Comprendre et Guider la Gestion des Ressources de Calcul dans unContexte Multi-Modèles de Programmation

With the advent of multicore and manycore processors as buildingblocks of HPC supercomputers, many applications shift from relying solely on a distributed programming model (e.g., MPI) to mixing distributed and shared-memory models (e.g., MPI+OpenMP). This leads to a better exploitation of shared-memory communications and reduces the overall memory footprint.However, this evolution has a large impact on the software stack as applications’ developers do typically mix several programming models to scale over a largenumber of multicore nodes while coping with their hiearchical depth. Oneside effect of this programming approach is runtime stacking: mixing multiplemodels involve various runtime libraries to be alive at the same time. Dealing with different runtime systems may lead to a large number of execution flowsthat may not efficiently exploit the underlying resources.We first present a study of runtime stacking. It introduces stacking configurations and categories to describe how stacking can appear in applications.We explore runtime-stacking configurations (spatial and temporal) focusing on thread/process placement on hardware resources from different runtime libraries. We build this taxonomy based on the analysis of state-of-the-artruntime stacking and programming models.We then propose algorithms to detect the misuse of compute resources when running a hybrid parallel application. We have implemented these algorithms inside a dynamic tool, called the Overseer. This tool monitors applications,and outputs resource usage to the user with respect to the application timeline, focusing on overloading and underloading of compute resources.Finally, we propose a second external tool called Overmind, that monitors the thread/process management and (re)maps them to the underlyingcores taking into account the hardware topology and the application behavior. By capturing a global view of resource usage the Overmind adapts theprocess/thread placement, and aims at taking the best decision to enhance the use of each compute node inside a supercomputer. We demonstrate the relevance of our approach and show that our low-overhead implementation is able to achieve good performance even when running with configurations that would have ended up with bad resource usage.La simulation numérique reproduit les comportements physiquesque l’on peut observer dans la nature. Elle est utilisée pour modéliser des phénomènes complexes, impossible à prédire ou répliquer. Pour résoudre ces problèmes dans un temps raisonnable, nous avons recours au calcul haute performance (High Performance Computing ou HPC en anglais). Le HPC regroupe l’ensemble des techniques utilisées pour concevoir et utiliser les super calcula-teurs. Ces énormes machines ont pour objectifs de calculer toujours plus vite,plus précisément et plus efficacement.Pour atteindre ces objectifs, les machines sont de plus en plus complexes. La tendance actuelle est d’augmenter le nombre cœurs de calculs sur les processeurs,mais aussi d’augmenter le nombre de processeurs dans les machines. Les ma-chines deviennent de plus en hétérogènes, avec de nombreux éléments différents à utiliser en même temps pour extraire le maximum de performances. Pour pallier ces difficultés, les développeurs utilisent des modèles de programmation,dont le but est de simplifier l’utilisation de toutes ces ressources. Certains modèles, dits à mémoire distribuée (comme MPI), permettent d’abstraire l’envoi de messages entre les différents nœuds de calculs, d’autres dits à mémoire partagée, permettent de simplifier et d’optimiser l’utilisation de la mémoire partagée au sein des cœurs de calcul.Cependant, ces évolutions et cette complexification des supercalculateurs à un large impact sur la pile logicielle. Il est désormais nécessaire d’utiliser plusieurs modèles de programmation en même temps dans les applications.Ceci affecte non seulement le développement des codes de simulations, car les développeurs doivent manipuler plusieurs modèles en même temps, mais aussi les exécutions des simulations. Un effet de bord de cette approche de la programmation est l’empilement de modèles (‘Runtime Stacking’) : mélanger plusieurs modèles implique que plusieurs bibliothèques fonctionnent en même temps. Gérer plusieurs bibliothèques peut mener à un grand nombre de fils d’exécution utilisant les ressources sous-jacentes de manière non optimaleL’objectif de cette thèse est d’étudier l’empilement des modèles de programmation et d’optimiser l’utilisation de ressources de calculs par ces modèles au cours de l’exécution des simulations numériques. Nous avons dans un premier temps caractérisé les différentes manières de créer des codes de calcul mélangeant plusieurs modèles. Nous avons également étudié les différentes interactions que peuvent avoir ces modèles entre eux lors de l’exécution des simulations.De ces observations nous avons conçu des algorithmes permettant de détecter des utilisations de ressources non optimales. Enfin, nous avons développé un outil permettant de diriger automatiquement l’utilisation des ressources par les différents modèles de programmation

