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Méthodes In-Situ et In-Transit : vers un continuum entre les applications interactives et offline à grande échelle.

Matthieu Dreher 1 
1 MOAIS - PrograMming and scheduling design fOr Applications in Interactive Simulation
Inria Grenoble - Rhône-Alpes, LIG - Laboratoire d'Informatique de Grenoble
Abstract : Parallel simulation has become a very useful tool in various scientific areas. In order to perform such simulations, large parallel machines are required. The computational power of these machine continues to grow, allowing scientists to construct larger and larger models. However, the I/O systems, used to store the data produced by simulation, have not improved at the same pace. Currently, it is already difficult for scientist to store all the accumulated data and to have enough computational power later on to process them. Yet, these data are the key toward major scientific discoveries. In-situ treatments are a promising solution to this problem. The idea is to analyze the data while the simulation is still running and the data are still living in memory. This approach allows avoiding the I/O bottleneck as well as taking benefit of the computational power provided by a supercomputer to perform the analysis. In this thesis, we propose to use the data flow paradigm to construct complex asynchronous in-situ applications. We use the middleware FlowVR to couple heterogeneous parallel codes and to form a graph. Our approach provides enough flexibility to facilitate various placement strategies for the analytics in order to minimize their impact on the simulation. We applied our approach exemplarily to a well-known software from the field of molecular dynamics, Gromacs. With of the of biology experts, we designed several realistic scenarios in which we evaluated both the flexibility of our approach and the capability of our infrastructure to support each step of the biologists' analysis workflow.
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Submitted on : Wednesday, August 31, 2016 - 9:57:29 PM
Last modification on : Wednesday, July 6, 2022 - 4:16:16 AM
Long-term archiving on: : Friday, December 2, 2016 - 12:54:36 AM


  • HAL Id : tel-01358477, version 1



Matthieu Dreher. Méthodes In-Situ et In-Transit : vers un continuum entre les applications interactives et offline à grande échelle.. Calcul parallèle, distribué et partagé [cs.DC]. Collège des Ecoles Doctorales de l'Université Grenoble Alpes, 2015. Français. ⟨tel-01358477⟩



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