A fast algorithm for particle simulations
Journal of Computational Physics
Algorithmic challenges in computational molecular biophysics
Journal of Computational Physics - Special issue on computational molecular biophysics
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Parallel programming in OpenMP
Parallel programming in OpenMP
Computing in Science and Engineering
Performance of hybrid message-passing and shared-memory parallelism for discrete element modeling
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
The quest for petascale computing
Computing in Science and Engineering
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
A comparison of three programming models for adaptive applications on the origin2000
Journal of Parallel and Distributed Computing
Scalable Molecular-Dynamics, Visualization, and Data-Management Algorithms for Materials Simulations
Computing in Science and Engineering
Multiscale Simulation of Nanosystems
Computing in Science and Engineering
Analysis of the Clustering Properties of the Hilbert Space-Filling Curve
IEEE Transactions on Knowledge and Data Engineering
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Message passing and shared address space parallelism on an SMP cluster
Parallel Computing
Immersive and interactive exploration of billion-atom systems
Presence: Teleoperators and Virtual Environments - special issue: IEEE virtual reality 2002 conference
The Grid 2: Blueprint for a New Computing Infrastructure
The Grid 2: Blueprint for a New Computing Infrastructure
Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Scalable atomistic simulation algorithms for materials research
Scientific Programming - Best papers from SC 2001
Parallel Lattice Boltzmann Flow Simulation on Emerging Multi-core Platforms
Euro-Par '08 Proceedings of the 14th international Euro-Par conference on Parallel Processing
The reverse-acceleration model for programming petascale hybrid systems
IBM Journal of Research and Development
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
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We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/ computation structures, as well as its implementation using hybrid grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations—1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids— in addition to 134 billion-atom non-reactive space—time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM/MD simulation on a grid consisting of 6 supercomputer centers in the US and Japan (in total of 150,000 processor hours), in which the number of processors change dynamically on demand and resources are allocated and migrated dynamically in response to faults. Furthermore, performance portability has been demonstrated on a wide range of platforms such as BlueGene/L, Altix 3000, and AMD Opteron-based Linux clusters.