Blue Gene: A vision for protein science using a petaflop supercomputer
F Allen and G Almasi and W Andreoni and D Beece and BJ Berne and A Bright and J Brunheroto and C Cascaval and J Castanos and P Coteus and P Crumley and A Curioni and M Denneau and W Donath and M Eleftheriou and B Fitch and B Fleischer and CJ Georgiou and R Germain and M Giampapa and D Gresh and M Gupta and R Haring and H Ho and P Hochschild and S Hummel and T Jonas and D Lieber and G Martyna and K Maturu and J Moreira and D Newns and M Newton and R Philhower and T Picunko and J Pitera and M Pitman and R Rand and A Royyuru and V Salapura and A Sanomiya and R Shah and Y Sham and S Singh and M Snir and F Suits and R Swetz and WC Swope and N Vishnumurthy and TJC Ward and H Warren and R Zhou, IBM SYSTEMS JOURNAL, 40, 310-327 (2001).
In December 1999, 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.
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