Parallel Performance of Blue Matter on Blue Gene, Application for Molecular Dynamics Simulations

The Blue Gene/L supercomputer will allow studies of biological systems to be performed on unprecedented length and size scales. Carrying out these calculations efficiently on a massively
parallel machine like BG/L may require rethinking algorithms with particular attention to their communication and load-balancing characteristics. General infrastructure and algorithms used in Blue Matter will be discussed and performance data presented for different molecular system sizes and number of nodes.

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