Parallel implementation of DNAml program on message-passing architectures

被引：16

作者：

Ceron, C ^{[1
]}

Dopazo, J

Zapata, EL

Carazo, JM

Trelles, O

机构：

[1] Univ Malaga, Comp Architecture Dept, E-29071 Malaga, Spain

[2] TDI, I&D Dept, Madrid 28028, Spain

[3] CSIC, Ctr Nacl Biotecnol, Biocomp Unit, E-28049 Madrid, Spain

来源：

PARALLEL COMPUTING | 1998年 / 24卷 / 5-6期

关键词：

parallel computers; run-time analysis; phylogenetic trees; DNAml program;

D O I：

10.1016/S0167-8191(98)00002-7

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

We present a new computing approach for the parallelization on message-passing computer architectures of the DNAml algorithm, one of the most powerful tools available for constructing phylogenetic trees from DNA sequences. An analysis of the data dependencies of the method gave little chances to develop an efficient parallel approach. However, a careful run-time analysis of the behaviour of the algorithm allowed us to propose a very efficient parallel implementation based on the combination of advanced dynamic scheduling strategies, speculative running-time execution decisions and I/O buffering. In this work, we discuss specific Parallel Virtual Machine (PVM)-based implementations for a cluster of workstations and for Distributed Memory multiprocessors, with high performance results. The code can be obtained from our public-domain sites. (C) 1998 Published by Elsevier Science B.V. All rights reserved.

引用

页码：701 / 716

页数：16

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