Copernicus: A new paradigm for parallel adaptive molecular dynamics
2011 (English)In: Proceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, 60- p.Conference paper (Refereed)
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.
Theoretical Chemistry Biophysics
Research subject SRA - E-Science (SeRC)
IdentifiersURN: urn:nbn:se:kth:diva-79168DOI: 10.1145/2063384.2063465ScopusID: 2-s2.0-83155193238ISBN: 9781450307710OAI: oai:DiVA.org:kth-79168DiVA: diva2:495189
2011 International Conference for High Performance Computing, Networking, Storage and Analysis, SC11; Seattle, WA; 12 November 2011 through 18 November 2011
FunderSwedish e‐Science Research Center
QC 201202232012-02-082012-02-082012-02-23Bibliographically approved