Reference : Parallel implementation of domain decomposition algorithm for molecular dynamics
Scientific congresses, symposiums and conference proceedings : Paper published in a book
Life sciences : Biochemistry, biophysics & molecular biology
Life sciences : Biotechnology
Engineering, computing & technology : Chemical engineering
Engineering, computing & technology : Computer science
Engineering, computing & technology : Energy
Engineering, computing & technology : Materials science & engineering
Engineering, computing & technology : Mechanical engineering
Computational Sciences
http://hdl.handle.net/10993/5994
Parallel implementation of domain decomposition algorithm for molecular dynamics
English
Berhe, Girma [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC) >]
Peters, Bernhard mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Engineering Research Unit >]
Varrette, Sébastien mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC) >]
Bouvry, Pascal mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC) >]
2009
PARENG 2007
Civil-Comp Press
1-19
Yes
International
978-1-905088-29-4
First International Conference on Parallel, Distributed and Grid Computing for Engineering
April 6-8, 2009
Pecs
Hungary
[en] solid-fuel particles ; domain decomposition ; parallel computing ; load-balancing ; discrete particle method ; molecular dynamics
[en] The objective of this study is to apply a domain decomposition algorithm to the La- grangian based Discrete Particle Method (DPM). The latter deals with the thermal decomposition of solid e.g. biomass fuel particles. It considers each particle as an individual entity that is represented by an instantiation of a class. Modelizing thermal conversion of biomass in real systems involves a large number of particles. This can be achieved in a reasonable computing time only through a parallel implementation able to distribute the particles e.g. objects onto the participating processors. This pa- per present such an implementation based on Orthogonal Recursive Bisection (ORB) method. Due to the fact that the particles may take arbitrary positions within the do- main, a particular issue addressed by the domain decomposition technic used in this work is to generate a load balance for each processors as uniform as possible. Fur- thermore, the particles are coupled via heat transfer. One challenge for the designed algorithm is then to identify the nearest neighbours of each particle so that the nec- essary information can be communicated between them. Since the positions of all particles are subject to change and may migrate from one processor to another, the communication links together with the number of neighbors are highly dynamic. The implementation is carried out using the KAAPI API, a C++ library for parallel pro- gramming that allows to execute ?ne/medium grain multithreaded computation with dynamic data ?ow synchronizations. First results are very promising since they indi- cate that our algorithm creates sub domains with an average imbalance ranging from 2.5% to 6.3% for uniformly distributed particles.
University of Luxembourg: High Performance Computing - ULHPC
http://hdl.handle.net/10993/5994
Proceedings of the First International Conference on Parallel, Distributed and Grid Computing for Engineering

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Limited access
girma_berhe_peng09.pdfNo commentaryAuthor postprint356.83 kBRequest a copy

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.