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检索条件"主题词=PARALLEL algorithms"

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A parallel algorithm for the constrained multiple sequence alignment problem

A parallel algorithm for the constrained multiple sequence a...

引用

IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： D. He A.N. Arslan Department of Computer Science University of Vermont Burlington VT USA

We propose a parallel algorithm for the constrained multiple sequence alignment (CMSA) problem that seeks an optimal multiple alignment constrained to include a given pattern. We consider the dynamic programming computations in layers indexed by the symbols of the given pattern. In each layer we compute as a potential part of an optimal alignment for the CMSA problem, shortest paths for multiple sources and multiple destinations. These shortest paths problems are independent from one another (which enables parallel execution), and each can be solved using an A* algorithm specialized for the shortest paths problem for multiple sources and multiple destinations. The final step of our algorithm solves a single source single destination shortest path problem. Our experiments on real sequences show that our algorithm is faster in general than the existing sequential dynamic programming solutions.

关键词： parallel algorithms Tin Dynamic programming Shortest path problem Helium Computer science Heuristic algorithms

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FPGA implementations of the massively parallel GCA model

FPGA implementations of the massively parallel GCA model

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International Symposium on parallel and Distributed Processing (IPDPS)

作者： W. Heenes R. Hoffmann S. Kanthak Computer Architecture Group Darmstadt University of Technology Darmstadt Germany

The GCA (global cellular automata) model is a very interesting and flexible model which can be used to implement all kind of parallel algorithms. The GCA model consists of afield of cells similar the cellular automata model. Each cell has links to a set of remote cells which can be dynamically changed from generation to generation. A cell reads the remote neighbors' states and then changes its own state according to a local rule. The model is massively parallel because all cells can change their states independently and in parallel. We have investigated how the GCA model can be implemented efficiently in hardware using a field-programmable gate array (FPGA) prototyping platform. We have implemented a fully parallel architecture where all cells operate fully in parallel and other architectures where the cells are stored in memories in order to handle a large number of cells. We are showing that in the fully parallel architecture a speed-up of around 190 is realistic on a modern FPGA platform compared to a software implementation on a PC. In the partially parallel architecture based on memories the speed-up will be lower but the number of cells is only restricted by the capacity of the memories.

关键词： Field programmable gate arrays Computer architecture Hardware parallel architectures Biological system modeling parallel algorithms Programmable logic arrays Prototypes Hydrodynamics Biomedical optical imaging

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Research on parallel algorithm of DC optimal power flow in large interconnection power grids

Research on parallel algorithm of DC optimal power flow in l...

引用

International Conference on Electrical Machines and Systems (ICEMS)

作者： Liu Keyan Sheng Wanxing Li Yun-hua Beijing Aeronautics and Astronautics University Beijing China China Electrical Power Research Institute Beijing China

This paper investigated an optimal method of optimal power flow in large interconnected power grids. A decomposition collaborative model based on partial duality is analyzed, and a parallel algorithm based on DC optimal power flow model is presented in multi-region decomposition of interconnected power grids. The OPF computation of large power grid is decomposed into subproblems of multi regions, which is a quadratic programming problem used to solve a DC optimal power flow. The optimal convergence condition of multi-region is discussed. The interchange information among regions is export price and boundary nodal bus phase angle. The IEEE RTS-96 with two and three interconnected regions is studied to illustrate the effect of the proposed approach and to prove a great future in interconnected power system

关键词： parallel algorithms Load flow Power grids Power system interconnection Power system reliability Lagrangian functions Power systems Grid computing Quadratic programming Convergence

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parallel implementation of 1-D fast Fourier transform without inter-processor communications

Parallel implementation of 1-D fast Fourier transform withou...

