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 …