Concurrent number cruncher - A GPU implementation of a general sparse linear solver

to appearInternational audienceA wide class of numerical methods needs to solve a linear system, where the matrix pattern of non-zero coefficients can be arbitrary. These problems can greatly benefit from highly multithreaded computational power and large memory bandwidth available on GPUs, especially since dedicated general purpose APIs such as CTM (AMD-ATI) and CUDA (NVIDIA) have appeared. CUDA even provides a BLAS implementation, but only for dense matrices (CuBLAS). Other existing linear solvers for the GPU are also limited by their internal matrix representation. This paper describes how to combine recent GPU programming techniques and new GPU dedicated APIs with high performance computing strategies (namely block compressed row storage, register blocking and vectorization), to implement a sparse general-purpose linear solver. Our implementation of the Jacobi-preconditioned Conjugate Gradient algorithm outperforms by up to a factor of 6.0x leading-edge CPU counterparts, making it attractive for applications which are content with single precision

Algorithmes sur GPU de visualisation et de calcul pour des maillages non-structurés

De nombreux domaines utilisent à présent de nouveaux types de grilles composées de polyèdres arbitraires, autrement dit des grilles fortement non-structurées. La problématique de cette thèse concerne la définition de nouveaux outils de visualisation et de calcul sur de telles grilles. Pour la visualisation, cela pose à la fois le problème du stockage et de l'adaptativité des algorithmes à une géométrie et une topologie variables. Pour le calcul, cela pose le problème de la résolution de grands systèmes linéaires creux non-structurés. Pour aborder ces problèmes, l'augmentation incessante de la puissance de calcul parallèle des processeurs graphiques nous fournit de nouveaux outils. Toutefois, l'utilisation de ces GPU nécessite de définir de nouveaux algorithmes adaptés aux modèles de programmation parallèle qui leur sont spécifiques. Nos contributions sont les suivantes : (1) Une méthode générique de visualisation tirant partie de la puissance de calcul des GPU pour extraire des isosurfaces à partir de grandes grilles fortement non-structurées. (2) Une méthode de classification de cellules qui permet d'accélérer l'extraction d'isosurfaces grâce à une pré-sélection des seules cellules intersectées. (3) Un algorithme d'interpolation temporelle d'isosurfaces. Celui-ci permet de visualiser de manière continue dans le temps l'évolution d'isosurfaces. (4) Un algorithme massivement parallèle de résolution de grands systèmes linéaires non-structurés creux sur le GPU. L'originalité de celui-ci concerne son adaptation à des matrices de motif arbitraire, ce qui le rend applicable à n'importe quel système creux, dont ceux issus de maillages fortement non-structurésThis thesis proposes new tools for visualization and computation on strongly unstructured grids. Visualization of such grids that have variable geometry and topology, poses the problem of how to store data and how algorithms could handle such variability. Doing computations on such grids poses the problem of solving large sparse unstructured linear systems. The ever-growing parallel power of GPUs makes them more and more valuable for handling theses tasks. However, using GPUs calls for defining new algorithms highly adapted to their specific programming model. Most recent algorithms for Geometry Processing or Computational Fluid Dynamics (CFD) are using new types of grids made of arbitrary polyhedra, in other words strongly unstructured grids. In case of CFD simulations, these grids can be mapped with scalar or vector fields representing physical properties (for example : density, porosity, permeability). Our contributions are: (1) An efficient generic visualization method that uses GPU's power to accelerate isosurface extraction for large unstructured grids. (2) An adaptative cell classification method that accelerates isosurface extraction by pre-selecting only intersected cells. (3) An efficient algorithm for temporal interpolation of isosurfaces. This algrithm helps to visualize in a continuous maner the evolution of isosurfaces through time. (4) A massively parallel algorithm for solving large sparse unstructured linear systems on the GPU. Its originality comes from its adaptation to sparse matrices with random pattern, which enables to solve any sparse linear system, thus the ones that come from strongly unstructured gridsNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Insights into the Intraspecific Variability of the above and Belowground Emissions of Volatile Organic Compounds in Tomato

International audienceThe in-vivo monitoring of volatile organic compound (VOC) emissions is a potential non-invasive tool in plant protection, especially in greenhouse cultivation. We studied VOC production from above and belowground organs of the eight parents of the Multi-Parent Advanced Generation Intercross population (MAGIC) tomato population, which exhibits a high genetic variability, in order to obtain more insight into the variability of constitutive VOC emissions from tomato plants under stress-free conditions. Foliage emissions were composed of terpenes, the majority of which were also stored in the leaves. Foliage emissions were very low, partly light-dependent, and differed significantly among genotypes, both in quantity and quality. Soil with roots emitted VOCs at similar, though more variable, rates than foliage. Soil emissions were characterized by terpenes, oxygenated alkanes, and alkenes and phenolic compounds, only a few of which were found in root extracts at low concentrations. Correlation analyses revealed that several VOCs emitted from foliage or soil are jointly regulated and that above and belowground sources are partially interconnected. With respect to VOC monitoring in tomato crops, our results underline that genetic variability, light-dependent de-novo synthesis, and belowground sources are factors to be considered for successful use in crop monitoring

An experimental test of the hypothesis of non-homeostatic consumer stoichiometry in a plant litter-microbe system

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A Comparative Analysis of Dung Beetle Assemblages (Coleoptera: Scarabaeidae: Scarabaeinae, Aphodiinae) Attracted to Sheep and Little Bustard Excrement in Southern France

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Male odor influences both female puberty and sexual perference in mice

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Peripubertal exposure to male odor influences both female puberty and adult sexual preference in mice

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The influence of plant odours on sexual readiness in an insectivorous songbird

International audienceMany organisms rely on environmental cues to predict and anticipate the annual optimal timing of reproduction. In insectivorous birds, preparation for breeding often coincides with the time vegetation starts to develop in spring. Whether there is a direct relationship between the two, and through which mechanisms this link could come about, has rarely been investigated. Plants release herbivore-induced plant volatiles (HIPVs) when they are attacked by insects, and recent studies have shown that birds can detect and orient to those odours when searching for food. Whether those volatiles also stimulate sexual reproductive development and timing of reproduction remains to be discovered. We tested this hypothesis by monitoring gonadal growth in pairs of blue tits (Cyanistes caeruleus) exposed to air from caterpillar-infested oak trees or from a control, in spring. We found that while males and females grew their gonads over time, gonads grew at the same rate in both odour treatments. More exploratory (i.e. a proxy of personality) females did, however, have larger ovarian follicle sizes when exposed to the HIPVs than to the control air, which is consistent with earlier results showing that fast explorers have larger gonads in spring and are more sensitive to HIPVs. If HIPVs constitute powerful attractants in foraging birds, their influence on gonadal development prior to breeding appears to be relatively subtle and to only enhance reproductive readiness in some individuals. These results are nevertheless important as they set olfaction as a new player in the seasonal timing of reproduction in birds