引用

Southeastern Symposium on System Theory

作者： R. Al Na'mneh D.W. Pan R. Adhami Electrical and Computer Engineering Department University of Alabama Huntsville Huntsville AL USA Electrical and computer Engineering Department University of Alabama Huntsville Huntsville AL USA

Computing 1-D fast Fourier transform (FFT) using the classical 4-step FFT on parallel computers requires intensive all-to-all communication. This all-to-all communication significantly reduces the performance of FFT. In this paper, we present the no-communication algorithm that is a parallel algorithm for 1-D FFT without inter-processors communication. The advantage of this algorithm is the absence of all-to-all communication between processors. The disadvantage of this algorithm is the extra computation compared to the classical 4-step FFT. The no-communication algorithm has been implemented and tested in 8-node symmetric multiprocessors (SMP). The results show that the no-communication algorithm performs better than the 4-step FFT for relatively small data sizes. However, 4-step FFT algorithm performs better than the no-communication for relatively large data sizes.

关键词： Fast Fourier transforms Signal processing algorithms Concurrent computing Testing Scalability Central Processing Unit parallel algorithms FETs Image processing Image analysis

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Associative parallel algorithms for computing functions defined on paths in trees

Associative parallel algorithms for computing functions defi...

引用

International Conference on parallel Computing in Electrical Engineering (PAR ELEC 2002)

作者： Nepomniaschaya, AS Russian Acad Sci Siberian Div Inst Computat Math & Math Geophys Novosibirsk 630090 Russia

ISBN: (纸本)0769517315

In this paper by means of an abstract model of the SIMD type with vertical data processing (the STAR-machine), we present a simple associative parallel algorithm for finding tree paths in undirected graphs. We study applications of this algorithm to update minimum spanning trees in undirected graphs, to determine maximum flow values in a multiterminal network, and to find a fundamental set of circuits with respect to a given spanning tree. These algorithms are given as the corresponding STAR procedures whose correctness is proved and time complexity is evaluated.

关键词： Associative processing Concurrent computing Data processing Electronic mail Geophysics computing Mathematics parallel algorithms parallel processing Registers Tree graphs

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Time-optimal parallel algorithms for constructing optimal virtual cellular networks 9

Time-optimal parallel algorithms for constructing optimal vi...

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9th International Conference on parallel and Distributed Systems (ICPADS 2002)

作者： Zhang, JY Vrbsky, S Fan, GB Univ Alabama Dept Comp Sci Tuscaloosa AL 35487 USA

ISBN: (纸本)0769517609

In a cellular network, the base stations are not necessarily uniformly distributed, and their corresponding cell sizes are not necessarily the same. For example, a cell in a well-populated city cell is usually smaller than a cell in a rural area. To study a cellular network with non-uniform cell sizes, one approach is to use a virtual cellular network with a uniform cell size such that each virtual cell contains at most one base station. This paper has proposed parallel algorithms for meshes with multiple broadcasting to construct virtual mesh and honeycomb cellular networks for non-uniformly distributed base stations. The constructed virtual cellular networks are optimal in the sense that their corresponding uniform cell sizes reach the largest possible. The algorithms run in O(logn) time on a mesh with multiple broadcasting of size nxn to construct optimal virtual mesh and honeycomb cellular networks for n non-uniformly distributed base stations. Furthermore, those algorithms are time-optimal.

关键词： Base stations Broadcasting Cities and towns Computational modeling Computer architecture Computer science Land mobile radio cellular systems parallel algorithms

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Fast parallel algorithms for computing trigonometric sums

Fast parallel algorithms for computing trigonometric sums

引用

International Conference on parallel Computing in Electrical Engineering (PAR ELEC 2002)

作者： Stpiczynski, P Marie Curie Sklodowska Univ Dept Comp Sci PL-20031 Lublin Poland

ISBN: (纸本)0769517315

In this paper we present new parallel versions of sequential Goertzel and Reinsch algorithms for calculating trigonometric sums. The new algorithms use a recently introduced, very efficient BLAS-based algorithm for solving linear recurrence systems with constant coefficients. To achieve their portability across different shared-memory parallel architectures, the algorithms have been implemented in Fortran 77 and OpenMP. We also present experimental results performed on a two processor Pentium III computer running under Linux operating system with Atlas as an efficient implementation of BLAS. The new algorithms are up to 60-90% faster than the equivalent sequential Goertzel and Reinsch algorithms, even on one processor.

