PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

Interconnection networks for parallel molecular dynamics simulation based on hamiltonian cubic symmetric topology
Dragan Marušič, Klavdija Kutnar, Urban Borštnik and Dušanka Janežič
J. math. chem Volume 45, Number 2, pp. 372-385, 2009. ISSN 0259-9791


A class of interconnection networks for efficient parallel MD simulations based on hamiltonian cubic symmetric graphs is presented. The cubic symmetric graphs have many desirable properties as interconnection networks since they have a low degree and are vertex- and edge-transitive. We present a method for scheduling collective communication routines that are used in parallel MD and are based on the property that the graphs in question have a Hamilton cycle, that is, a cycle going through all vertices of the graph. Analyzing these communication routines shows that hamiltonian cubic symmetric graphs of small diameter are good candidates for a topology that gives rise to an interconnection network with excellent properties, allowing faster communication and thus speeding up parallel MD simulation.

EPrint Type:Article
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Theory & Algorithms
ID Code:8228
Deposited By:Boris Horvat
Deposited On:21 February 2012