Parallelization and Distribution Strategies of Large Bioinformatics Requests over the Grid

Authors:
Eddy Caron;Frédéric Desprez;Gaël Mahec
Affiliations:
University of Lyon, ENS Lyon, INRIA,;LIP. UMR 5668, ENS Lyon, INRIA, CNRS, UCBL, France;LPC de Clermont-Ferrand, CNRS, IN2P3, UBP Université Blaise Pascal, France
Venue:
ICA3PP '08 Proceedings of the 8th international conference on Algorithms and Architectures for Parallel Processing
Year:
2008

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Abstract

This paper focuses on simultaneous scheduling of computation and data replication for life science applications on the grid. We present an adaptive algorithm based on the SRA algorithm (Static Joint Replication and Scheduling) [4] with more dynamicity for the jobs frequencies. The use of a linear program giving a databases mapping on the nodes and a jobs distribution schema, ensures us that our data placement and jobs distribution will be near the optimal solution, as long as the informations about the jobs frequencies are right. We validate our results with large jobs submissions simulations on a realistic platform.