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

被引：165

作者：

Allen, F ^{[1
]}

Almasi, G ^{[1
]}

Andreoni, W ^{[1
]}

Beece, D ^{[1
]}

Berne, BJ ^{[1
]}

Bright, A ^{[1
]}

Brunheroto, J ^{[1
]}

Cascaval, C ^{[1
]}

Castanos, J ^{[1
]}

Coteus, P ^{[1
]}

Crumley, P ^{[1
]}

Curioni, A ^{[1
]}

Denneau, M ^{[1
]}

Donath, W ^{[1
]}

Eleftheriou, M ^{[1
]}

Fitch, B ^{[1
]}

Fleischer, B ^{[1
]}

Georgiou, CJ ^{[1
]}

Germain, R ^{[1
]}

Giampapa, M ^{[1
]}

Gresh, D ^{[1
]}

Gupta, M ^{[1
]}

Haring, R ^{[1
]}

Ho, H ^{[1
]}

Hochschild, P ^{[1
]}

Hummel, S ^{[1
]}

Jonas, T ^{[1
]}

Lieber, D ^{[1
]}

Martyna, G ^{[1
]}

Maturu, K ^{[1
]}

Moreira, J ^{[1
]}

Newns, D ^{[1
]}

Newton, M ^{[1
]}

Philhower, R ^{[1
]}

Picunko, T ^{[1
]}

Pitera, J ^{[1
]}

Pitman, M ^{[1
]}

Rand, R ^{[1
]}

Royyuru, A ^{[1
]}

Salapura, V ^{[1
]}

Sanomiya, A ^{[1
]}

Shah, R ^{[1
]}

Sham, Y ^{[1
]}

Singh, S ^{[1
]}

Snir, M ^{[1
]}

Suits, F ^{[1
]}

Swetz, R ^{[1
]}

Swope, WC ^{[1
]}

Vishnumurthy, N ^{[1
]}

Ward, TJC ^{[1
]}

机构：

[1] IBM Corp, Div Res, Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA

来源：

IBM SYSTEMS JOURNAL | 2001年 / 40卷 / 02期

关键词：

D O I：

10.1147/sj.402.0310

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

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.

引用

页码：310 / 327

页数：18

共 46 条

[1] Allen M. P., 1989, COMPUTER SIMULATION
[2] RATTLE - A VELOCITY VERSION OF THE SHAKE ALGORITHM FOR MOLECULAR-DYNAMICS CALCULATIONS
ANDERSEN, HC
[J]. JOURNAL OF COMPUTATIONAL PHYSICS, 1983, 52 (01) : 24 - 34
[3] ANDREONI W, 2001, IBM J RES DEV, V45
[4] Parametrizing a polarizable force field from ab initio data.: I.: The fluctuating point charge model
Banks, JL
Kaminski, GA
Zhou, RH
Mainz, DT
Berne, BJ
Friesner, RA
[J]. JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (02) : 741 - 754
[5] BEETEM J, 1987, EXPT PARALLEL COMPUT
[6] MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH
BERENDSEN, HJC
POSTMA, JPM
VANGUNSTEREN, WF
DINOLA, A
HAAK, JR
[J]. JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) : 3684 - 3690
[7] Transition path sampling: throwing ropes over mountains in the dark
Bolhuis, PG
Dellago, C
Geissler, PL
Chandler, D
[J]. JOURNAL OF PHYSICS-CONDENSED MATTER, 2000, 12 (8A) : A147 - A152
[8] BRUNNER RK, 2000, SUP 2000 P DALL TX
[9] Variant Creutzfeldt-Jakob disease
Collinge, J
[J]. LANCET, 1999, 354 (9175) : 317 - 323
[10] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES
CORNELL, WD
CIEPLAK, P
BAYLY, CI
GOULD, IR
MERZ, KM
FERGUSON, DM
SPELLMEYER, DC
FOX, T
CALDWELL, JW
KOLLMAN, PA
[J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) : 5179 - 5197

← 1 2 3 4 5 →