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Multi-core computing: A novel accelerating method for chemometrics calculation

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS 2009年第1期96卷 94-97页

作者： Zhang, Zhi-Min Liang, Yi-Zeng Xu, Qing-Song Cent S Univ Res Ctr Modernizat Chinese Med Coll Chem & Chem Engn Changsha 410083 Hunan Peoples R China Cent S Univ Sch Math Sci & Comp Technol Changsha 410083 Peoples R China

The higher speed is the eternal pursuit of any chemometric algorithm. In order to take full advantage of the multi-core processor's computing resources (the prevailing current of personal computer) and accelerate the time-consuming algorithms in chemometrics, a novel multi-core computing method is introduced. Leave-one-out cross-validation is taken as an example to show the powerful capability of the multi-core computing. The comparison results show that the execution time drops rapidly with the increasing number of computing cores, which demonstrates that the multi-core computing is a promising tool for solving computing-intensive and data-intensive problems in chemometrics. (C) 2008 Published by Elsevier B.V.

关键词： Multi-core computing Cross-validation parallel algorithm Message Passing Interface

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A Lattice Boltzmann Method for Image Denoising

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IEEE TRANSACTIONS ON IMAGE PROCESSING 2009年第12期18卷 2797-2802页

作者： Chang, Qianshun Yang, Tong Chinese Acad Sci Inst Appl Math Acad Math & Syst Sci Beijing Peoples R China City Univ Hong Kong Dept Math Hong Kong Hong Kong Peoples R China

In this paper, we construct a Lattice Boltzmann scheme to simulate the well known total variation based restoration model, that is, ROF model. The advantages of the Lattice Boltzmann method include the fast computational speed and the easily implemented fully parallel algorithm. A conservative property of the LB method is discussed. The macroscopic PDE associated with the LB algorithm is derived which is just the ROF model. Moreover, the linearized stability of the method is analyzed. The numerical computations demonstrate that the LB algorithm is efficient and robust. Even though the quality of the restored images is slightly lower than those by using the ROF model, the restored images of the LB method are satisfactory. Furthermore, computational speed of the LB method is much faster than ROF model. In general, CPU time of the LB method for restored images is about one tenth of ROF model.

关键词： algorithm of denoising fast algorithm image restoration lattice Boltzmann method parallel algorithm

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Some theoretical challenges in digital geometry: A perspective

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DISCRETE APPLIED MATHEMATICS 2009年第16期157卷 3362-3371页

作者： Asano, Tetsuo Brimkov, Valentin E. Barneva, Reneta P. SUNY Coll Buffalo Dept Math Buffalo NY 14222 USA Japan Adv Inst Sci & Technol Sch Informat Sci Nomi Ishikawa 9231292 Japan SUNY Coll Fredonia Dept Comp Sci Fredonia NY 14063 USA

In recent years image analysis has become a research field of exceptional significance, due to its relevance to real life problems in important societal and governmental sectors, Such as medicine, defense, and security. The explicit purpose of the present Perspective is to suggest a number of strategic objectives for theoretical research, with all emphasis oil the combinatorial approach in image analysis. Most of the proposed objectives relate to the need to make the theoretical foundations of combinatorial image analysis better integrated within a number of well-established subjects of theoretical computer science and discrete applied mathematics, such as the theory of algorithms and problem complexity, combinatorial optimization and polyhedral combinatorics, integer and linear programming, and computational geometry. Published by Elsevier B.V.

关键词： Combinatorial image analysis Digital geometry Computational geometry Complexity theory Polyhedral reconstruction parallel algorithm In-place algorithm Voronoi diagram Zone diagram

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Fast Tensor-Product Solvers: Partially Deformed Three-dimensional Domains

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JOURNAL OF SCIENTIFIC COMPUTING 2009年第1期39卷 28-48页

作者： Bjontegaard, Tormod Maday, Yvon Ronquist, Einar M. Norwegian Univ Sci & Technol Dept Math Sci N-7491 Trondheim Norway Univ Paris 06 Lab Jacques Louis Lions Paris France

We discuss the numerical solution of partial differential equations in a particular class of three-dimensional geometries;the two-dimensional cross section (in the xy-plane) can have a general shape, but is assumed to be invariant with respect to the third direction. Earlier work has exploited such geometries by approximating the solution as a truncated Fourier series in the z-direction. In this paper we propose a new solution algorithm which also exploits the tensor-product feature between the xy-plane and the z-direction. However, the new algorithm is not limited to periodic boundary conditions, but works for general Dirichlet and Neumann type of boundary conditions. The proposed algorithm also works for problems with variable coefficients as long as these can be expressed as a separable function with respect to the variation in the xy-plane and the variation in the z-direction. For problems where the new method is applicable, the computational cost is very competitive with the best iterative solvers. The new algorithm is easy to implement, and useful, both in a serial and parallel context. Numerical results demonstrating the superiority of the method are presented for three-dimensional Poisson and Helmholtz problems using both low order finite elements and high order spectral element discretizations.

关键词： Fast solver Tensor-product Partial differential equation parallel algorithm

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A parallel computing algorithm for 16S rRNA probe design

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JOURNAL OF parallel AND DISTRIBUTED COMPUTING 2006年第12期66卷 1546-1551页

作者： Zhu, Dianhui Fofanov, Yuriy Willson, Richard C. Fox, George E. Univ Houston Dept Comp Sci Houston TX 77204 USA Univ Houston Dept Chem Engn Houston TX 77204 USA Univ Houston Dept Biol & Biochem Houston TX 77204 USA

With the continuing rapid increase in the number of available 16S ribosomal RNA (rRNA) sequences, it is a significant computational challenge to efficiently design 16S rRNA targeted probes. In our previous work, we designed a fast software tool called ProkProbePicker (PPP) that takes 0(log N) time for a worst-case scenario search. Despite this improvement, it can still take many hours for PPP to extract probes for all the clusters in a phylogenetic tree. Herein, a parallelized version of PPP is described. When run on 80 processors, this version of PPP took only 67 min to extract probes, while some 87 h were needed by the sequential version of PPP. The speedup increased linearly with the increase of CPU numbers, which revealed the outstanding scalability of the parallelized version of PPP. (C) 2006 Elsevier Inc. All rights reserved.