Mise en forme topologique : lumière et cristaux liquides

The enclosed work deals with the study of the topological shaping of light and matter and will bedivided into two categories of research. The first focuses on the topological shaping of light from liquid-crystal based spin-orbit interfaces. In particular, we show in this manuscript, that different systems based on the use of natural topological defects behave as highly efficient natural optical spin-orbit encoders, for distinct topological charges, at the micron scale and with spatial control.The operating wave length and operation mode of such interfaces can be tuned in real-time using low voltage electric fields. This breakthrough opens the path to the ultra-broadband control of the light’sorbital state. The second category concerns the topological shaping of a cholesteric liquid crystal film in context of mass data storage. We show the potential to generate metastable topological mi-crostructures in a controlled and reconfigurable way, both in time and space and with a low energy cost. We also demonstrated a new, unique type of rewritable memory, controlled by the«spin»ofthe laser-generated incident photonCe travail de thèse consiste en l’étude de la mise en forme topologique de la lumière et de la matière et s’articule autour de deux axes de recherche. Le premier concerne la mise en forme topologique de la lumière à partir d’interfaces spin-orbite à base de cristaux liquides. En l’occurrence, nous montrons dans ce manuscrit que différents systèmes de défauts topologiques naturels permettent de générer des vortex optiques par interaction spin-orbite de la lumière, de manière efficace, accordable en longueur d’onde et reconfigurable en temps réel et donnant accès à des charges topologiques diverses. Tout ceci nous a permis de travailler à des échelles microscopiques et de manière spatialement contrôlée. Ces avancées ouvrent la voie au contrôle de l’état orbital de la lumière sur une large bande spectrale.Le second axe concerne la mise en forme topologique d’un film de cristal liquide cholestérique dans le cadre du stockage de l’information de nature topologique. Nous avons démontré la possibilité de générer une grande diversité de défauts topologiques métastables, de manière contrôlée et reconfigurable, à la fois dans le temps et dans l’espace. Nous avons développé une approche permettant de réduire drastiquement le coût énergétique d’écriture de ces défauts. Nous avons également montré qu’il était possible d’obtenir un nouveau type de mémoire réinscriptible contrôlé par le degré de liberté «spin» du photon

Fabrication of Capacitive Acoustic Resonators Combining 3D Printing and 2D Inkjet Printing Techniques

International audienceA capacitive acoustic resonator developed by combining three-dimensional (3D) printing and two-dimensional (2D) printed electronics technique is described. During this work, a patterned bottom structure with rigid backplate and cavity is fabricated directly by a 3D printing method, and then a direct write inkjet printing technique has been employed to print a silver conductive layer. A novel approach has been used to fabricate a diaphragm for the acoustic sensor as well, where the conductive layer is inkjet-printed on a pre-stressed thin organic film. After assembly, the resulting structure contains an electrically conductive diaphragm positioned at a distance from a fixed bottom electrode separated by a spacer. Measurements confirm that the transducer acts as capacitor. The deflection of the diaphragm in response to the incident acoustic single was observed by a laser Doppler vibrometer and the corresponding change of capacitance has been calculated, which is then compared with the numerical result. Observation confirms that the device performs as a resonator and provides adequate sensitivity and selectivity at its resonance frequency

Analysis of acute brain slices by electron microscopy: A correlative light-electron microscopy workflow based on Tokuyasu cryo-sectioning.

Acute brain slices are slices of brain tissue that are kept vital in vitro for further recordings and analyses. This tool is of major importance in neurobiology and allows the study of brain cells such as microglia, astrocytes, neurons and their inter/intracellular communications via ion channels or transporters. In combination with light/fluorescence microscopies, acute brain slices enable the ex vivo analysis of specific cells or groups of cells inside the slice, e.g. astrocytes. To bridge ex vivo knowledge of a cell with its ultrastructure, we developed a correlative microscopy approach for acute brain slices. The workflow begins with sampling of the tissue and precise trimming of a region of interest, which contains GFP-tagged astrocytes that can be visualised by fluorescence microscopy of ultrathin sections. The astrocytes and their surroundings are then analysed by high resolution scanning transmission electron microscopy (STEM). An important aspect of this workflow is the modification of a commercial cryo-ultramicrotome to observe the fluorescent GFP signal during the trimming process. It ensured that sections contained at least one GFP astrocyte. After cryo-sectioning, a map of the GFP-expressing astrocytes is established and transferred to correlation software installed on a focused ion beam scanning electron microscope equipped with a STEM detector. Next, the areas displaying fluorescence are selected for high resolution STEM imaging. An overview area (e.g. a whole mesh of the grid) is imaged with an automated tiling and stitching process. In the final stitched image, the local organisation of the brain tissue can be surveyed or areas of interest can be magnified to observe fine details, e.g. vesicles or gold labels on specific proteins. The robustness of this workflow is contingent on the quality of sample preparation, based on Tokuyasu's protocol. This method results in a reasonable compromise between preservation of morphology and maintenance of antigenicity. Finally, an important feature of this approach is that the fluorescence of the GFP signal is preserved throughout the entire preparation process until the last step before electron microscopy

Correlation of fluorescence microscopy, electron microscopy, and NanoSIMS stable isotope imaging on a single tissue section.

