A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

Mubarak, Misbah; Seol, Seegyoung; Lu, Qiukai; Shephard, Mark S.

doi:10.1155/2013/654971

Title: A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

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Abstract

Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order in a 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood datamore » to carry out computation.« less

Authors:

Mubarak, Misbah ^[1]; Seol, Seegyoung ^[1]; Lu, Qiukai ^[1]; Shephard, Mark S. ^[1]

Scientific Computation Research Center, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180, USA

Publication Date:: Tue Jan 01 00:00:00 EST 2013

Sponsoring Org.:: USDOE

OSTI Identifier:: 1197889

Grant/Contract Number:: FC02-06ER25769

Resource Type:: Published Article

Journal Name:: Scientific Programming

Additional Journal Information:: Journal Name: Scientific Programming Journal Volume: 21 Journal Issue: 1-2; Journal ID: ISSN 1058-9244

Publisher:: Hindawi Publishing Corporation

Country of Publication:: Egypt

Language:: English

Citation Formats


                    Mubarak, Misbah, Seol, Seegyoung, Lu, Qiukai, and Shephard, Mark S. A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database.  Egypt: N. p., 2013. 
Web.  doi:10.1155/2013/654971.

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                    Mubarak, Misbah, Seol, Seegyoung, Lu, Qiukai, & Shephard, Mark S. A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database.  Egypt.  https://doi.org/10.1155/2013/654971

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                    Mubarak, Misbah, Seol, Seegyoung, Lu, Qiukai, and Shephard, Mark S. Tue .  
"A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database".  Egypt.  https://doi.org/10.1155/2013/654971.

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@article{osti_1197889,

  title        = {A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database},

  author       = {Mubarak, Misbah and Seol, Seegyoung and Lu, Qiukai and Shephard, Mark S.},

  abstractNote = {Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order in a 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.},

  doi          = {10.1155/2013/654971},

  journal      = {Scientific Programming},

  number       = 1-2,

  volume       = 21,

  place        = {Egypt},

  year         = {Tue Jan 01 00:00:00 EST 2013},

  month        = {Tue Jan 01 00:00:00 EST 2013}

}

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