Parallel Out-of-Core Algorithm for Genome-Scale Enumeration of Metabolic Systemic Pathways
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
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We parallelized the serial extreme pathways algorithm presented by Schilling et al., in J. Theor. Biol. 203 (2000) using the Message Passing Interface (MPI). The parallel algorithm exhibits super-linear scalability because the number of independence tests performed decreases as the number of MPI nodes increases. A subsystem of the metabolic network of Escherichia coli with 140 reactions and 96 metabolites (without preprocessing) is used as a benchmark. The extreme pathways of this system are computed in under 280 seconds using 70 2.4 GHz Intel Pentium-IV CPUs with Myrinet interconnection among the dual-CPU nodes of the Linux cluster.