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Parallel Megabase DNA Sequence Comparison with OpenCL

Published: 16 December 2015 Publication History

Abstract

Biological sequence comparison is a very common task in Bioinformatics applications. Many parallel solutions have been proposed for this problem, using different HPC platforms, programmed usually with platform-specific languages and frameworks. With this approach, it is difficult to port solutions among different platforms such as CPUs and GPUs, for instance. To tackle this problem, this paper proposes and evaluates an OpenCL parallel solution for Biological Sequence Comparison, which was integrated to the CUDAlign Megabase Sequence Comparison tool. The evaluation of our solution shows we were able to obtain a program for CPUs and GPUs (NVidia and AMD) with basically the same OpenCL code. In addition, in the comparison with SW# and CUDAlign optimized CUDA codes, we show that the performance of our OpenCL version has comparable and, many times, superior performance.
  1. Parallel Megabase DNA Sequence Comparison with OpenCL

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    cover image Guide Proceedings
    HIPC '15: Proceedings of the 2015 IEEE 22nd International Conference on High Performance Computing (HiPC)
    December 2015
    476 pages
    ISBN:9781467384889

    Publisher

    IEEE Computer Society

    United States

    Publication History

    Published: 16 December 2015

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