In this paper, we are concerned with a number of parallel algorithms for comparing three different synchronization mechanisms when applied to a particular problem. The problem is the reduction of a general matrix to u...
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In this paper, we are concerned with a number of parallel algorithms for comparing three different synchronization mechanisms when applied to a particular problem. The problem is the reduction of a general matrix to upper Hessenberg form. The algorithms were written in C++ programming language using the Encore parallel Threads [Encore Computer Corporation, Encore parallel Threads Manual. No. 724-06210 Rev. A, 1988] package using a shared memory MIMD computer. (C) 2004 Elsevier Inc. All rights reserved.
The multiple genome sequence alignment problem falls in the domain of problems that can be parallelized to address large sequence lengths. Although there is communication required for the computation of the aligned se...
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ISBN:
(纸本)0769523129
The multiple genome sequence alignment problem falls in the domain of problems that can be parallelized to address large sequence lengths. Although there is communication required for the computation of the aligned sequences, the proper distribution can reduce the overall problem to a set of tasks to be solved independently and then merged. A parallel algorithm for the alignment of multiple genome sequences is described. The algorithm is experimentally evaluated in a distributed Grid environment that provides very scalable and low cost computation performance. The Grid environment is evaluated with respect to a traditional cluster environment and results are compared to evaluate the effectiveness of a Grid environment for large computational biology.
This paper presents a lock-free parallel algorithm for garbage collection in a realistic model using synchronization primitives offered by machine architectures. Mutators and collectors can simultaneously operate on t...
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Biological sequence comparison is one of the most important and basic problems in computational biology. Due to its high demands for computational power and memory, it is a very challenging task. Most of sequence comp...
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This paper discusses a parallel quicksort algorithm that is cost optimal, in average, using O(n/log(n)) processors. The cost optimality is mainly due to a cost optimal partitioning algorithm that utilizes all the proc...
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Computing reversal distance of two signed permutations has gained increasing attention over the last decade with the study of genome rearrangements in computational molecular biology. In this paper, we present a paral...
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In this paper, we develop parallel algorithms for pricing American-style Asian options employing binomial tree method. We describe the algorithm, explain the complexities, and study the performance. We have extended o...
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In this paper, we parallelize a new algorithm for solving nonsymmetric Toeplitz linear systems. This algorithm embeds the Toeplitz matrix in a larger structured matrix, then transforms it into an embedded Cauchy-like ...
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This paper introduces new approaches to the data distribution-partition problem for sparse matrices in a multiprocessor environment. In this work, the data partition problem of a sparse matrix is modeled as a Min-Max ...
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This paper introduces new approaches to the data distribution-partition problem for sparse matrices in a multiprocessor environment. In this work, the data partition problem of a sparse matrix is modeled as a Min-Max Problem subject to the uniformity constrain when the goal is to balance the load for both sparse and dense operations. This problem is NP-Complete and two heuristic solutions (ABO and GPB) are proposed. The key of ABO and GPB is to determine the permutation of rows/columns of the input sparse matrix to obtain a sorted matrix with a homogeneous density of nonzero elements. Due to the heuristic nature of the proposed methods their validation is carried out by a comparative study of the parallel efficiency of two types of problems (sparse and mixed) when ABO, GPB, Block, Cyclic and MRD data distributions are applied.
An ultrametric tree is an evolutionary tree in which the distances from the root to all leaves in the tree are equal. The Minimum Ultrametric Tree construction problem is the problem of constructing an ultrametric tre...
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