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Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflop Computer

by George S. Almasi, Calin Cascaval, C Cascaval, Monty Denneau Wilm Donath, Jose G. Castanos, Monty Denneau, Wilm Donath, Maria Eleftheriou, Mark Giampapa, Howard Ho, Derek Lieber, Jose E. Moreira, Dennis Newns, Marc Snir, Henry S. Warren - International Journal of Parallel Programming , 2001
"... The IBM Blue Gene project has endeavored to develop a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges of this project is demonstrating that applications can successfully exploit this massive amount of parallelism. Starting from the sequent ..."
Abstract - Cited by 24 (3 self) - Add to MetaCart
The IBM Blue Gene project has endeavored to develop a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges of this project is demonstrating that applications can successfully exploit this massive amount of parallelism. Starting from

Scalable molecular dynamics with NAMD.

by James C Phillips , Rosemary Braun , Wei Wang , James Gumbart , Emad Tajkhorshid , Elizabeth Villa , Christophe Chipot , Robert D Skeel , Laxmikant Kalé , Klaus Schulten - J Comput Chem , 2005
"... Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and la ..."
Abstract - Cited by 849 (63 self) - Add to MetaCart
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop

The anatomy of the Grid: Enabling scalable virtual organizations.

by Ian Foster , • , Carl Kesselman , Steven Tuecke - The International Journal of High Performance Computing Applications , 2001
"... Abstract "Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation. In this article, we define this new field. First, ..."
Abstract - Cited by 2673 (86 self) - Add to MetaCart
Abstract "Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation. In this article, we define this new field. First

Recovering High Dynamic Range Radiance Maps from Photographs

by Paul E. Debevec, Jitendra Malik
"... We present a method of recovering high dynamic range radiance maps from photographs taken with conventional imaging equipment. In our method, multiple photographs of the scene are taken with different amounts of exposure. Our algorithm uses these differently exposed photographs to recover the respon ..."
Abstract - Cited by 859 (15 self) - Add to MetaCart
demonstrate a few applications of having high dynamic range radiance maps, such as synthesizing realistic motion blur and simulating the response of the human visual system.

Coupled hidden Markov models for complex action recognition

by Matthew Brand, Nuria Oliver, Alex Pentland , 1996
"... We present algorithms for coupling and training hidden Markov models (HMMs) to model interacting processes, and demonstrate their superiority to conventional HMMs in a vision task classifying two-handed actions. HMMs are perhaps the most successful framework in perceptual computing for modeling and ..."
Abstract - Cited by 501 (22 self) - Add to MetaCart
We present algorithms for coupling and training hidden Markov models (HMMs) to model interacting processes, and demonstrate their superiority to conventional HMMs in a vision task classifying two-handed actions. HMMs are perhaps the most successful framework in perceptual computing for modeling

The design and implementation of an intentional naming system

by William Adjie-Winoto, Elliot Schwartz, Hari Balakrishnan, Jeremy Lilley - 17TH ACM SYMPOSIUM ON OPERATING SYSTEMS PRINCIPLES (SOSP '99) PUBLISHED AS OPERATING SYSTEMS REVIEW, 34(5):186--201, DEC. 1999 , 1999
"... This paper presents the design and implementation of the Intentional Naming System (INS), a resource discovery and service location system for dynamic and mobile networks of devices and computers. Such environments require a naming system that is (i) expressive, to describe and make requests based o ..."
Abstract - Cited by 518 (14 self) - Add to MetaCart
This paper presents the design and implementation of the Intentional Naming System (INS), a resource discovery and service location system for dynamic and mobile networks of devices and computers. Such environments require a naming system that is (i) expressive, to describe and make requests based

Grid Information Services for Distributed Resource Sharing

by Karl Czajkowski , Steven Fitzgerald, Ian Foster, Carl Kesselman , 2001
"... Grid technologies enable large-scale sharing of resources within formal or informal consortia of individuals and/or institutions: what are sometimes called virtual organizations. In these settings, the discovery, characterization, and monitoring of resources, services, and computations are challengi ..."
Abstract - Cited by 712 (52 self) - Add to MetaCart
are challenging problems due to the considerable diversity, large numbers, dynamic behavior, and geographical distribution of the entities in which a user might be interested. Consequently, information services are a vital part of any Grid software infrastructure, providing fundamental mechanisms for discovery

Tabu Search -- Part I

by Fred Glover , 1989
"... This paper presents the fundamental principles underlying tabu search as a strategy for combinatorial optimization problems. Tabu search has achieved impressive practical successes in applications ranging from scheduling and computer channel balancing to cluster analysis and space planning, and more ..."
Abstract - Cited by 680 (11 self) - Add to MetaCart
of computational experience for a variety of applications. Part I1 of this study (to appear in a subsequent issue) examines more advanced considerations, applying the basic ideas to special settings and outlining a dynamic move structure to insure finiteness. Part I1 also describes tabu search methods for solving

NAMD2: Greater Scalability for Parallel Molecular Dynamics

by Laxmikant Kale , Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, Klaus Schulten - JOURNAL OF COMPUTATIONAL PHYSICS , 1998
"... Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this ..."
Abstract - Cited by 322 (45 self) - Add to MetaCart
Molecular dynamics programs simulate the behavior of biomolecular systems, leading to insights and understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness

Petaflop Computing for Protein Folding

by Petaflop Computing For, Shannon K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesus Izaguirre, Peter M. Kogge - In Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing
"... This paper addresses the mapping of protein folding to a million-processor array for petaflop performance. A new scalability model is defined which incorporates the characteristics of highly-distributed multithreaded architectures. The model is used to compare the scalability of various algorithms a ..."
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and decompositions and facilitates the prototyping of a million node Processing-In-Memory array to achieve petaflop performance during a molecular dynamics simulation typical of protein folding. In addition, simulations are used to validate the model and parallel implementations are demonstrated. Although parallel
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