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Design and performance analysis of a distributed HPC molecular dynamics code on distributed resources

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MG '08: Proceedings of the 15th ACM Mardi Gras conference: From lightweight mash-ups to lambda grids: Understanding the spectrum of distributed computing requirements, applications, tools, infrastructures, interoperability, and the incremental adoption of key capabilities

Article No.: 21, Page 1

https://doi.org/10.1145/1341811.1341835

Published: 29 January 2008 Publication History

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Abstract

Molecular Dynamics (MD) is an important step towards understanding the behavior of biological systems. Even though, the state-of-the-art computational resource and techniques have made it feasible to do large-scale MD simulations, MD remains a very compute-intensive job, especially for large realistic systems. Thus there exists interest in developing and understanding the performance of MD code on multiple distributed HPC resources. To realize this goal, we have developed a preliminary parallel and distributed MD code and benchmarked it on the LONI (Louisiana Optical Network Interface) grid, which uses dedicated light-path networks to connect supercomputers across Louisiana.

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Chakraborty PJha SKatz D(2009)Novel submission modes for tightly coupled jobs across distributed resources for reduced time-to-solutionPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences10.1098/rsta.2009.0054367:1897(2545-2556)Online publication date: 28-Jun-2009
https://doi.org/10.1098/rsta.2009.0054

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Design and performance analysis of a distributed HPC molecular dynamics code on distributed resources

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Published In

January 2008

178 pages

ISBN:9781595938350

DOI:10.1145/1341811

General Chair:
Daniel S. Katz
LSU
,
Program Chair:
Craig Lee
Aerospace Corporation

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SIGAPP: ACM Special Interest Group on Applied Computing

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Association for Computing Machinery

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Published: 29 January 2008

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Mardi Gras'08: 15th Mardi Gras Conference on Distributed Applications

January 29 - February 3, 2008

Louisiana, Baton Rouge, USA

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Chakraborty PJha SKatz D(2009)Novel submission modes for tightly coupled jobs across distributed resources for reduced time-to-solutionPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences10.1098/rsta.2009.0054367:1897(2545-2556)Online publication date: 28-Jun-2009
https://doi.org/10.1098/rsta.2009.0054

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An investigation of molecular dynamics simulation and molecular docking: Interaction of citrus flavonoids and bovine β-lactoglobulin in focus

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Computational insights into human UCP1 activators through molecular docking, MM-GBSA, and molecular dynamics simulation studies

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