Computational Aerodynamics on unstructed meshes

New 2D and 3D unstructured-grid based flow solvers have been developed for simulating steady compressible flows for aerodynamic applications. The codes employ the full compressible Euler/Navier-Stokes equations. The Spalart-Al Imaras one equation turbulence model is used to model turbulence effects of flows. The spatial discretisation has been obtained using a cell-centred finite volume scheme on unstructured-grids, consisting of triangles in 2D and of tetrahedral and prismatic elements in 3D. The temporal discretisation has been obtained with an explicit multistage Runge-Kutta scheme. An "inflation" mesh generation technique is introduced to effectively reduce the difficulty in generating highly stretched 2D/3D viscous grids in regions near solid surfaces. The explicit flow method is accelerated by the use of a multigrid method with consideration of the high grid aspect ratio in viscous flow simulations. A solution mesh adaptation technique is incorporated to improve the overall accuracy of the 2D inviscid and viscous flow solutions. The 3D flow solvers are parallelised in a MIMD fashion aimed at a PC cluster system to reduce the computing time for aerodynamic applications. The numerical methods are first applied to several 2D inviscid flow cases, including subsonic flow in a bump channel, transonic flow around a NACA0012 airfoil and transonic flow around the RAE 2822 airfoil to validate the numerical algorithms. The rest of the 2D case studies concentrate on viscous flow simulations including laminar/turbulent flow over a flat plate, transonic turbulent flow over the RAE 2822 airfoil, and low speed turbulent flows in a turbine cascade with massive separations. The results are compared to experimental data to assess the accuracy of the method. The over resolved problem with mesh adaptation on viscous flow simulations is addressed with a two phase mesh reconstruction procedure. The solution convergence rate with the aspect ratio adaptive multigrid method and the direct connectivity based multigrid is assessed in several viscous turbulent flow simulations. Several 3D test cases are presented to validate the numerical algorithms for solving Euler/Navier-Stokes equations. Inviscid flow around the M6 wing airfoil is simulated on the tetrahedron based 3D flow solver with an upwind scheme and spatial second order finite volume method. The efficiency of the multigrid for inviscid flow simulations is examined. The efficiency of the parallelised 3D flow solver and the PC cluster system is assessed with simulations of the same case with different partitioning schemes. The present parallelised 3D flow solvers on the PC cluster system show satisfactory parallel computing performance. Turbulent flows over a flat plate are simulated with the tetrahedron based and prismatic based flow solver to validate the viscous term treatment. Next, simulation of turbulent flow over the M6 wing is carried out with the parallelised 3D flow solvers to demonstrate the overall accuracy of the algorithms and the efficiency of the multigrid method. The results show very good agreement with experimental data. A highly stretched and well-formed computational grid near the solid wall and wake regions is generated with the "inflation" method. The aspect ratio adaptive multigrid displayed a good acceleration rate. Finally, low speed flow around the NREL Phase 11 Wind turbine is simulated and the results are compared to the experimental data

Reverse engineering a gene network using an asynchronous parallel evolution strategy.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: The use of reverse engineering methods to infer gene regulatory networks by fitting mathematical models to gene expression data is becoming increasingly popular and successful. However, increasing model complexity means that more powerful global optimisation techniques are required for model fitting. The parallel Lam Simulated Annealing (pLSA) algorithm has been used in such approaches, but recent research has shown that island Evolutionary Strategies can produce faster, more reliable results. However, no parallel island Evolutionary Strategy (piES) has yet been demonstrated to be effective for this task. RESULTS: Here, we present synchronous and asynchronous versions of the piES algorithm, and apply them to a real reverse engineering problem: inferring parameters in the gap gene network. We find that the asynchronous piES exhibits very little communication overhead, and shows significant speed-up for up to 50 nodes: the piES running on 50 nodes is nearly 10 times faster than the best serial algorithm. We compare the asynchronous piES to pLSA on the same test problem, measuring the time required to reach particular levels of residual error, and show that it shows much faster convergence than pLSA across all optimisation conditions tested. CONCLUSIONS: Our results demonstrate that the piES is consistently faster and more reliable than the pLSA algorithm on this problem, and scales better with increasing numbers of nodes. In addition, the piES is especially well suited to further improvements and adaptations: Firstly, the algorithm's fast initial descent speed and high reliability make it a good candidate for being used as part of a global/local search hybrid algorithm. Secondly, it has the potential to be used as part of a hierarchical evolutionary algorithm, which takes advantage of modern multi-core computing architectures

Grenoble Traffic Lab: An experimental platform for advanced traffic monitoring and forecasting

International audienceThis paper describes the main features of the "Grenoble Traffic Lab" (GTL), a new experimental platform for the collection of traffic data coming from a dense network of wireless sensors installed in the south ring of Grenoble, in France. The main challenges related to the configuration of the platform and data validation are discussed, and two relevant traffic monitoring and forecasting applications are presented to illustrate the operation of GTL

