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The Blue Genet/L computer is a massively parallel supercomputer based on IBM system-on-a-chip technology. It is designed to scale to 65,536 dual-processor nodes, with a peak performance of 360 teraflops. This paper describes the project objectives and provides an overview of the system architecture that resulted. We discuss our application-based approach and rationale for a low-power, highly integrated design. The key architectural features of Blue Gene/L are introduced in this paper: the link chip component and five Blue Gene/L networks, the PowerPCt 440 core and floatingpoint enhancements, the on-chip and off-chip distributed memory system, the node-and system-level design for high reliability, and the comprehensive approach to fault isolation.

The main interconnect of the massively parallel Blue Genet/L is a three-dimensional torus network with dynamic virtual cut-through routing. This paper describes both the architecture and the microarchitecture of the torus and a network performance simulator. Both simulation results and hardware measurements are presented.

, IBM announced the start of a five-year effort to build a massively parallel computer, to be applied to the study of biomolecular phenomena such as protein folding. The project has two main goals: to advance our understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively parallel machine architecture and software. This project should enable biomolecular simulations that are orders of magnitude larger than current technology permits. Major areas of investigation include: how to most effectively utilize this novel platform to meet our scientific goals, how to make such massively parallel machines more usable, and how to achieve performance targets, with reasonable cost, through novel machine architectures. This paper provides an overview of the Blue Gene project at IBM Research. It includes some of the plans that have been made, the intended goals, and the anticipated challenges regarding the scientific work, the software application, and the hardware design.

Abstract. This paper presents strong scaling performance data for the Blue Matter molecular dynamics framework using a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time per time-step of under 2.3 milliseconds for a 43,222 atom protein/lipid system. This is equivalent to a simulation rate of over 76 nanoseconds per day and represents an unprecedented time-to-solution for biomolecular simulation as well as continued speed-up to fewer than three atoms per node. On a smaller, solvated lipid system with 13,758 atoms, we have achieved continued speedups through fewer than one atom per node and less than 2 milliseconds/time-step. On a 92,224 atom system, we have achieved floating point performance of over 1.8 TeraFlops/second on 16,384 nodes. Strong scaling of fixed-size classical molecular dynamics of biological systems to large numbers of nodes is necessary to extend the simulation time to the scale required to make contact with experimental data and derive biologically relevant insights.