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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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.
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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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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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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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 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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The parallel multiple front method is used in mechanical engineering to solve large sparse linear systems issued from finite element modeling. It is a parallel direct method based on a nonoverlapping domain decomposit...
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ISBN:
(纸本)0769523129
The parallel multiple front method is used in mechanical engineering to solve large sparse linear systems issued from finite element modeling. It is a parallel direct method based on a nonoverlapping domain decomposition method. The decomposition is usually built with a graph partitioning approach. However this approach is not well suited to all parallel applications. It provides computing times over the subdomains which can vary from simple to double for our parallel multiple method. We show that its computing time can be decreased by load balancing the computational volume over the subdomains. We present in this communication a sequential and a parallel version of our load balancing method which corrects in computational volume an initial decomposition issued from graph partitioning tools.
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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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 compu...
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