Parallelization on Heterogeneous Multicore and Multi-GPU Systems of the Fast Multipole Method for the Helmholtz Equation Using a Runtime System

International audienceThe Fast Multipole Method (FMM) is considered as one of the top ten algorithms of the 20th century. The FMM can speed up solving of electromagnetic scattering problems. With N being the number of unknowns, the complexity usually O(N 2) becomes O(N log N ) allowing a problem with hundreds of millions of complex unknowns to be solved. The FMM applied in our context has a serious drawback: the parallel version is not very scalable. In this paper, we present a new approach in order to overcome this limit. We use StarPU, a runtime system for heterogeneous multicore architectures. Thus, our aim is to have good efficiency on a cluster with hundreds of CPUs, and GPUs. Much work have been done on parallelization with advanced distribution techniques but never with such a runtime system. StarPU is very useful, especially for the multi-level algorithm on a hybrid machine. At present, we have developed a multi-core and a GPU version. The techniques for distributing and grouping the data are detailed in this paper. The first results of the strategy used are promising

LXXIII.— On the habits of Evania Desjardinsii, Blanch

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Site symmetry and crystal symmetry: a spherical tensor analysis

The relation between the properties of a specific crystallographic site and the properties of the full crystal is discussed by using spherical tensors. The concept of spherical tensors is introduced and the way it transforms under the symmetry operations of the site and from site to site is described in detail. The law of spherical tensor coupling is given and illustrated with the example of the electric dipole and quadrupole transitions in x-ray absorption spectroscopy. The main application of the formalism is the reduction of computation time in the calculation of the properties of crystals by band structure methods. The general approach is illustrated by the examples of substitutional chromium in spinel and substitutional vanadium in garnet.Comment: 27 pages, 3 figure

Phonon effects on x-ray absorption and nuclear magnetic resonance spectroscopies

In material sciences, spectroscopic approaches combining ab initio calculations with experiments are commonly used to accurately analyze the experimental spectral data. Most state-of-the-art first-principle calculations are usually performed assuming an equilibrium static lattice. Yet, nuclear motion affects spectra even when reduced to the zero-point motion at 0 K. We propose a framework based on Density-Functional Theory that includes quantum thermal fluctuations in theoretical X- ray Absorption Near-Edge Structure (XANES) and solid-state Nuclear Magnetic Resonance (NMR) spectroscopies and allows to well describe temperature effects observed experimentally. Within the Born-Oppenheimer and quasi-harmonic approximations, we incorporate the nuclear motion by generating several non-equilibrium configurations from the dynamical matrix. The averaged calculated XANES and NMR spectral data have been compared to experiments in MgO, proof-of-principle compound. The good agreement obtained between experiments and calculations validates the developed approach, which suggests that calculating the XANES spectra at finite temperature by averaging individual non-equilibrium configurations is a suitable approximation. This study high- lights the relevance of phonon renormalization and the relative contributions of thermal expansion and nuclear dynamics on NMR and XANES spectra on a wide range of temperatures.Comment: 13 pages, 6 figures, 1 appendi

Perceptions chrétiennes de l'islamisation et de l'arabisation de l'espace du Bilâd al-Shâm durant les XIIe et XIIIe siècles

Résumé : Suite à la première croisade (1096-1099) qui aboutit à l’établissement de quatre États latins au Proche-Orient, les chrétiens et les musulmans s’engagent durant les deux siècles suivants dans une lutte pour le contrôle du territoire syro-palestinien, également connu sous le nom de Bilâd al-Shâm. Toutefois, l’essor de nouvelles dynasties musulmanes, soit les zengides, les ayyoubides et les mameloukes, permet avec le regain du jihad une reconquête graduelle des possessions chrétiennes, mettant fin à l’existence des États latins d’Orient en 1291 malgré plusieurs croisades. Cette reconquête progressive menée par les musulmans s’accompagne de divers processus d’appropriation et de marquage de l’espace obéissant à un cadre islamique et pouvant être regroupés selon deux concepts : l’islamisation et l’arabisation. En analysant plusieurs sources chrétiennes latines, telles des chroniques, des récits de pèlerinage et des projets de croisade, nous constatons que les chrétiens affichent une certaine connaissance de ces processus d’appropriation religieuse, politique, sociale et culturelle. À la lumière des perceptions chrétiennes de l’islam et de la polémique anti-musulmane, la présente étude se penche sur les différents processus d’islamisation et d’arabisation perçus par les chrétiens latins et démontre comment ces processus sont interprétés par ces derniers. // Abstract : After the First Crusade (1096-1099) and the establishment of four Crusader states in the Near East, Christians and Muslims initiate a two century struggle for the control of the Levant, also known as Bilâd al-Shâm. However, the rise of new Muslim powers, such as the Zengid, Ayyubid and Mamluk dynasties, allows a revival of jihad and a gradual conquest of Christian territories, thus putting an end to the Crusader states in 1291. This conquest is accompanied by several mechanisms of territorial appropriation in the newly captured territories, linked to processes of Islamization and Arabization. By analyzing many Latin sources, such as chronicles, pilgrimage relations and Crusade manifestos, we find that Christians show a certain knowledge of these processes of religious, political, social and cultural appropriation. In light of Christian perceptions of Islam and of the anti-Islamic polemic, this study examines the different processes of Islamization and Arabization as seen by Christians and shows how these processes were understood

First-principles calculations of X-ray absorption spectra at the K-edge of 3d transition metals: an electronic structure analysis of the pre-edge

