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

: Liu, Weiguo; Müller-Wittig, Wolfgang K.; Schmidt, Bertil


Journal of VLSI signal processing systems for signal, image and video technology 48 (2007), Nr.3, S.209-221
ISSN: 0922-5773
ISSN: 1573-109X
Fraunhofer IGD ()
graphic hardware; dynamic programming; performance analysis; general purpose computation on graphics processing unit (GPGPU); sequence alignment

Using modern graphics processing units for no-graphics high performance computing is motivated by their enhanced programmability, attractive cost/performance ratio and incredible growth in speed. Although the pipeline of a modern graphics processing unit (GPU) permits high throughput and more concurrency, they bring more complexities in analyzing the performance of GPU-based applications. In this paper, we identify factors that determine performance of GPU-based applications. We then classify them into three categories: data-linear, data-constant and computation-dependent. According to the characteristics of these factors, we propose a performance model for each factor. These models are then used to predict the performance of bio-sequence database scanning application on GPUs. Theoretical analyses and measurements show that our models can achieve precise performance predictions.