Analytic Performance Modeling and Analysis of Detailed Neuron Simulations

Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel computer performance has been supporting these developments, and at the same time maintainers of neuroscientific simulation code have strived to optimally and efficiently exploit new hardware features. Current state of the art software for the simulation of biological networks has so far been developed using performance engineering practices, but a thorough analysis and modeling of the computational and performance characteristics, especially in the case of morphologically detailed neuron simulations, is lacking. Other computational sciences have successfully used analytic performance engineering and modeling methods to gain insight on the computational properties of simulation kernels, aid developers in performance optimizations and eventually drive co-design efforts, but to our knowledge a model-based performance analysis of neuron simulations has not yet been conducted. We present a detailed study of the shared-memory performance of morphologically detailed neuron simulations based on the Execution-Cache-Memory (ECM) performance model. We demonstrate that this model can deliver accurate predictions of the runtime of almost all the kernels that constitute the neuron models under investigation. The gained insight is used to identify the main governing mechanisms underlying performance bottlenecks in the simulation. The implications of this analysis on the optimization of neural simulation software and eventually co-design of future hardware architectures are discussed. In this sense, our work represents a valuable conceptual and quantitative contribution to understanding the performance properties of biological networks simulations.Comment: 18 pages, 6 figures, 15 table

Gauge/gravity duality and the interplay of various fractional branes

We consider different types of fractional branes on a Z_2 orbifold of the conifold and analyze in detail the corresponding gauge/gravity duality. The gauge theory possesses a rich and varied dynamics, both in the UV and in the IR. We find the dual supergravity solution which contains both untwisted and twisted 3-form fluxes, related to what are known as deformation and N=2 fractional branes respectively. We analyze the resulting RG flow from the supergravity perspective, by developing an algorithm to easily extract it. We find hints of a generalization of the familiar cascade of Seiberg dualities due to a non-trivial interplay between the different types of fractional branes. We finally consider the IR behavior in several limits, where the dominant effective dynamics is either confining, in a Coulomb phase or runaway, and discuss the resolution of singularities in the dual geometric background.Comment: 38 pages + appendices, 15 figures; v2: refs added and typos correcte

A multi-range approach for Cultural Heritage survey: a case study in Mantua Unesco site

In this paper, a Cultural Heritage survey, performed by employing and integrating different type of acquisition technologies (imagebased and active sensor based) is presented. The aim of the survey is to create a 3D multiscale database, therefore, different restitution scales, from the architectural-urban one to a detail one are taken in consideration. This research is part of a project financed by the Unesco for the study of historical gardens located in Mantua and Sabbioneta, and in particular for the Palazzo Te renaissance gardens in Mantua, which are reported in this paper. First of all, a general survey of the area has been realized by employing the classical aerial photogrammetry in order to provide the actual arboreal and urban furniture conditions of the gardens (1:500 scale). Next, a detailed photogrammetric survey of the Esedra courtyard in Palazzo Te has been performed by using a UAV system. At the end, laser scanning and traditional topography have been used for the terrestrial detailed acquisition of gardens and architectural façades (1:50???1:20 scale). The aim of this research is to create a suitable graphical documentation support for the study of the structure of the gardens, to analyze how they have been modified over the years and as an effective support for eventual future re-design. Moreover, the research has involved a certain number of botanic and archeological investigations, which have been duly acquired and modeled with image based systems. Starting from the acquired datasets with their acquisition scales, a series of comparative analysis have been performed, especially for those areas in which all the systems have been employed. The comparisons have been extracted by analyzing point cloud models obtained by using a topographical network. As a result, the multi-range approach efficiency, obtained by employing the actual available technologies have been illustrated in the present work

Technical and economic analysis of a cogeneration plant fueled by biogas produced from livestock biomass

AbstractThis technical report illustrates an anaerobic digestion plant for the production of biogas designed to be powered by livestock biomass, combined with a 330 kWe CHP unit co-generator, installed in a cattle farm located in the province of Reggio Emilia. The plant consists essentially of a pre-treatment system of the effluents to the load, two anaerobic continuously stirred tank reactors and heated under mesophilic regime sheltered with gasometric coverings with double membrane; at the end of the process of fermentation, the digestate converges in a solid-liquid separation system with helical compression and a storage tank of the clarified fraction, sheltered with a covering for the containment of residual gaseous emissions into the atmosphere. The produced biogas is collected in gasometers placed above the tanks and, after desulfurization, dehumidification and cooling, it fuels the co-generator. The report is determined to illustrate the experimental results for the first 12 months of operation of the plant that confirmed, both in terms of energy and from a financial perspective, the efficiency of biogas plants fueled only by livestock effluents

A basal slip model for Lagrangian finite element simulations of 3D landslides

A Lagrangian numerical approach for the simulation of rapid landslide runouts is presented and discussed. The simulation approach is based on the so-called Particle Finite Element Method. The moving soil mass is assumed to obey a rigid-viscoplastic, non-dilatant DruckerâPrager constitutive law, which is cast in the form of a regularized, pressure-sensitive Bingham model. Unlike in classical formulations of computational fluid mechanics, where no-slip boundary conditions are assumed, basal slip boundary conditions are introduced to account for the specific nature of the landslide-basal surface interface. The basal slip conditions are formulated in the form of modified Navier boundary conditions, with a pressure-sensitive threshold. A special mixed EulerianâLagrangian formulation is used for the elements on the basal interface to accommodate the new slip conditions into the Particle Finite Element Method framework. To avoid inconsistencies in the presence of complex shapes of the basal surface, the no-flux condition through the basal surface is relaxed using a penalty approach. The proposed model is validated by simulating both laboratory tests and a real large-scale problem, and the critical role of the basal slip is elucidated. Copyright © 2016 John Wiley & Sons, Ltd