5,453 research outputs found

    A low-cost parallel implementation of direct numerical simulation of wall turbulence

    Full text link
    A numerical method for the direct numerical simulation of incompressible wall turbulence in rectangular and cylindrical geometries is presented. The distinctive feature resides in its design being targeted towards an efficient distributed-memory parallel computing on commodity hardware. The adopted discretization is spectral in the two homogeneous directions; fourth-order accurate, compact finite-difference schemes over a variable-spacing mesh in the wall-normal direction are key to our parallel implementation. The parallel algorithm is designed in such a way as to minimize data exchange among the computing machines, and in particular to avoid taking a global transpose of the data during the pseudo-spectral evaluation of the non-linear terms. The computing machines can then be connected to each other through low-cost network devices. The code is optimized for memory requirements, which can moreover be subdivided among the computing nodes. The layout of a simple, dedicated and optimized computing system based on commodity hardware is described. The performance of the numerical method on this computing system is evaluated and compared with that of other codes described in the literature, as well as with that of the same code implementing a commonly employed strategy for the pseudo-spectral calculation.Comment: To be published in J. Comp. Physic

    Exploiting different levels of parallelism in the biological sequence comparison problem

    Get PDF
    In the last years the fast growth of bioinformatics field has atracted the attention of computer scientists. At the same time, de exponential growth of databases that contains biological information (such as protein and DNA data) demands great efforts to improve the performance of computational platforms. In this work, we investigate how bioinformatics applications benefit from parallel architectures that combine different alternatives to exploit coarse- and fine-grain parallelism. As a case of analysis, we study the performance behavior of the Ssearch application that implements the Smith-Waterman algorithm (SW), which is a dynamic programing approach that explores the similarity between a pair of sequences. The inherent large parallelism of the application makes it ideal for architectures supporting multiple dimensions of parallelism (thread-level parallelism, TLP; data-level parallelism, DLP; instruction-level parallelism, ILP). We study how this algorithm can take advantage of different parallel machines like the SGI Altix, IBM Power6, IBM Cell BE and MareNostrum machines. Our study includes a qualitative analysis of the parallelization opportunities and also the quantification of the performance in terms of speedup and execution time. These measures are collected taking into account the specific characteristics of each architecture. As an example, our results show that a share memory multiprocessor architecture (SMP) like the PowerPC 970MP of Marenostrum machine can surpasses a heterogeneous multi- processor machine like the current IBM Cell BE.Peer ReviewedPostprint (published version
    corecore