Radial Basis Functions: Biomedical Applications and Parallelization

Radial basis function (RBF) is a real-valued function whose values depend only on the distances between an interpolation point and a set of user-specified points called centers. RBF interpolation is one of the primary methods to reconstruct functions from multi-dimensional scattered data. Its abilities to generalize arbitrary space dimensions and to provide spectral accuracy have made it particularly popular in different application areas, including but not limited to: finding numerical solutions of partial differential equations (PDEs), image processing, computer vision and graphics, deep learning and neural networks, etc. The present thesis discusses three applications of RBF interpolation in biomedical engineering areas: (1) Calcium dynamics modeling, in which we numerically solve a set of PDEs by using meshless numerical methods and RBF-based interpolation techniques; (2) Image restoration and transformation, where an image is restored from its triangular mesh representation or transformed under translation, rotation, and scaling, etc. from its original form; (3) Porous structure design, in which the RBF interpolation used to reconstruct a 3D volume containing porous structures from a set of regularly or randomly placed points inside a user-provided surface shape. All these three applications have been investigated and their effectiveness has been supported with numerous experimental results. In particular, we innovatively utilize anisotropic distance metrics to define the distance in RBF interpolation and apply them to the aforementioned second and third applications, which show significant improvement in preserving image features or capturing connected porous structures over the isotropic distance-based RBF method. Beside the algorithm designs and their applications in biomedical areas, we also explore several common parallelization techniques (including OpenMP and CUDA-based GPU programming) to accelerate the performance of the present algorithms. In particular, we analyze how parallel programming can help RBF interpolation to speed up the meshless PDE solver as well as image processing. While RBF has been widely used in various science and engineering fields, the current thesis is expected to trigger some more interest from computational scientists or students into this fast-growing area and specifically apply these techniques to biomedical problems such as the ones investigated in the present work

Automated Hardware Prototyping for 3D Network on Chips

Vor mehr als 50 Jahren stellte Intel® Mitbegründer Gordon Moore eine Prognose zum Entwicklungsprozess der Transistortechnologie auf. Er prognostizierte, dass sich die Zahl der Transistoren in integrierten Schaltungen alle zwei Jahre verdoppeln wird. Seine Aussage ist immer noch gültig, aber ein Ende von Moores Gesetz ist in Sicht. Mit dem Ende von Moore’s Gesetz müssen neue Aspekte untersucht werden, um weiterhin die Leistung von integrierten Schaltungen zu steigern. Zwei mögliche Ansätze für "More than Moore” sind 3D-Integrationsverfahren und heterogene Systeme. Gleichzeitig entwickelt sich ein Trend hin zu Multi-Core Prozessoren, basierend auf Networks on chips (NoCs). Neben dem Ende des Mooreschen Gesetzes ergeben sich bei immer kleiner werdenden Technologiegrößen, vor allem jenseits der 60 nm, neue Herausforderungen. Eine Schwierigkeit ist die Wärmeableitung in großskalierten integrierten Schaltkreisen und die daraus resultierende Überhitzung des Chips. Um diesem Problem in modernen Multi-Core Architekturen zu begegnen, muss auch die Verlustleistung der Netzwerkressourcen stark reduziert werden. Diese Arbeit umfasst eine durch Hardware gesteuerte Kombination aus Frequenzskalierung und Power Gating für 3D On-Chip Netzwerke, einschließlich eines FPGA Prototypen. Dafür wurde ein Takt-synchrones 2D Netzwerk auf ein dreidimensionales asynchrones Netzwerk mit mehreren Frequenzbereichen erweitert. Zusätzlich wurde ein skalierbares Online-Power-Management System mit geringem Ressourcenaufwand entwickelt. Die Verifikation neuer Hardwarekomponenten ist einer der zeitaufwendigsten Schritte im Entwicklungsprozess hochintegrierter digitaler Schaltkreise. Um diese Aufgabe zu beschleunigen und um eine parallele Softwareentwicklung zu ermöglichen, wurde im Rahmen dieser Arbeit ein automatisiertes und benutzerfreundliches Tool für den Entwurf neuer Hardware Projekte entwickelt. Eine grafische Benutzeroberfläche zum Erstellen des gesamten Designablaufs, vom Erstellen der Architektur, Parameter Deklaration, Simulation, Synthese und Test ist Teil dieses Werkzeugs. Zudem stellt die Größe der Architektur für die Erstellung eines Prototypen eine besondere Herausforderung dar. Frühere Arbeiten haben es versäumt, eine schnelles und unkompliziertes Prototyping, insbesondere von Architekturen mit mehr als 50 Prozessorkernen, zu realisieren. Diese Arbeit umfasst eine Design Space Exploration und FPGA-basierte Prototypen von verschiedenen 3D-NoC Implementierungen mit mehr als 80 Prozessoren

