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SCHEDULE: NOV 12-18, 2011

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Copernicus: A New Paradigm for Parallel Adaptive Molecular Dynamics

SESSION: Molecular Dynamics and Computational Physics


TIME: 10:30AM - 11:00AM

AUTHOR(S):Sander Pronk, Per Larsson, Iman Pouya, Greg Bowman, Imran Haque, Kyle Beauchamp, Berk Hess, Vijay Pande, Peter Kasson, Erik Lindahl


Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring. Copernicus enables execution as single parallel jobs with automatic resource allocation. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. Starting from extended chains we observe structures 0.6Å from the native state within 30h, and achieve sufficient sampling to predict the native state without a priori knowledge after 80-90h. To match Copernicus' efficiency, a classical simulation would have to exceed 50 microseconds per day, currently infeasible even with custom hardware designed for simulations.

Chair/Author Details:

Sander Pronk - KTH Royal Institute of Technology

Per Larsson - University of Virginia

Iman Pouya - KTH Royal Institute of Technology

Greg Bowman - Stanford University

Imran Haque - Stanford University

Kyle Beauchamp - Stanford University

Berk Hess - KTH Royal Institute of Technology

Vijay Pande - Stanford University

Peter Kasson - University of Virginia

Erik Lindahl - KTH Royal Institute of Technology

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The full paper can be found in the ACM Digital Library

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