混合平台生物序列快速比对

S. Kedad-Sidhoum, F. Mendonca, Florence Monna, G. Mounié, D. Trystram
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引用次数: 5

摘要

今天,许多高性能计算平台使用混合架构,将多核处理器和gpu(图形处理单元)等硬件加速器结合在一起。提出了一种基于cpu和gpu的生物序列比较应用的任务调度新方法。这种策略被称为SWDUAL,它基于双重近似方案来确定哪些任务最适合在gpu上执行。目标是获得快速的执行时间并最小化每个PE(处理元素)上的空闲时间。它是使用主从模型实现的。将序列与五个公共基因组数据库进行比较的结果表明,与其他公共可用实现相比,该方法可以减少混合平台上的执行时间。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Fast Biological Sequence Comparison on Hybrid Platforms
Today, many high performance computing platforms use hybrid architectures combining multi-core processors and hardware accelerators like GPUs (Graphic Processing Units). This paper presents a new method for scheduling tasks for biological sequence comparison applications with CPUs and GPUs. This strategy is called SWDUAL and is based on a dual approximation scheme for determining which tasks are most suitable to be executed on the GPUs. The objective is to obtain fast execution time and minimize the idle time on each PE (Processing Element). It is implemented using a master-slave model. Results obtained when sequences were compared to five public genomic databases show that this method allows to reduce the execution time on hybrid platforms when compared to other public available implementations.
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