关键词： 16S rRNA targeted probes genetic affinity parallel algorithm

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Application of the Krawczyk-Moore-Jones algorithm to Electric Circuit Analysis and Its Further Development

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JAPAN JOURNAL OF INDUSTRIAL AND APPLIED MATHEMATICS 2009年第2-3期26卷 145-167页

作者： Okumura, Kohshi Hiroshima Inst Technol Fac Appl Informat Sci Hiroshima Japan

This paper surveys applications of Krawczyk-Moore-Jones's algorithm and presents its further developments. The application is focused on nonlinear electric circuit analysis. The further developments are described ... 详细信息

关键词： interval operation Krawczyk-Moore-Jones's algorithm parallel algorithm FPGA implementation Gray code all solutions

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Communication contention in APN list scheduling algorithm

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Science in China(Series F) 2009年第1期52卷 59-69页

作者： TANG XiaoYong LI KenLi PADUA Divid School of Computer and Communication Hunan University Changsha 410082 China Oriental Science & Technology College Hunan Agricultural University Changsha 410128 China Department of Computer Science University of Illinois at Urbana-Champaign Champaign 61801 USA

Task scheduling is an essential aspect of parallel process system. This NP-hard problem assumes fully connected homogeneous processors and ignores contention on the communication links. However, as arbitrary processor network （APN）, communication contention has a strong influence on the execution time of a parallel application. This paper investigates the incorporation of contention awareness into task scheduling. The innovation is the idea of dynamically scheduling edges to links, for which we use the earliest finish communication time search algorithm based on shortest-path search method. The other novel idea proposed in this paper is scheduling priority based on recursive rank computation on heterogeneous arbitrary processor network. In the end, to reduce time complexity of algorithm, a parallel algorithm is proposed and speedup O（PPE） is achieved. The comparison study, based on both randomly generated graphs and the graphs of some real applications, shows that our scheduling algorithm significantly surpasses classic and static communication contention awareness algorithm, especially for high data transmission rate parallel application.

关键词： list scheduling arbitrary processor network DAG communication contention parallel algorithm

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parallel algorithms for continuous competitive location problems

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OPTIMIZATION METHODS & SOFTWARE 2008年第5期23卷 779-791页

作者： Redondo, Juana L. Fernandez, Jose Garcia, Inmaculada Ortigosa, Pilar M. Univ Almeria Dept Comp Architecture & Elect Almeria Spain Univ Murcia Dept Stat & Operat Res Murcia Spain

A continuous location problem in which a firm wants to set up a single new facility in a competitive environment is considered. Other facilities offering the same product or service already exist in the area. Both the location and the quality of the new facility are to be found so as to maximize the profit obtained by the firm. This is a hard-to-solve global optimization problem. An evolutionary algorithm called Universal Evolutionary Global Optimizer (UEGO) seems to be the best procedure to cope with it, but the algorithm needs several hours of CPU time for solving large instances. In this paper, four parallelizations of UEGO are presented. They all are coarse-grain methods which differ in their migratory policies. A computational study is carried out to compare the performance of the parallel algorithms. The results show that one of the parallelizations always gives the best objective function value and has an almost linear speed-up for up to 16 processing elements for large instances.

关键词： parallel algorithm coarse-grain method migratory policy evolutionary algorithm continuous location computational study

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parallel rapid relaxation inversion of 3D magnetotelluric data

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Applied Geophysics 2009年第1期6卷 77-83,104页

作者：林昌洪谭捍东佟拓中国地质大学地质过程与矿产资源国家重点实验室北京100083 中国地质大学(北京)地球物理与信息技术学院北京100083

We implement a parallel algorithm with the advantage of MPI （Message Passing Interface） to speed up the rapid relaxation inversion for 3D magnetotelluric data. We test the parallel rapid relaxation algorithm with synthetic and real data. The execution efficiency of the algorithm for several different situations is also compared. The results indicate that the parallel rapid relaxation algorithm for 3D magnetotelluric inversion is effective. This parallel algorithm implemented on a common PC promotes the practical application of 3D magnetotelluric inversion and can be suitable for the other geophysical 3D modeling and inversion.

关键词： Magnetotelluric MPI 3D rapid relaxation inversion parallel algorithm

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Studies of Stock Leverage Effect Model Based on parallel algorithm

Studies of Stock Leverage Effect Model Based on Parallel Alg...

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2006年国际电子、工程及科学领域的分布式计算和应用学术研讨会

作者： Yu LIANG,Xi-nan ZHAO School of Business Administration,Northeastern University Shenyang,Liaoning,China Quan-bo GE Dept of Electrical Automation,Shanghai Maritime University, Shanghai,China

parallel algorithm was introduced into the estimation and forecasting of stock return *** the stock return rnodel, discrete event risk was described by random jump-diffusion process and the leverage effect was described by asymmetric Autoregression Conditional Heteroscedasticity *** samples were classified into five groups according to the existing of day-of-the-week *** estimation and the simulation were processed by parallel computing in five groups of *** empirical study on index of Shenzhen security market shows that parallel algorithm can not only increase the computing speed largely but also make the accuracy.

关键词： Jump-diffusion process Leverage Effect parallel algorithm Simulated annealing Stock Market

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