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SCHEDULE: NOV 16-21, 2014

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Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer

SESSION: ACM Gordon Bell Finalist II

EVENT TYPE: Award Presentations & Award Talks, ACM Gordon Bell Finalists, Best Paper Finalists

TIME: 1:30PM - 2:00PM

SESSION CHAIR: Subhash Saini

AUTHOR(S):David E. Shaw, J.P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, Ron O. Dror, Amos Even, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Brian Greskamp, C. Richard Ho, Douglas J. Ierardi, Lev Iserovich, Jeffrey S. Kuskin, Richard H. Larson, Timothy Layman, Li-Siang Lee, Adam K. Lerer, Chester Li, Daniel Killebrew, Kenneth M. Mackenzie, Shark Yeuk-Hai Mok, Mark A. Moraes, Rolf Mueller, Lawrence J. Nociolo, Jon L. Peticolas, Terry Quan, Daniel Ramot, John K. Salmon, Daniele P. Scarpazza, U. Ben Schafer, Naseer Siddique, Christopher W. Snyder, Jochen Spengler, Ping Tak Peter Tang, Michael Theobald, Horia Toma, Brian Towles, Benjamin Vitale, Stanley C. Wang, Cliff Young

ROOM:New Orleans Theater

ABSTRACT:

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 μs/day—180 times faster than any commodity hardware platform or general-purpose supercomputer.

Chair/Author Details:

Subhash Saini (Chair) - NASA Ames Research Center

David E. Shaw - D. E. Shaw Research

J.P. Grossman - D. E. Shaw Research

Joseph A. Bank - D. E. Shaw Research

Brannon Batson - D. E. Shaw Research

J. Adam Butts - D. E. Shaw Research

Jack C. Chao - D. E. Shaw Research

Martin M. Deneroff - D. E. Shaw Research

Ron O. Dror - D. E. Shaw Research

Amos Even - D. E. Shaw Research

Christopher H. Fenton - D. E. Shaw Research

Anthony Forte - D. E. Shaw Research

Joseph Gagliardo - D. E. Shaw Research

Gennette Gill - D. E. Shaw Research

Brian Greskamp - D. E. Shaw Research

C. Richard Ho - D. E. Shaw Research

Douglas J. Ierardi - D. E. Shaw Research

Lev Iserovich - D. E. Shaw Research

Jeffrey S. Kuskin - D. E. Shaw Research

Richard H. Larson - D. E. Shaw Research

Timothy Layman - D. E. Shaw Research

Li-Siang Lee - D. E. Shaw Research

Adam K. Lerer - D. E. Shaw Research

Chester Li - D. E. Shaw Research

Daniel Killebrew - D. E. Shaw Research

Kenneth M. Mackenzie - D. E. Shaw Research

Shark Yeuk-Hai Mok - D. E. Shaw Research

Mark A. Moraes - D. E. Shaw Research

Rolf Mueller - D. E. Shaw Research

Lawrence J. Nociolo - D. E. Shaw Research

Jon L. Peticolas - D. E. Shaw Research

Terry Quan - D. E. Shaw Research

Daniel Ramot - D. E. Shaw Research

John K. Salmon - D. E. Shaw Research

Daniele P. Scarpazza - D. E. Shaw Research

U. Ben Schafer - D. E. Shaw Research

Naseer Siddique - D. E. Shaw Research

Christopher W. Snyder - D. E. Shaw Research

Jochen Spengler - D. E. Shaw Research

Ping Tak Peter Tang - D. E. Shaw Research

Michael Theobald - D. E. Shaw Research

Horia Toma - D. E. Shaw Research

Brian Towles - D. E. Shaw Research

Benjamin Vitale - D. E. Shaw Research

Stanley C. Wang - D. E. Shaw Research

Cliff Young - D. E. Shaw Research

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Paper provided by the ACM Digital Library

Paper also available from IEEE Computer Society