5,453 research outputs found
A low-cost parallel implementation of direct numerical simulation of wall turbulence
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
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
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