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

被引：504

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

页码：41 / 53

页数：13

共 55 条

[1]

Acellera, ACEMD HIGH THROUGHP

[2]

ALAM SR, 2007, IEEE COMPUT, V40, P66

[3] MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms [J].

Andoh, Yoshimichi ;

Yoshii, Noriyuki ;

Fujimoto, Kazushi ;

Mizutani, Keisuke ;

Kojima, Hidekazu ;

Yamada, Atsushi ;

Okazaki, Susumu ;

Kawaguchi, Kazutomo ;

Nagao, Hidemi ;

Iwahashi, Kensuke ;

Mizutani, Fumiyasu ;

Minami, Kazuo ;

Ichikawa, Shin-ichi ;

Komatsu, Hidemi ;

Ishizuki, Shigeru ;

Takeda, Yasuhiro ;

Fukushima, Masao .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9 (07) :3201-3209

[4] Architecture and Membrane Interactions of the EGF Receptor [J].

Arkhipov, Anton ;

Shan, Yibing ;

Das, Rahul ;

Endres, Nicholas F. ;

Eastwood, Michael P. ;

Wemmer, David E. ;

Kuriyan, John ;

Shaw, David E. .

CELL, 2013, 152 (03) :557-569

[5]

Bhatia A., 2008, Proc. IEEE Int'l Conf. Network (ICON), P1, DOI [10.1002/9780470414811, DOI 10.1002/9780470414811]

[6]

Bowers K.J., 2006, 2006 ACM IEEE C SUP

[7] The classical equation of state of gaseous helium, neon and argon [J].

Buckingham, RA .

PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-MATHEMATICAL AND PHYSICAL SCIENCES, 1938, 168 (A933) :264-283

[8] A gating mechanism of pentameric ligand-gated ion channels [J].

Calimet, Nicolas ;

Simoes, Manuel ;

Changeux, Jean-Pierre ;

Karplus, Martin ;

Taly, Antoine ;

Cecchini, Marco .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (42) :E3987-E3996

[9] The Amber biomolecular simulation programs [J].

Case, DA ;

Cheatham, TE ;

Darden, T ;

Gohlke, H ;

Luo, R ;

Merz, KM ;

Onufriev, A ;

Simmerling, C ;

Wang, B ;

Woods, RJ .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1668-1688

[10]

Chow E., DESRESTR200801

← 1 2 3 4 5 6 →