Proceedings of the 2001 ACM/IEEE conference on Supercomputing
Overview of GridRPC: A Remote Procedure Call API for Grid Computing
GRID '02 Proceedings of the Third International Workshop on Grid Computing
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
MPICH-G2: a Grid-enabled implementation of the Message Passing Interface
Journal of Parallel and Distributed Computing - Special issue on computational grids
The Grid 2: Blueprint for a New Computing Infrastructure
The Grid 2: Blueprint for a New Computing Infrastructure
GRID '04 Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing
International Journal of High Performance Computing Applications
Distributing MCell Simulations on the Grid
International Journal of High Performance Computing Applications
Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Scalable atomistic simulation algorithms for materials research
Scientific Programming - Best papers from SC 2001
The Journal of Supercomputing
De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers
International Journal of High Performance Computing Applications
GridFMO Quantum chemistry of proteins on the grid
GRID '07 Proceedings of the 8th IEEE/ACM International Conference on Grid Computing
The Grid Enablement and Sustainable Simulation of Multiscale Physics Applications
CCGRID '09 Proceedings of the 2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid
Rescheduling co-allocation requests based on flexible advance reservations and processor remapping
GRID '08 Proceedings of the 2008 9th IEEE/ACM International Conference on Grid Computing
GRID '08 Proceedings of the 2008 9th IEEE/ACM International Conference on Grid Computing
Future Generation Computer Systems
The design, usage, and performance of GridUFO: A Grid based Unified Framework for Optimization
Future Generation Computer Systems
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We propose a reservation-based sustainable adaptive Grid supercomputing paradigm to enable tightly coupled computations of considerable scale (involving over 1,000 processors) and duration (over tens of continuous days) on a Grid of geographically distributed parallel supercomputers. The paradigm is demonstrated for an adaptive multiscale simulation application, in which accurate but compute-intensive quantum mechanical (QM) simulations are embedded within a classical molecular dynamics (Md) simulation only when and where high fidelity is required. Key technical innovations include: 1) an embedded divide-and-conquer algorithmic framework to maximally expose data and computation localities for enhanced scalability; 2) a buffered-cluster hybridization scheme to adaptively adjust MD/QM boundaries to maintain the model accuracy; and 3) a hybrid Grid remote procedure call (GridRPC) + message passing interface (MPI) Grid application framework to combine flexibility (adaptive resource allocation and migration), fault tolerance (automated fault recovery), and efficiency (scalable management of large computing resources). We have achieved an automated execution of multiscale MD/QM simulation on a Grid consisting of 6 supercomputer centers in Japan and the US (in total of 150 thousand processor-hours) for the dynamic simulation of implanted oxygen atoms in a silicon substrate, in which the number of processors changes dynamically on demand and resources are allocated and migrated dynamically according to both reservations and unexpected faults. The simulation results reveal a strong dependence of the oxygen penetration depth on the incident oxygen-beam position, which is useful information to further advance SIMOX (separation by implanted oxygen) technique to fabricate high speed and low power-consumption semiconductor devices.