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Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko
SiPS, INESC-ID/IST Universidade Tecnica de Lisboa Rua Alves Redol 9, 1000-029 Lisbon, Portugal
Parallel Computing (August 2011)

@article{pratas2011fine,

   title={Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems},

   author={Pratas, F. and Trancoso, P. and Sousa, L. and Stamatakis, A. and Shi, G. and Kindratenko, V.},

   journal={Parallel Computing},

   year={2011},

   publisher={Elsevier}

}

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Currently, we are facing a situation where applications exhibit increasing computational demands and where a large variety of parallel processor systems are available. In this paper we focus on exploiting fine-grain parallelism for three applications with distinct characteristics: a Bioinformatics application (MrBayes), a Molecular Dynamics application (NAMD), and a Database application (TPC-H). We assess, side-by-side, the performance of the three applications on general-purpose multi-core processors, the Cell Broadband Engine (Cell/BE), and Graphical Processor Units GPUs. Our results indicate that application performance depends on the characteristics of the parallel architectures and on the computational requirements of the core functions of the respective applications. For MrBayes the best overall performance is achieved on general-purpose multi-core processors, for NAMD on the Cell/BE, and for TPC-H on GPUs.
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