Correlative light and electron microscopy allows localization of specific molecules at the ultrastructural level in biological tissue but does not provide information about metabolic turnover or the distribution of labile molecules, such as micronutrients. We present a method to directly correlate (immuno)fluorescent microscopy, (immuno)TEM imaging and NanoSIMS isotopic mapping of the same tissue section, with nanometer-scale spatial precision. The process involves chemical fixation of the tissue, cryo sectioning, thawing, and air-drying under a thin film of polyvinyl alcohol. It permits to effectively retain labile compounds and strongly increases NanoSIMS sensitivity for 13C-enrichment. The method is illustrated here with correlated distribution maps of a carbonic anhydrase enzyme isotype, β-tubulin proteins, and 13C- and 15N-labeled labile micronutrients (and their anabolic derivates) within the tissue of a reef-building symbiotic coral. This broadly applicable workflow expands the wealth of information that can be obtained from multi-modal, sub-cellular observation of biological tissue

Toxoplasma gondii F-actin forms an extensive filamentous network required for material exchange and parasite maturation

Apicomplexan actin is important during the parasite's life cycle. Its polymerization kinetics are unusual, permitting only short, unstable F-actin filaments. It has not been possible to study actin in vivo and so its physiological roles have remained obscure, leading to models distinct from conventional actin behaviour. Here a modified version of the commercially available actin-chromobody was tested as a novel tool for visualising F-actin dynamics in Toxoplasma gondii. Cb labels filamentous actin structures within the parasite cytosol and labels an extensive F-actin network that connects parasites within the parasitophorous vacuole and allows vesicles to be exchanged between parasites. In the absence of actin, parasites lack a residual body and inter-parasite connections and grow in an asynchronous and disorganized manner. Collectively, these data identify new roles for actin in the intracellular phase of the parasites lytic cycle and provide a robust new tool for imaging parasitic F-actin dynamics

Correlative Light, Electron Microscopy and Raman Spectroscopy Workflow To Detect and Observe Microplastic Interactions with Whole Jellyfish.

Many researchers have turned their attention to understanding microplastic interaction with marine fauna. Efforts are being made to monitor exposure pathways and concentrations and to assess the impact such interactions may have. To answer these questions, it is important to select appropriate experimental parameters and analytical protocols. This study focuses on medusae of Cassiopea andromeda jellyfish: a unique benthic jellyfish known to favor (sub-)tropical coastal regions which are potentially exposed to plastic waste from land-based sources. Juvenile medusae were exposed to fluorescent poly(ethylene terephthalate) and polypropylene microplastics (<300 μm), resin embedded, and sectioned before analysis with confocal laser scanning microscopy as well as transmission electron microscopy and Raman spectroscopy. Results show that the fluorescent microplastics were stable enough to be detected with the optimized analytical protocol presented and that their observed interaction with medusae occurs in a manner which is likely driven by the microplastic properties (e.g., density and hydrophobicity)

Temperature and feeding induce tissue level changes in autotrophic and heterotrophic nutrient allocation in the coral symbiosis – A NanoSIMS study

Corals access inorganic seawater nutrients through their autotrophic endosymbiotic dinoflagellates, but also capture planktonic prey through heterotrophic feeding. Correlating NanoSIMS and TEM imaging, we visualized and quantified the subcellular fate of autotrophic and heterotrophic C and N in the coral Stylophora pistillata using stable isotopes. Six scenarios were compared after 6 h: autotrophic pulse (13C-bicarbonate, 15N-nitrate) in either unfed or regularly fed corals, and heterotrophic pulse (13C-, 15N-labelled brine shrimps) in regularly fed corals; each at ambient and elevated temperature. Host assimilation of photosynthates was similar under fed and unfed conditions, but symbionts assimilated 10% more C in fed corals. Photoautotrophic C was primarily channelled into host lipid bodies, whereas heterotrophic C and N were generally co-allocated to the tissue. Food-derived label was detected in some subcellular structures associated with the remobilisation of host lipid stores. While heterotrophic input generally exceeded autotrophic input, it was more negatively affected by elevated temperature. The reduced input from both modes of nutrition at elevated temperature was accompanied by a shift in the partitioning of C and N, benefiting epidermis and symbionts. This study provides a unique view into the nutrient partitioning in corals and highlights the tight connection of nutrient fluxes in symbiotic partners