Automatic efficient data layout for multithreaded stencil codes on CPUs and GPUs

International audienceStencil based computation on structured grids is a kernel at the heart of a large number of scientific applications. The variety of stencil kernels used in practice make this computation pattern difficult to assemble into a high performance computing library. With the multiplication of cores on a single chip, answering architectural alignment requirements became an even more important key to high performance. In addition to vector accesses, data layout optimization must also consider concurrent parallel accesses. In this paper, we develop a strategy to automatically generate stencil codes for multicore vector architectures, searching for the best data layout possible to answer architectural alignment problems. We introduce a new method for aligning multidimensional data structures, called multipadding, that can be adapted to specificities of multicores and GPUs architectures. We present multiple methods with different level of complexity. We show on different stencil patterns that generated codes with multipadding display better performances than existing optimizations

Phases of granular segregation in a binary mixture

We present results from an extensive experimental investigation into granular segregation of a shallow binary mixture in which particles are driven by frictional interactions with the surface of a vibrating horizontal tray. Three distinct phases of the mixture are established viz; binary gas (unsegregated), segregation liquid and segregation crystal. Their ranges of existence are mapped out as a function of the system's primary control parameters using a number of measures based on Voronoi tessellation. We study the associated transitions and show that segregation can be suppressed is the total filling fraction of the granular layer, $C$, is decreased below a critical value, $C_{c}$, or if the dimensionless acceleration of the driving, $\gamma$, is increased above a value $\gamma_{c}$.Comment: 12 pages, 12 figures, submitted to Phys. Rev.

Experiences pour évaluer le recouvrement calcul/communication des collectoves non-bloquates de MP

We present experimental results for evaluating non-blocking MPI collectives. We compute several metrics to asses the efficiency of the overlap for different MPI library, with different configurations and for different hardware.Nous présentons les résultats d’expériences pour l’évaluation des collectives non bloquantes dans MPI. Nous calculons différentes métriques pour évaluer l’efficacité du recouvrement pour différentes bibliothèques MPI avec différentes configurations et pour différents types de matériels

One core dedicated to MPI nonblocking communication progression? A model to assess whether it is worth it

International audienceOverlapping communications with computation is an efficient way to amortize the cost of communications of an HPC application. To do so, it is possible to utilize MPI nonblocking primitives so that communications run in background alongside computation. However, these mechanisms rely on communications actually making progress in the background, which may not be true for all MPI libraries. Some MPI libraries leverage a core dedicated to communications to ensure communication progression. However, taking a core away from the application for such purpose may have a negative impact on the overall execution time. It may be difficult to know when such dedicated core is actually helpful. In this paper, we propose a model for the performance of applications using MPI nonblocking primitives running on top of an MPI library with a dedicated core for communications. This model is used to understand the compromise between computation slowdown due to the communication core not being available for computation, and the communication speed-up thanks to the dedicated core; evaluate whether nonblocking communication is actually obtaining the expected performance in the context of the given application; predict the performance of a given application if ran with a dedicated core. We describe the performance model and evaluate it on different applications. We compare the predictions of the model with actual executions

Electronic and physico-chemical properties of nanmetric boron delta-doped diamond structures

Heavily boron doped diamond epilayers with thicknesses ranging from 40 to less than 2 nm and buried between nominally undoped thicker layers have been grown in two different reactors. Two types of [100]-oriented single crystal diamond substrates were used after being characterized by X-ray white beam topography. The chemical composition and thickness of these so-called deltadoped structures have been studied by secondary ion mass spectrometry, transmission electron microscopy, and spectroscopic ellipsometry. Temperature-dependent Hall effect and four probe resistivity measurements have been performed on mesa-patterned Hall bars. The temperature dependence of the hole sheet carrier density and mobility has been investigated over a broad temperature range (6K<T<450 K). Depending on the sample, metallic or non-metallic behavior was observed. A hopping conduction mechanism with an anomalous hopping exponent was detected in the non-metallic samples. All metallic delta-doped layers exhibited the same mobility value, around 3.660.8 cm2/Vs, independently of the layer thickness and the substrate type. Comparison with previously published data and theoretical calculations showed that scattering by ionized impurities explained only partially this low common value. None of the delta-layers showed any sign of confinement-induced mobility enhancement, even for thicknesses lower than 2 nm.14 page

Spatial heterogeneity of tectonic stress and friction in the crust

The complex geometry of faults, seismicity, and diversity of earthquake mechanisms suggest that the stress and strength in Earth's crust are spatially heterogeneous. We investigated the degree of heterogeneity using the following two end-member models. In one end-member model, we assumed that the orientation of stress is uniform in the crust as is assumed in many stress inversion studies. In this model, the variability of earthquake mechanisms means that friction during faulting must vary for each event. We computed friction μ from the ratio of the resolved shear stress to the effective normal stress on the fault plane with the assumption of hydrostatic pore pressure. The values of μ vary over a large range from 0 to 1.5. In the other extreme model we assumed optimally oriented slip and a constant μ = 0.6, as is suggested by Byerlee's law, for all the earthquakes, and determined the local stress orientation for each earthquake. The orientation of the stress changes drastically from one earthquake to another, and the assumption of uniform stress field commonly used in stress inversion is not warranted. An important conclusion is that a regionally uniform stress field and constant friction on optimally oriented faults are mutually exclusive. The actual situation in the crust is most likely to be intermediate between these two end-member models. From the existing data alone, we cannot determine the degree of heterogeneity uniquely, but both μ and the local stress field near earthquake faults are likely to vary substantially, and studies on earthquake rupture dynamics must take these heterogeneities into consideration

Aqueous dune-like bedforms in Athabasca Valles and neighbouring locations utilized in palaeoflood reconstruction

Putative fluvial dunes have been identified within the Athabasca Valles and associated network of channels on Mars. Previous published work identified and measured bedforms in Athabasca Valles using photoclinometry methods on 2–3 m/pixel resolution Mars Orbiter Camera Narrow Angle images, and argued that these were created by an aqueous megaflood that occurred between 2 and 8 million years ago. This event is likely to have occurred due to geological activity associated with the Cerberus Fossae fracture system at the source of Athabasca Vallis. The present study has used higher resolution, 25 cm/pixel images from the Mars Reconnaissance Orbiter HiRISE camera, as well as stereo-derived digital terrain models and GIS software, to re-measure and evaluate these bedforms together with data from newly discovered neighbouring fields of bedforms. The analysis indicates that the bedforms are aqueous dunes, in that they occur in channel locations where dunes would be expected to be preserved and moreover they have geometries very similar to megaflood dunes on Earth. Dune geometries are used to estimate megaflood discharge rates, including uncertainty, which results support previous flood estimates that indicate that a flood with a discharge of ∼2 × 106m3s−1 created these bedforms

SYNERGISTIC ON AUXIN AND CYTOKININ 1 positively regulates growth and attenuates soil pathogen resistance

Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens. Cytokinin and auxin are two major hormonal regulators of plant growth. Here the authors identify SYAC1, a gene that is synergistically activated by the two hormones being applied together, and show that it is required for normal growth while negatively impacting pathogen resistance