Scientific Applications:
OpenAtom - Ab Initio Molecular Dynamics
Proper homepage of OpenAtom project is here.
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 then 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, Klaus Schulten on the MD side and Jack Dongarra on performance optimization for ORNL LCF. Currently, the OpenAtom project is a collaboration of Kale with Glenn Martyna and Sohrab Ismail-Beigi.
OpenAtom Project
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 then 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, Klaus Schulten on the MD side and Jack Dongarra on performance optimization for ORNL LCF. Currently, the OpenAtom project is a collaboration of Kale with Glenn Martyna and Sohrab Ismail-Beigi.
OpenAtom Project
People
Papers/Talks
16-05
2016
[Paper]
[Paper]
OpenAtom: Scalable Ab-Initio Molecular Dynamics with Diverse Capability [ISC 2016]
14-49
2014
[Talk]
[Talk]
Adaptive runtime systems for computational chemistry [ACS 2014]
14-14
2014
[Paper]
[Paper]
Optimizing the performance of parallel applications on a 5D torus via task mapping [HiPC 2014]
14-07
2014
[Paper]
[Paper]
Parallel Programming with Migratable Objects: Charm++ in Practice [SC 2014]
14-04
2014
[Paper]
[Paper]
Maximizing Throughput on a Dragonfly Network [SC 2014]
13-42
2013
[Paper]
[Paper]
Parallel Science and Engineering Applications: The Charm++ Approach: Chapter 5: OpenAtom: Ab-initio Molecular Dynamics for Petascale Platforms [Book 2013]
13-16
2013
[Paper]
[Paper]
Parallel Science and Engineering Applications: The Charm++ Approach [Book 2013]
10-04
2010
[Paper]
[Paper]
Optimizing Communication for Charm++ Applications by Reducing Network Contention [Concurrency and Computation: Practice and Experience 2010]
09-24
2009
[Talk]
[Talk]
A Case Study of Communication Optimizations on 3D Interconnects [Euro-Par 2009]
09-16
2009
[Poster]
[Poster]
Topology Aware Task Mapping Techniques: An API and Case Study [PPoPP 2009]
08-20
2008
[Talk]
[Talk]
Application-specific Topology-aware Mapping for Three Dimensional Topologies [LSPP 2008]
08-18
2008
[Poster]
[Poster]
Effects of Contention on Message Latencies in Large Supercomputers [SC 2008]
08-17
2008
[Poster]
[Poster]
Automatic Topology-Aware Task Mapping for Parallel Applications Running on Large Parallel Machines [IPDPS 2008]
08-10
2009
[Paper]
[Paper]
A Case Study of Communication Optimizations on 3D Mesh Interconnects [Euro-Par 2009]
08-02
2008
[Paper]
[Paper]
Application-specific Topology-aware Mapping for Three Dimensional Topologies [LSPP 2008]
07-12
2007
[MS Thesis]
[MS Thesis]
Application-specific Topology-aware Mapping and Load Balancing for three-dimensional Torus Topologies [Thesis 2007]
07-03
2007
[Paper]
[Paper]
Fine Grained Parallelization of the Car-Parrinello ab initio MD Method on Blue Gene/L [IBM Journal of Research and Development 2007]
05-15
2005
[Paper]
[Paper]
Scalable, Fine Grain, Parallelization of the Car-Parrinello ab initio Molecular Dynamics Method [PPL Technical Report 2005]
04-17
2004
[Paper]
[Paper]
Scalable Fine-Grained Parallelization of Plane-Wave-Based ab initio Molecular Dynamics for Large Supercomputers [Journal of Computational Chemistry 2004]
03-22
2003
[Talk]
[Talk]
Parallelization of CPAIMD using Charm++ [No Conference 2003]
03-18
2003
[MS Thesis]
[MS Thesis]
Parallelizing CPAIMD Using Charm++ [Thesis 2003]
03-06
2003
[Paper]
[Paper]
Scalable Parallelization of Ab Initio Molecular Dynamics [PPL Technical Report 2003]