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The scaling of molecular dynamics on the KSR1
Hawaii, USA January 04-January 07
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/HICSS.1995.37534228th Hawaii International Conference ...
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R. Haacke, B. Montgomery Pettitt, "The scaling of molecular dynamics on the KSR1," Hawaii International Conference on System Sciences, pp. 142, 28th Hawaii International Conference on System Sciences (HICSS'95), 1995.
 
 
BibTex
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@article{ 10.1109/HICSS.1995.375342,
author = {R. Haacke and B. Montgomery Pettitt},
title = {The scaling of molecular dynamics on the KSR1},
journal ={Hawaii International Conference on System Sciences},
volume = {0},
year = {1995},
issn = {1060-3425},
pages = {142},
doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.1995.375342},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - Hawaii International Conference on System Sciences
TI - The scaling of molecular dynamics on the KSR1
SN - 1060-3425
SP
EP
A1 - R. Haacke,
A1 - B. Montgomery Pettitt,
PY - 1995
KW - molecular dynamics method; physics; physics computing; digital simulation; parallel machines; parallel algorithms; molecular dynamics; particle based simulation techniques; highly parallelizable; concurrency; irreproducible trajectories; reproducible simulations; performance penalty; ESP; KSR1 parallel computer
VL - 0
JA - Hawaii International Conference on System Sciences
ER -
 
R. Haacke, Dept. of Chem. & Comput. Sci., Houston Univ., TX, USA
B. Montgomery Pettitt, Dept. of Chem. & Comput. Sci., Houston Univ., TX, USA
Molecular dynamics and many other particle based simulation techniques are often highly parallelizable in principle. In practice many algorithms for concurrency can lead to irreproducible trajectories. We suggest a method for providing reproducible simulations that suffers only a small performance penalty. Results for scaling of the molecular dynamics code ESP to the KSR1 parallel computer are also given and the effects of trying to overlap computation and communication on the KSR are discussed. Algorithms are discussed with particular attention focused on the force summation aspects.
Index Terms:
molecular dynamics method; physics; physics computing; digital simulation; parallel machines; parallel algorithms; molecular dynamics; particle based simulation techniques; highly parallelizable; concurrency; irreproducible trajectories; reproducible simulations; performance penalty; ESP; KSR1 parallel computer
Citation:
R. Haacke, B. Montgomery Pettitt, "The scaling of molecular dynamics on the KSR1," hicss, pp.142, 28th Hawaii International Conference on System Sciences (HICSS'95), 1995
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