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Parallélisation et multiprogrammation pour une application irrégulière de dynamique moléculaire opérationnelle

Abstract : Many numerical parallel methods are implemented to use the modern super computer, but those methods rarely use the technics of regulation and lose their efficiency on unstructured problems. In particular, the numerical simulation of the motion of atoms inside biological structures is one of the irregular problems that need many computational power. The subject concerned in this thesis, through the achievement of a parallel molecular dynamics (MD) software to study proteins, show how threads (or light-weight processes) are useful to parallelize such an application. This work take part of the INRIA-IMAG APACHE project that carry out ATHAPASCAN, a runtime system for the irregular parallel applications, and in collaboration with the laboratory BMC CEA-Grenoble. After an introduction on parallelization technics for applications, we present basic concept of a parallelization technics using threads and message passing. The second part of this document give a synthetic view of the MD models used to study proteins and presents the cut off radius method to approximate forces. Next we propose a parallel implementation of this cut off method using a spatial decomposition of the domain. We study some mapping strategies to find the better compromise between load balancing and communication minimization. Then, we show how multiprogramming is able to overlap communication with computation. Finally, we propose a dynamic load balancing technics of computational load. Many performance measurement on the IBM-SP1 and on the CRAY-T3E are done, and they show scalability of our parallel algorithms.
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https://tel.archives-ouvertes.fr/tel-00004919
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Submitted on : Friday, February 20, 2004 - 10:14:10 AM
Last modification on : Wednesday, March 10, 2021 - 1:50:03 PM
Long-term archiving on: : Thursday, September 13, 2012 - 2:00:43 PM

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  • HAL Id : tel-00004919, version 1

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Pierre-Eric Bernard. Parallélisation et multiprogrammation pour une application irrégulière de dynamique moléculaire opérationnelle. Autre [cs.OH]. Institut National Polytechnique de Grenoble - INPG, 1997. Français. ⟨tel-00004919⟩

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