose computation on commodity graphics hardware: A case study using bioinformatics

Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology

Volumn 48, Issue 3, 2007, Pages 209-221

  Liu, Weiguo ^a   Müller Wittig, Wolfgang ^a   Schmidt, Bertil ^b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b Division of Engineering Science and Technology   (Singapore)

Author keywords

Dynamic programming; GPGPU; Graphics hardware; Pairwise sequence alignment; Performance prediction

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL COMPLEXITY; DATA MINING; DATABASE SYSTEMS; DYNAMIC PROGRAMMING; PIPELINE PROCESSING SYSTEMS; PROGRAM PROCESSORS;

GRAPHICS HARDWARE; PAIRWISE SEQUENCE ALIGNMENT; PERFORMANCE PREDICTION;

COMPUTER GRAPHICS;

EID: 34548458883     PISSN: 13875485     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11265-007-0064-7     Document Type: Article

References (15)

1. J. Owens, D. Luebke, N. Govindaraju, M. Harris, J. Kruger, A. Lefohn and T. Purcell, "A Survey of General-Purpose Computation on Graphics Hardware," in Eurographics 2005, 2005, pp. 21-51.
2. D. Manocha, "General-Purpose Computations Using Graphics Processors," Computer, vol. 38, no. 8, 2005, pp. 85-88.
3. J. Kruger and R. Westermann, "Linear Algebra Operators for GPU Implementation of Numerical Algorithms," ACM Trans. Graph, vol. 22, 2003, pp. 908-916.
4. P. Agarwal, S. Krishnan, N. Mustafa and S. Venkatasubramanian, "Streaming Geometric Optimization Using Graphics Hardware," in Proc. 11th European Symposium on Algorithms, 2003.
5. N. Govindaraju, B. Lloyd, W. Wang, M. Lin and D. Manocha, "Fast Computation of Database Operations Using Graphics Processors," in SIGMOD'04, 2004, pp. 215-226.
6. F. Xu and K. Mueller, "Ultra-fast 3d Filtered Backprojection on Commodity Graphics Hardware," in IEEE International Symposium on Biomedical Imaging'04, 2004.
7. W. Liu, B. Schmidt, G. Voss, A. Schröder and W. Müller-Wittig, "Bio-sequence Database Scanning on a GPU," in Proceedings of 20th IEEE International Parallel & Distributed Processing Symposium (HICOMB Workshop), 2006.
8. W. Liu, B. Schmidt, G. Voss and W. Müller-Wittig, "GPU-clustalw: Using Graphics Hardware to Accelerate Multiple Sequence Alignment," in 13th Annual IEEE International Conference on High Performance Computing (HiPC 2006), LNCS 4297, 2006, pp. 363-374.
9. Y. Liu, W. Huang, J. Johnson and S. Vaidya, "GPU Accelerated Smith-Waterman," in International Conference on Computational Science 2006 (ICCS 2006), LNCS 3994, pp. 188-195.
10. D. Horn, M. Houston and P. Hanrahan, "ClawHMMer: A Streaming HMMer-Search Implementation," in Proceedings of Supercomputing 2005, 2005.
11. M. Charalambous, P. Trancoso and A. Stamatakis, "Initial Experiences Porting a Bioinformatics Application to a Graphics Processor," in Proceedings of 10th Panhellenic Conference on Informatics, 2005.
12. I. Buck, K. Fatahalian and P. Hanrahan, "Evaluating GPU Performance for Numerical and Scientific Applications," in Proceedings the 2004 ACM. Workshop on General-Purpose Computing on Graphics Processors, 2004.
13. T. Smith and M. Waterman, "Identification of Common Molecular Subsequences," J. Mol. Biol., vol. 147, 1981, pp. 195-197.
14. J. Kessenich, D. Baldwin, and R. Rost, "The OpenGL Shading Language, Document Revision 59." http://www.opengl.org/documentation/oglsl.html, Tech. Rep., 2005.
15. W. Dally, P. Hanrahan, M. Erez, T. Knight, F. Labonte, J.-.H.A., N. Jayasena, U. Kapasi, A. Das, J. Gummaraju and I. Buck, "Merrimac: Supercomputing with Streams," in SC'03, Phoenix, Arizona, November 2003.