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Flexible, efficient and robust algorithm for parallel execution and coupling of components in a framework

COMPUTER PHYSICS COMMUNICATIONS 2006年第10期174卷 793-802页

作者： Toth, Gabor Univ Michigan Ctr Space Environm Modeling Ann Arbor MI 48109 USA

We describe a general algorithm suitable for executing and coupling components of a software framework on a parallel computer. The requirements of a flexible, efficient and robust algorithm are defined precisely, and the motivation for the requirements is demonstrated on several examples. In short, the requirements are the following: (i) the algorithm should allow arbitrary distribution of processors among the components, (ii) it should allow arbitrary coupling schedule between the components, (iii) it should not use any inter-processor communication other than already required by the components and their couplings, and (iv) it should never get into a dead-lock. We show that the proposed algorithm based on the Temporal and Predefined Ordering of Tasks (TPOT) satisfies all these requirements. The TPOT algorithm has been implemented in the Space Weather Modeling Framework. The flexibility and efficiency of the algorithm is demonstrated with several examples. (c) 2006 :Elsevier B.V. All rights reserved.

关键词： software framework concurrent execution parallel algorithm space weather

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A model-based parallel origin and for cryoTEM and its application orientation refinement algorithm to the study of virus structures

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JOURNAL OF STRUCTURAL BIOLOGY 2006年第1期154卷 1-19页

作者： Ji, YC Marinescu, DC Zhang, W Zhang, X Yan, XD Baker, TS Univ Cent Florida Sch Comp Sci Orlando FL 32816 USA Purdue Univ Dept Sci Biol W Lafayette IN 47907 USA Univ Calif San Diego Dept Chem & Biochem La Jolla CA 92093 USA Univ Calif San Diego Div Biol Sci La Jolla CA 92093 USA

We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called pO(2)R, has been used for the refinement of several virus structures, includine those of the 500 A diameter dengue virus (to 9.5 angstrom resolution), the 850 A mammalian reovirus (to better than 7 angstrom), and the 1800 angstrom paramecium bursaria chlorella virus (to 15 angstrom). (c) 2005 Elsevier Inc. All rights reserved.

关键词： virus structure determination 3D reconstruction orientation and origin refinement electron cryo-microscopy cryoTEM parallel algorithm cluster of PCs

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parallel algorithm for near tridiagonal Toeplitz equations on distributed-memory multicomputer

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Jisuanji Yanjiu yu Fazhan/Computer Research and Development 2004年第7期41卷 1281-1285页

作者： Shan, Run-Hong Gao, Feng Song, Jun-Qiang Li, Xiao-Mei Sch. of Comp. Sci. Natl. Univ. of Defense Technol. Changsha 410073 China Lab. of Antenna and Microwave Tech. Xidian Univ. Xi'an 710071 China

Making use of the special structure of near tridiagonal Toeplitz matrix, a new fast algorithm is presented to solve near tridiagonal Toeplitz equations. Based on the near LU factorization of tridiagonal Toeplitz matrix and by making use of the principle of divide and rule, a fast distributed parallel algorithm is put forward for near tridiagonal Toeplitz equations. By introducing Qing-Jiushao algorithm and special mathematic skill, the new parallel algorithm avoids redundant operations. Also proved in theory is that the algorithm's speedup is closed to linearity. Finally, numerical experiments show that the new parallel algorithm have a high parallel efficiency. And above all, if n is large enough, the speedup is approximate to linearity.

关键词： parallel algorithm Speedup Toeplitz Tridiagonal equations

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parallel algorithm for k-nearest-neighbor on reconfigurable meshes

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Jisuanji Yanjiu yu Fazhan/Computer Research and Development 2004年第9期41卷 1559-1564页

作者： Zhao, Jian-Yong Xu, Yin-Long Chen, Long-Bin Natl. High Performance Comp. Ctr. Dept. of Comp. Sci. and Technology Univ. of Sci. and Technol. of China Hefei 230027 China

Nearest neighbor query is a basic problem of computational geometry. As an extension of nearest neighbor query, k-nearest-neighbor is widely applied in the fields of VLSI design, data retrieval, pattern matching, graph processing, etc. A parallel algorithm is presented on a reconfigurable mesh of size N × N for k-nearest-neighbor search in a planar point set S of N points. The time complexity of this algorithm is O(k). It attains the lower bound of this problem.

关键词： K-nearest-neighbor parallel algorithm Reconfigurable mesh

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Study on parallel algorithms for power system small signal stability based on PC clusters

Study on parallel algorithms for power system small signal s...

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International Conference on Power Systems Technology (POWERCON)

作者： Li Fang Guo Jian Wu Zhongxi Zhou Xiaoxin China Electric Power Reserch China China Electric Power Reserch

ISBN: (纸本)9781424401109

With the interconnection of power systems, interarea low frequency oscillation occurs frequently, insufficient damping of the weak-interconnected power grid has become a serious issue affecting power system stability. Considering the high rank of algebraic and differential equations and the geographical distributed data of interconnected power systems, it is necessary to analyze small signal stability problems in parallel mode with distributed computers. Based on the 'Multi-port Inverse Matrix parallel algorithm' proposed by China EPRI, the parallel implementation methods of the Simultaneous Iteration algorithm and the Inverse Iteration/Rayleigh Quotient Iteration algorithm are described in detail in this paper. With the characteristics of limited communication time and good load balancing, the proposed parallel algorithms can run well on distributed PC clusters. Numerical simulation results on actual large-scale power systems show that the proposed algorithms are correct and efficient.

