Many important problems in material science, chemistry, solid-state physics, and biophysics require a modeling
approach based on fundamental quantum mechanical principles. A particular approach that has proven to be relatively
efficient and useful is Car-Parrinello ab initio molecular dynamics (CPAIMD). Parallelization of this approach beyond a
few hundred processors is challenging, due to the complex dependencies among various subcomputations, which lead to
complex communication optimization and load balancing problems. We are parallelizing CPAIMD using Charm++. The computation is modeled using a large number of virtual processors, which are mapped flexibly to
available processors with assistance from the Charm++ runtime system.
This project began as a NSF funded collaboration involving us (PPL : Laxmikant Kale)
and Drs. Roberto Car, Michael Klein, Glenn Martyna, Mark Tuckerman, Nick Nystrom and Josep Torrellas. It has now shifted to a collaborative development to scale both OpenAtom and NAMD under the LCF ORNL grant "Scalable Atomistic Modeling Tools with Chemical Reactivity for
Life Sciences", as a continuing collaboration with PPL, Kale on
computer scienece, Martyna and Tuckerman on the QM side, now joined by
Klaus Schulten on the MD side and Jack Dongarra on performance
optimization for ORNL LCF.
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Scaling Water on BG/L
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This code has been shown to scale efficiently to tens of thousands of processors on BG/L.
These water experiments show strong scaling for each water system and
also demonstrate effective weak scaling as system size increases. In
this graph, perfect scaling is horizontal, and the green diagonals
represent no scaling. This software was released under the production
name OpenAtom in January 2008.
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- 10-04
Abhinav Bhatele, Eric Bohm and Laxmikant V. Kale, Optimizing communication for Charm++ applications by reducing network contention, Concurrency and Computation: Practice and Experience (EuroPar special issue), Vol: 23, Issue: 2, Pages: 211-222, 2011
- 08-10
Abhinav Bhatele, Eric Bohm and Laxmikant V. Kale, A Case Study of Communication Optimizations on 3D Mesh Interconnects, Proceedings of Euro-Par (Topic 13 - High Performance Networks), 2009
Distinguished Paper Award at Euro-Par 2009
- 08-02
Abhinav Bhatele, Laxmikant V. Kale, Application-specific Topology-aware Mapping for Three Dimensional Topologies, Workshop on Large-Scale Parallel Processing (IPDPS), 2008
- 07-12
Abhinav Bhatele, Application-specific Topology-aware Mapping and Load Balancing for three-dimensional Torus Topologies, Master's Thesis, Department of Computer Science, University of Illinois, 2007
- 07-03
Eric Bohm, Abhinav Bhatele, Laxmikant V. Kale, Mark E. Tuckerman, Sameer Kumar, John A. Gunnels and Glenn J. Martyna, Fine grained parallelization of the Car-Parrinello ab initio MD method on Blue Gene/L, IBM Journal of Research and Development, Volume 52, No. 1/2, 2007
- 05-15
Sameer Kumar, Yan Shi, Eric Bohm, L. V. Kale, Scalable, fine grain, parallelization of the Car-Parrinello ab initio molecular dynamics method, Technical Report
- 04-17
Ramkumar V. Vadali , Yan Shi , Sameer Kumar , L. V. Kale , Mark E. Tuckerman , Glenn J. Martyna, Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers,, Journal of Computational Chemistry Volume 25, No. 16, pp. 2006-2022, 2004
- 03-18
Ramkumar Venkat Vadali , Parallelizing CPAIMD Using Charm++, Master's Thesis, Dept. of Computer Science, University of Illinois 2003
- 03-06
Ramkumar Vadali, L. V. Kale, Glenn Martyna, Mark Tuckerman, Scalable Parallelization of Ab Initio Molecular Dynamics, Technical Report, communicated to SC 2003
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