Abstract
Cell dynamics simulation is a very promising approach to model dynamic processes in block copolymer systems at the mesoscale level. A parallel algorithm for large-scale simulation is described in detail. Several performance tuning methods based on SGI Altix are introduced. With the efficient strategy of domain decomposition and the fast method of neighboring points location, we greatly reduce the calculating and communicating cost and successfully perform simulations of large-scale systems with up to 5123 grids. The algorithm is implemented on 32 processors with the speedup of 28.4 and the efficiency of 88.9%.
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References
Dongarra, J., Foster, I., Fox, G., Gropp, W., Kennedy, K., Torczon, L., White, A. (eds.): Sourcebook of Parallel Computing. Elsevier Science, San Francisco (2003)
Guo, X., Pinna, M., Zvelindovsky, A.V.: Parallel algorithm for cell dynamics simulation of block copolymers. Macromolecular Theory and Simulations 16(9), 779–784 (2007)
Oono, Y., Puri, S.: Study of phase-separation dynamics by use of cell dynamical systems. I. Modeling. Physical Review A 38(1), 434–453 (1988)
Pinna, M., Zvelindovsky, A.V.: Kinetic pathways of gyroid-to-cylinder transitions in diblock copolymers under external fields: cell dynamics simulation. Soft Matter 4(2), 316–327 (2008)
Pinna, M., Zvelindovsky, A.V., Todd, S., Goldbeck-Wood, G.: Cubic phases of block copolymers under shear and electric fields by cell dynamics simulation. I. Spherical phase. The Journal of Chemical Physics 125(15), 154905–(1–10) (2006)
Ren, S.R., Hamley, I.W.: Cell dynamics simulations of microphase separation in block copolymers. Macromolecules 34(1), 116–126 (2001)
SGI: Message Passing Toolkit (MPT) User’s Guide. http://docs.sgi.com
Snir, M., Gropp, W.: MPI: The Complete Reference. MIT Press, Cambridge, Massachusetts (1998)
Zvelindovsky, A.V. (ed.): Nanostructured Soft Matter: Experiment, Theory, Simulation and Perspectives. Springer, Dordrecht (2007)
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Guo, X., Pinna, M., Zvelindovsky, A.V. (2009). Parallel Algorithm for Cell Dynamics Simulation of Soft Nano-Structured Matter. In: Parallel Scientific Computing and Optimization. Springer Optimization and Its Applications, vol 27. Springer, New York, NY. https://doi.org/10.1007/978-0-387-09707-7_22
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DOI: https://doi.org/10.1007/978-0-387-09707-7_22
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-09706-0
Online ISBN: 978-0-387-09707-7
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