International audienceWe first present an extended introduction of the various methods used to extract electronic and structural information from the K pre-edge X-ray absorption spectra of 3d transition metal ions. The K pre-edge structure is then modelled for a selection of 3d transition metal compounds and analyzed using first-principles calculations based on the density functional theory (DFT) in the local density approximation (LDA). The selected compounds under study are presented in an ascending order of electronic structure complexity, starting with the Ti K-edge of rutile and anatase, and finishing with the Fe K-edge of the cyanomet-myoglobin. In most cases, the calculations are compared to polarized experimental spectra. It is shown that DFT-LDA methods enable us to reproduce satisfactorily the experimental features and to understand the nature of the electronic transitions involved in the pre-edge region. The limiting aspects of such methods in modelling the core-hole electron interaction and the 3d electron-electron repulsion are also pointed out

Organ specificity in the plant circadian clock

Circadian clocks are endogenous oscillators that control many physiological processes and confer functional and adaptive advantages in various organisms. These molecular oscillators comprise several interlocked feedback loops at the gene expression level. In plants, the circadian clock was recently shown to be organ specific. The root clock seemed to involve only a morning loop whereas the shoot clock also includes an evening loop in a more complex structure. My work aimed at refining the differences and similarities between the shoot and root clocks, using a combination of experimental and theoretical approaches. I developed an imaging method to obtain more data from the shoot and root clocks over time in various conditions. Some previous results were confirmed: the free running periods (FRPs) are longer in roots compared to shoots under constant light (LL). In addition, the amplitude of clock gene expression rhythms is lower in roots compared to shoots. However, the expression of several evening genes is circadian in roots, contrary to previous conclusions. This was confirmed with qPCR, and was observed in both light- and dark-grown roots. Yet light affects clock gene expression in roots, so an automatic covering system was designed to keep the roots in darkness and obtain data in more physiological conditions. Clock genes behaved differently in shoots and light-grown roots that were in the same environmental conditions, and may be differentially affected by blue and red light. However shoot and root clocks were more similar under constant darkness (DD). My imaging and RT-qPCR data, together with new microarray results and preliminary studies on clock mutants suggest that shoot and root circadian systems may have a similar structure but different input pathways. Entrainment is a fundamental property of circadian systems, which can be reset by cues such as light/dark (LD) cycles. I demonstrated that light can directly entrain the root clock in decapitated plants. The root clock could be entrained by a broad range of T cycles using low light intensity. In addition, rhythms were preferably entrained by low light than by any putative signal from shoots in experiments using conflicting LD cycles of different strengths. My results indicate that direct entrainment by LD cycles could be the main mechanism that synchronise the shoot and root clocks at constant temperature. This is physiologically relevant because dark-grown roots can perceive light channelled by the exposed tissues, in a fibre optic way. I also showed for the first time that clock and output genes could be rapidly entrained by temperature cycles in roots. Several mathematical models of the shoot circadian clock were used to try and fit the root clock data by optimising some parameters. The best set of parameters gave a good qualitative fit to root data under LD, LL and DD. It reproduced the long FRP observed in roots under LL and captured the entrainment under LD with lower amplitude in roots. The parameters that were changed for these simulations were all related to light input, which supports the idea of similar clock structures in shoots and roots but with different input pathways. Together my results confirmed that the plant circadian clock is organ specific and suggest that it is organ autonomous

Local, Short-term Effects of Forest Harvesting on Breeding Waterfowl and Common Loon in Forest-Dominated Landscapes of Quebec

Northern forests are major breeding habitats for several waterfowl and other waterbird species. In Quebec, as in many other areas within the boreal region, clear-cut logging is an important human activity, and it is likely to affect ground- and cavity-nesting species differently. We used Black Duck Joint Venture/Canadian Wildlife Service aerial survey data, together with Quebec digital forest maps, to investigate local, i.e., within 2 km of clear-cut areas, short-term (~ 4 yr) effects of forest harvesting on waterfowl and Common Loon. Our predictions were that clear-cut logging would not affect ground nesters, but would negatively affect pair settling patterns in cavity nesters through nesting habitat disturbance. Our study spanned a 540,000-km² territory in which we considered over 30,000 ha of clear-cut areas that were dispersed into 42 different locations. We controlled for interannual variation in population size by comparing the pre- and post-harvest percentages of potentially hospitable nesting cover disturbed by timber harvesting within a 1-km radius of indicated breeding pairs. Our results suggest that timber harvesting positively influenced local populations of Canada Goose and American Green-winged Teal. No other ground-nesting species showed a significant response. For the cavity-nesting guild and species, we detected no local, short-term effect of clear-cutting. This result was unexpected because many previous studies of nest-box provisioning reported increased breeding pair densities, indicating that availability of natural holes may limit cavity-nesting duck populations. Moreover, because cavity-nesting ducks are considered among the most vulnerable bird species to forest management, our results are consistent with the hypothesis that boreal bird populations exhibit some resilience to disturbance. This conclusion follows from a study in landscapes where forests were mostly first-growth. It is not evident that it will remain valid following subsequent clear-cutting episodes and long-term forestry

Description et comparaison de la socioconstruction des connaissances dans trois contextes d’apprentissage différents du milieu scolaire

L’étude décrit et compare la socioconstruction des connaissances dans trois contextes scolaires d’apprentissage. Elle s’appuie sur les concepts clés du socioconstructivisme. Chaque interaction est décrite sous trois dimensions linguistique, sociocognitive et socio‐émotionnelle. L’étude décrit et compare la socioconstruction des connaissances sous les angles de l’égalité de la participation, du type sociocognitif et du climat socioémotionnel. On observe qu’elle est plus présente dans l’environnement où les interactants communiquent par écrit, sans présence physique et de façon asynchrone; elle est moins marquée là où les interactants sont présents physiquement ou communiquent par vidéoconférence. Favoriser l’expression d’opinions et traiter les désaccords pour augmenter les consensus amélioreraient la socioconstruction