关键词： small signal stability parallel algorithm inverse iteration Rayleigh quotient iteration simultaneous iteration PC cluster power system

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BPA-A parallel shortest path algorithm for cluster-router

BPA-A parallel shortest path algorithm for cluster-router

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18th IASTED International Conference on parallel and Distributed Computing and Systems

作者： Zhang, Xiaoping Wu, Jianping Zhang, Ning Zhao, Youjian Tsinghua Univ 4-104 FIT Bldg Beijing 100084 Peoples R China

ISBN: (纸本)9780889866386

To keep up with the pace of fast development of Internet, cluster architecture has been proposed for next generation core routers. In a cluster router, parallel computation is expected. Computing shortest path tree (SPT) is a fundamental problem implementing OSPF, which is one of the most popular routing protocols. This paper presents a parallel algorithm BPA (Branching parallel algorithm) for computing SPT, analyzes the performance of BPA, and finally validates the BPA performance by experiments

关键词： cluster router shortest path shortest path tree parallel algorithm complexity

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parallel sequence alignment algorithm for clustering system

Parallel sequence alignment algorithm for clustering system

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PROLAMAT 2006 Conference on Knowledge Enterprise

作者： Chen, Yang Yu, Songnian Leng, Ming Shanghai Univ Sch Engn & Comp Sci Shanghai Peoples R China

ISBN: (纸本)0387344020

Sequence alignment is one of the most important fundamental operations in bioinformatics. It has been successfully applied to predict the function, structure and evolution of biological sequences. In this paper, the sequence alignment algorithms based on dynamic programming are analyzed and compared. We present a parallel algorithm for pairwise alignment and implement it on a clustering system with MPI. The experimental results demonstrate the effectiveness in performance promotion. We encapsulate the algorithm into a grid service for practical use.

关键词： bioinformatics sequence alignment parallel algorithm clustering system MPI

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Study on parallel Computing

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Journal of Computer Science & Technology 2006年第5期21卷 665-673页

作者：陈国良孙广中张云泉莫则尧 Anhui Province-MOST Key Co-Lab of High Performance Computing and Its Applications Department of Computer Science and Technology University of Science and Technology of China Hefei 230027 P.R. China Laboratory of Parallel Computing Institute of Software Chinese Academy of Sciences Beijing 100080 P.R. China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing 100088 P.R. China

In this paper, we present a general survey on parallel computing. The main contents include parallel computer system which is the hardware platform of parallel computing, parallel algorithm which is the theoretical base of parallel computing, parallel programming which is the software support of parallel computing. After that, we also introduce some parallel applications and enabling technologies. We argue that parallel computing research should form an integrated methodology of ＂architecture algorithm programming application＂. Only in this way, parallel computing research becomes continuous development and more realistic.

关键词： parallel computing parallel architecture parallel programming parallel algorithm parallel application

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Improved parallel Three-List algorithm for the Knapsack Problem without Memory Conflicts

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Journal of Southwest Jiaotong University(English Edition) 2006年第1期14卷 7-14页

作者：潘军李肯立李庆华 School of Computer Science and Technology Huazhong University of Science and Technology Wuhan 430074 China

Based on the two-list algorithm and the parallel three-list algorithm, an improved parallel three-list algorithm for knapsack problem is proposed, in which the method of divide and conquer, and parallel merging without memory conflicts are adopted. To find a solution for the n-element knapsack problem, the proposed algorithm needs O（2^3n/8） time when O（2^3n/8） shared memory units and O（2^n/4） processors are available. The comparisons between the proposed algorithm and 10 existing algorithms show that the improved parallel three-fist algorithm is the first exclusive-read exclusive-write （EREW） parallel algorithm that can solve the knapsack instances in less than O（2^n/2） time when the available hardware resource is smaller than O（2^n/2） , and hence is an improved result over the past researches.

关键词： Knapsack problem NP-Hard parallel algorithm Memory conflicts Hardware-time tradeoff

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parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2006年第3期27卷 352-362页

作者： Dudley, TJ Olson, RM Schmidt, MW Gordon, MS Villanova Univ Villanova PA 19085 USA Iowa State Univ Dept Chem Ames IA 50011 USA

A parallel algorithm for solving the coupled-perturbed MCSCF (CPMCSCF) equations and analytic nuclear second derivatives of CASSCF wave functions is presented. A parallel scheme for evaluating derivative integrals and their subsequent use in constructing other derivative quantities is described. The task of solving the CPMCSCF equations is approached using a parallelization scheme that partitions the electronic hessian matrix over all processors as opposed to simple partitioning of the 3 N solution vectors among the processors. The scalability of the current algorithm, up to 128 processors, is demonstrated. Using three test cases, results indicate that the parallelization of derivative integral evaluation through a simple scheme is highly effective regardless of the size of the basis set employed in the CASSCF energy calculation. parallelization of the construction of the MCSCF electronic hessian during solution of the CPMCSCF equations varies quantitatively depending on the nature of the hessian itself, but is highly scalable in all cases. (c) 2005 Wiley Periodicals, Inc.

关键词： CASSCF analytic harmonic frequencies CPMCSCF parallel algorithm GAMESS

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