Blue Matter, An Application Framework for Molecular Simulation on Blue Gene

In this paper we describe the context, architecture, and challenges of Blue Matter, the application framework being developed in conjunction with the science effort within IBM’s Blue Gene project. The study of the mechanisms behind protein folding and related topics can require long time simulations on systems with a wide range of sizes and the application supporting these studies must map efficiently onto a large range of parallel partition sizes to optimize scientific throughput for a particular study. The design goals for the Blue Matter architecture include separating the complexities of the parallel implementation on a particular machine from those of the scientific simulation as well as minimizing system environmental dependencies so that running an application within a very lightweight kernel with minimal services is possible. We describe some of the parallel decompositions currently being explored that target the first member of the Blue Gene family, BG/L, and present simple performance models for these decompositions that we are using to prioritize our development work. Preliminary results indicate that the high performance networks on BG/L will allow us to use FFT-based techniques for periodic electrostatics with reasonable efficiencies on 512 node count partitions even for systems with as few as 5000 atoms.

A previous version of this report appeared as RC 22683 (12/17/02).

By: Blake G. Fitch, Robert S. Germain, Mark Mendell, Jed W. Pitera, Mike C. Pitman, Aleksandr Rayshubski, Yuk Sham, Frank Suits, William C. Swope, T. J. C. Ward, Yuriy Zhestkov, Ruhong Zhou

Published in: RC22683 in 2003


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