关键词： Character generation Clustering algorithms Computer science Concurrent computing Interpolation Linux Operating systems parallel algorithms parallel architectures Scientific computing

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Performance evaluation of parallel algorithms for pricing multidimensional financial derivatives

Performance evaluation of parallel algorithms for pricing mu...

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31st International Conference on parallel Processing (ICPP 2002)

作者： Thulasiram, RK Bondarenko, DA Univ Manitoba Dept Comp Sci Winnipeg MB R3T 2N2 Canada

ISBN: (纸本)0769516807

In this paper, we develop parallel algorithms for pricing a class of multidimensional financial derivatives employing binomial lattice approach. We describe the algorithms, explain their complexities, and study their performance. The limitations posed by the problem size on the recursive algorithm and the solution to overcome this problem by the iterative algorithm are explained through the experimental results using MPL We first present analytical results for the number of computations and communications for both the algorithms. Since the number of nodes in a recombining lattice grows linearly with the problem size, it is feasible to price long-dated options using a recombining lattice. We have extended our algorithm to handle derivatives with many underlying assets and shown that the multi-asset derivatives offer a better problem for parallel computation. This is very important for finance industry since long-dated derivatives with many underlying assets are common in practice.

关键词： parallel algorithms

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parallel algorithm for hardware implementation of inverse halftoning

Parallel algorithm for hardware implementation of inverse ha...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： U.F. Siddiqi S.M. Sait A.A. Farooqui Department of Computer Engineering King Fahd University of Petroleum and Minerals Dhahran Saudi Arabia Synopsys Module Compiler Synopsys Inc. Mountain View CA USA

A parallel algorithm and its hardware implementation are proposed for an inverse halftone operation. The algorithm is based on lookup tables from which the inverse halftone value of a pixel is directly determined using a pattern of pixels. A method has been developed that allows accessing more than one value from the lookup table at any time. The lookup table is divided into smaller lookup tables, such that each pattern selected at any time goes to a separate smaller lookup table. The 15-pixel parallel version of the algorithm was tested on sample images and a simple and effective method has been used to overcome quality degradation due to pixel loss in the proposed algorithm. It can provide at least 4 times decrease in lookup table size when compared with a serial lookup table method implemented multiple times for the same number of pixels.

关键词： parallel algorithms Hardware Table lookup Pixel Image processing Concurrent computing Petroleum Minerals Testing Degradation

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Space and time efficient parallel algorithms and software for EST clustering

Space and time efficient parallel algorithms and software fo...

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31st International Conference on parallel Processing (ICPP 2002)

作者： Kalyanaraman, A Aluru, S Kothari, S Iowa State Univ Dept CS Ames IA 50011 USA

ISBN: (纸本)0769516777

Expressed sequence tags, abbreviated ESTs, are DNA molecules experimentally derived from expressed portions of genes. Clustering of ESTs is essential for gene recognition and understanding important genetic variations such as those resulting in diseases. In this paper, we present the design and development of a parallel software system for EST clustering. To our knowledge, this is the first such effort to address the problem of EST clustering in parallel. The novel features of our approach include 1) design of space efficient algorithms to keep the space requirement linear in the size of the input data set, 2) a combination of algorithmic techniques to reduce the total work without sacrificing the quality of EST clustering, and 3) use of parallel processing to reduce the run-time and facilitate the clustering of large data sets. Using a combination of these techniques, we report the clustering of 81,414 Arabidopsis ESTs in under 2.5 minutes on a 64-processor IBM SP, a problem that is estimated to take 9 hours of run-time with a state-of-the-art software, provided the memory required to run the software can be made available.

关键词： Algorithm design and analysis Clustering algorithms Diseases DNA Genetics parallel algorithms parallel processing Runtime Sequences Software systems

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