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Copernicus: A new paradigm for parallel adaptive molecular dynamics
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. (Erik Lindahl)
Stockholm University.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. (Erik Lindahl)
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2011 (English)In: Proceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, 60- p.Conference paper, Published paper (Refereed)
Abstract [en]

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 0.6 Å 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.

Place, publisher, year, edition, pages
2011. 60- p.
National Category
Theoretical Chemistry Biophysics
Research subject
SRA - E-Science (SeRC)
Identifiers
URN: urn:nbn:se:kth:diva-79168DOI: 10.1145/2063384.2063465Scopus ID: 2-s2.0-83155193238ISBN: 9781450307710 (print)OAI: oai:DiVA.org:kth-79168DiVA: diva2:495189
Conference
2011 International Conference for High Performance Computing, Networking, Storage and Analysis, SC11; Seattle, WA; 12 November 2011 through 18 November 2011
Funder
Swedish e‐Science Research Center
Note
QC 20120223Available from: 2012-02-08 Created: 2012-02-08 Last updated: 2012-02-23Bibliographically approved

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Hess, BerkLindahl, Erik

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