Blue Matter, an application framework for molecular simulation on Blue Gene

• Published in: Journal of parallel and distributed computing 2003, Vol.63 (7), p.759-773
• Main Authors: Fitch, B.G, Germain, R.S, Mendell, M, Pitera, J, Pitman, M, Rayshubskiy, A, Sham, Y, Suits, F, Swope, W, Ward, T.J.C, Zhestkov, Y, Zhou, R
• Format: Article
• Language: English
• Subjects: Biomolecular simulation; Molecular dynamics; N-body problem; Parallel computing
• ISSN: 0743-7315; 1096-0848
• DOI: 10.1016/S0743-7315(03)00084-4

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 low overhead 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 speedups on 512–1024 node count partitions even for systems with as few as 5000 atoms.