Anton 2: Raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer

被引:488
作者
Shaw, David E. [1 ,2 ]
Grossman, J. P. [1 ]
Bank, Joseph A. [1 ]
Batson, Brannon [1 ]
Butts, J. Adam [1 ]
Chao, Jack C. [1 ,3 ]
Deneroff, Martin M. [1 ,4 ]
Dror, Ron O. [1 ,5 ]
Even, Amos [1 ]
Fenton, Christopher H. [1 ]
Forte, Anthony [1 ]
Gagliardo, Joseph [1 ]
Gill, Gennette [1 ]
Greskamp, Brian [1 ]
Ho, C. Richard [1 ,6 ]
Ierardi, Douglas J. [1 ]
Iserovich, Lev [1 ]
Kuskin, Jeffrey S. [1 ]
Larson, Richard H. [1 ,8 ]
Layman, Timothy [1 ,9 ]
Lee, Li-Siang [1 ,10 ]
Lerer, Adam K. [1 ]
Li, Chester [1 ,6 ]
Killebrew, Daniel [1 ,7 ]
Mackenzie, Kenneth M. [1 ]
Mok, Shark Yeuk-Hai [1 ,8 ]
Moraes, Mark A. [1 ]
Mueller, Rolf [1 ,6 ]
Nociolo, Lawrence J. [1 ]
Peticolas, Jon L. [1 ]
Quan, Terry [1 ]
Ramot, Daniel [1 ,11 ]
Salmon, John K. [1 ]
Scarpazza, Daniele P. [1 ]
Ben Schafer, U. [1 ,6 ]
Siddique, Naseer [1 ]
Snyder, Christopher W. [1 ,12 ]
Spengler, Jochen [1 ]
Tang, Ping Tak Peter [1 ,13 ]
Theobald, Michael [1 ]
Toma, Horia [1 ,14 ]
Towles, Brian [1 ]
Vitale, Benjamin [1 ,6 ]
Wang, Stanley C. [1 ]
Young, Cliff [1 ,6 ]
机构
[1] DE Shaw Res, New York, NY 10036 USA
[2] Columbia Univ, Dept Biochem & Mol Biophys, New York, NY 10032 USA
[3] Columbia Univ, New York, NY 10027 USA
[4] GreenWave Syst, Orange, CA USA
[5] Stanford Univ, Stanford, CA 94305 USA
[6] Google, Mountain View, CA USA
[7] DNAnexus, Mountain View, CA USA
[8] Apple, Cupertino, CA USA
[9] Cadence Design Syst, San Jose, CA USA
[10] Barefoot Networks, Palo Alto, CA USA
[11] Via, New York, NY USA
[12] Edgeflip, Chicago, IL USA
[13] Intel, Santa Clara, CA USA
[14] Synopsys, Mountain View, CA USA
来源
SC14: INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS | 2014年
关键词
FORCE-FIELD; SIMULATIONS;
D O I
10.1109/SC.2014.9
中图分类号
TP301 [理论、方法];
学科分类号
081202 ;
摘要
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its predecessor, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations. A 512-node Anton 2 machine, currently in operation, is up to ten times faster than Anton 1 with the same number of nodes, greatly expanding the reach of all-atom biomolecular simulations. Anton 2 is the first platform to achieve simulation rates of multiple microseconds of physical time per day for systems with millions of atoms. Demonstrating strong scaling, the machine simulates a standard 23,558-atom benchmark system at a rate of 85 mu s/day-180 times faster than any commodity hardware platform or general-purpose supercomputer.
引用
收藏
页码:41 / 53
页数:13
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