Blue Gene: A vision for protein science using a petaflop supercomputer

F. Allen; G. Almasi; W. Andreoni; D. Beece; B. J. Berne; A. Bright; J. Brunheroto; C. Cascaval; J. Castanos; P. Coteus; P. Crumley; A. Curioni; M. Denneau; W. Donath; M. Eleftheriou; B. Fitch; B. Fleischer; C. J. Georgiou; R. Germain; M. Giampapa; D. Gresh; M. Gupta; R. Haring; H. Ho; P. Hochschild; S. Hummel; T. Jonas; D. Lieber; G. Martyna; K. Maturu; J. Moreira; D. Newns; M. Newton; R. Philhower; T. Picunko; J. Pitera; M. Pitman; R. Rand; A. Royyuru; V. Salapura; A. Sanomiya; R. Shah; Y. Sham; S. Singh; M. Snir; F. Suits; R. Swetz; W. C. Swope; N. Vishnumurthy; T. J.C. Ward

doi:10.1147/sj.402.0310

Blue Gene: A vision for protein science using a petaflop supercomputer

F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, C. Cascaval, J. Castanos, P. Coteus, P. Crumley, A. Curioni, M. Denneau, W. Donath, M. Eleftheriou, B. Fitch, B. Fleischer, C. J. Georgiou, R. Germain, M. GiampapaD. Gresh, M. Gupta, R. Haring, H. Ho, P. Hochschild, S. Hummel, T. Jonas, D. Lieber, G. Martyna, K. Maturu, J. Moreira, D. Newns, M. Newton, R. Philhower, T. Picunko, J. Pitera, M. Pitman, R. Rand, A. Royyuru, V. Salapura, A. Sanomiya, R. Shah, Y. Sham, S. Singh, M. Snir, F. Suits, R. Swetz, W. C. Swope, N. Vishnumurthy, T. J.C. Ward

University of Minnesota Informatics Institute

Research output: Contribution to journal › Article › peer-review

216 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	310-327
Number of pages	18
Journal	IBM Systems Journal
Volume	40
Issue number	2
DOIs	https://doi.org/10.1147/sj.402.0310
State	Published - 2001

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Allen, F., Almasi, G., Andreoni, W., Beece, D., Berne, B. J., Bright, A., Brunheroto, J., Cascaval, C., Castanos, J., Coteus, P., Crumley, P., Curioni, A., Denneau, M., Donath, W., Eleftheriou, M., Fitch, B., Fleischer, B., Georgiou, C. J., Germain, R., ... Ward, T. J. C. (2001). Blue Gene: A vision for protein science using a petaflop supercomputer. IBM Systems Journal, 40(2), 310-327. https://doi.org/10.1147/sj.402.0310

Allen, F, Almasi, G, Andreoni, W, Beece, D, Berne, BJ, Bright, A, Brunheroto, J, Cascaval, C, Castanos, J, Coteus, P, Crumley, P, Curioni, A, Denneau, M, Donath, W, Eleftheriou, M, Fitch, B, Fleischer, B, Georgiou, CJ, Germain, R, Giampapa, M, Gresh, D, Gupta, M, Haring, R, Ho, H, Hochschild, P, Hummel, S, Jonas, T, Lieber, D, Martyna, G, Maturu, K, Moreira, J, Newns, D, Newton, M, Philhower, R, Picunko, T, Pitera, J, Pitman, M, Rand, R, Royyuru, A, Salapura, V, Sanomiya, A, Shah, R, Sham, Y, Singh, S, Snir, M, Suits, F, Swetz, R, Swope, WC, Vishnumurthy, N & Ward, TJC 2001, 'Blue Gene: A vision for protein science using a petaflop supercomputer', IBM Systems Journal, vol. 40, no. 2, pp. 310-327. https://doi.org/10.1147/sj.402.0310

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abstract = "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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AU - Allen, F.

AU - Almasi, G.

AU - Andreoni, W.

AU - Beece, D.

AU - Berne, B. J.

AU - Bright, A.

AU - Brunheroto, J.

AU - Cascaval, C.

AU - Castanos, J.

AU - Coteus, P.

AU - Crumley, P.

AU - Curioni, A.

AU - Denneau, M.

AU - Donath, W.

AU - Eleftheriou, M.

AU - Fitch, B.

AU - Fleischer, B.

AU - Georgiou, C. J.

AU - Germain, R.

AU - Giampapa, M.

AU - Gresh, D.

AU - Gupta, M.

AU - Haring, R.

AU - Ho, H.

AU - Hochschild, P.

AU - Hummel, S.

AU - Jonas, T.

AU - Lieber, D.

AU - Martyna, G.

AU - Maturu, K.

AU - Moreira, J.

AU - Newns, D.

AU - Newton, M.

AU - Philhower, R.

AU - Picunko, T.

AU - Pitera, J.

AU - Pitman, M.

AU - Rand, R.

AU - Royyuru, A.

AU - Salapura, V.

AU - Sanomiya, A.

AU - Shah, R.

AU - Sham, Y.

AU - Singh, S.

AU - Snir, M.

AU - Suits, F.

AU - Swetz, R.

AU - Swope, W. C.

AU - Vishnumurthy, N.

AU - Ward, T. J.C.

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Blue Gene: A vision for protein science using a petaflop supercomputer

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