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BLAST Application with Data-aware Desktop Grid Middleware

Haiwu He 1 Gilles Fedak 1 Bing Tang 2 Franck Cappello 3, 4 
1 GRAAL - Algorithms and Scheduling for Distributed Heterogeneous Platforms
Inria Grenoble - Rhône-Alpes, LIP - Laboratoire de l'Informatique du Parallélisme
3 GRAND-LARGE - Global parallel and distributed computing
LRI - Laboratoire de Recherche en Informatique, LIFL - Laboratoire d'Informatique Fondamentale de Lille, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France, CNRS - Centre National de la Recherche Scientifique : UMR8623
Abstract : There exists numerous Grid middleware to develop and execute programs on the computational Grid, but they still require intensive work from their users. BitDew is made to facilitate the usage of large scale Grid with dynamic, heterogeneous, volatile and highly distributed computing resources for applications that require a huge amount of data processing. Data-intensive applications form an important class of applications for the e-Science community which require secure and coordinated access to large datasets, wide-area transfers and broad distribution of TeraBytes of data while keeping track of multiple data replicas. In genetic biology, gene sequences comparison and analysis are the most basic routines. With the considerable increase of sequences to analyze, we need more and more computing power as well as efficient solution to manage data. In this work, we investigate the advantages of using a new Desktop Grid middleware BitDew, designed for large scale data management.Our contribution is two-fold: firstly, we introduce a data-driven Master/Slave programming model and we present an implementation of BLAST over BitDew following this model, secondly, we present extensive experimental and simulation results which demonstrate the effectiveness and scalability of our approach. We evaluate the benefit of multi-protocol data distribution to achieve remarkable speedups, we report on the ability to cope with highly volatile environment with relative performance degradation, we show the benefit of data replication in Grid with heterogeneous resource performance and we evaluate the combination of data fault tolerance and data replication when computing on volatile resources.
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Submitted on : Tuesday, April 3, 2012 - 1:36:07 PM
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Haiwu He, Gilles Fedak, Bing Tang, Franck Cappello. BLAST Application with Data-aware Desktop Grid Middleware. CCGrid'09: Proceedings of the 9th IEEE International Symposium on Cluster Computing and the Grid, May 2009, Shanghai, China. ⟨10.1109/CCGRID.2009.91⟩. ⟨hal-00684869⟩



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