Morphogenesis in robot swarms

Morphogenesis allows millions of cells to self-organize into intricate structures with a wide variety of functional shapes during embryonic development. This process emerges from local interactions of cells under the control of gene circuits that are identical in every cell, robust to intrinsic noise, and adaptable to changing environments. Constructing human technology with these properties presents an important opportunity in swarm robotic applications ranging from construction to exploration. Morphogenesis in nature may use two different approaches: hierarchical, top-down control or spontaneously self-organizing dynamics such as reaction-diffusion Turing patterns. Here, we provide a demonstration of purely self-organizing behaviors to create emergent morphologies in large swarms of real robots. The robots achieve this collective organization without any self-localization and instead rely entirely on local interactions with neighbors. Results show swarms of 300 robots that self-construct organic and adaptable shapes that are robust to damage. This is a step toward the emergence of functional shape formation in robot swarms following principles of self-organized morphogenetic engineering

Data-driven deep-learning methods for the accelerated simulation of Eulerian fluid dynamics

Deep-learning (DL) methods for the fast inference of the temporal evolution of fluid-dynamics systems, based on the previous recognition of features underlying large sets of fluid-dynamics data, have been studied. Specifically, models based on convolution neural networks (CNNs) and graph neural networks (GNNs) were proposed and discussed. A U-Net, a popular fully-convolutional architecture, was trained to infer wave dynamics on liquid surfaces surrounded by walls, given as input the system state at previous time-points. A term for penalising the error of the spatial derivatives was added to the loss function, which resulted in a suppression of spurious oscillations and a more accurate location and length of the predicted wavefronts. This model proved to accurately generalise to complex wall geometries not seen during training. As opposed to the image data-structures processed by CNNs, graphs offer higher freedom on how data is organised and processed. This motivated the use of graphs to represent the state of fluid-dynamic systems discretised by unstructured sets of nodes, and GNNs to process such graphs. Graphs have enabled more accurate representations of curvilinear geometries and higher resolution placement exclusively in areas where physics is more challenging to resolve. Two novel GNN architectures were designed for fluid-dynamics inference: the MuS-GNN, a multi-scale GNN, and the REMuS-GNN, a rotation-equivariant multi-scale GNN. Both architectures work by repeatedly passing messages from each node to its nearest nodes in the graph. Additionally, lower-resolutions graphs, with a reduced number of nodes, are defined from the original graph, and messages are also passed from finer to coarser graphs and vice-versa. The low-resolution graphs allowed for efficiently capturing physics encompassing a range of lengthscales. Advection and fluid flow, modelled by the incompressible Navier-Stokes equations, were the two types of problems used to assess the proposed GNNs. Whereas a single-scale GNN was sufficient to achieve high generalisation accuracy in advection simulations, flow simulation highly benefited from an increasing number of low-resolution graphs. The generalisation and long-term accuracy of these simulations were further improved by the REMuS-GNN architecture, which processes the system state independently of the orientation of the coordinate system thanks to a rotation-invariant representation and carefully designed components. To the best of the author’s knowledge, the REMuS-GNN architecture was the first rotation-equivariant and multi-scale GNN. The simulations were accelerated between one (in a CPU) and three (in a GPU) orders of magnitude with respect to a CPU-based numerical solver. Additionally, the parallelisation of multi-scale GNNs resulted in a close-to-linear speedup with the number of CPU cores or GPUs.Open Acces

An efficient and effective convolutional neural network for visual pattern recognition

Convolutional neural networks (CNNs) are a variant of deep neural networks (DNNs) optimized for visual pattern recognition, which are typically trained using first order learning algorithms, particularly stochastic gradient descent (SGD). Training deeper CNNs (deep learning) using large data sets (big data) has led to the concept of distributed machine learning (ML), contributing to state-of-the-art performances in solving computer vision problems. However, there are still several outstanding issues to be resolved with currently defined models and learning algorithms. Propagations through a convolutional layer require flipping of kernel weights, thus increasing the computation time of a CNN. Sigmoidal activation functions suffer from gradient diffusion problem that degrades training efficiency, while others cause numerical instability due to unbounded outputs. Common learning algorithms converge slowly and are prone to hyperparameter overfitting problem. To date, most distributed learning algorithms are still based on first order methods that are susceptible to various learning issues. This thesis presents an efficient CNN model, proposes an effective learning algorithm to train CNNs, and map it into parallel and distributed computing platforms for improved training speedup. The proposed CNN consists of convolutional layers with correlation filtering, and uses novel bounded activation functions for faster performance (up to 1.36x), improved learning performance (up to 74.99% better), and better training stability (up to 100% improvement). The bounded stochastic diagonal Levenberg-Marquardt (B-SDLM) learning algorithm is proposed to encourage fast convergence (up to 5.30% faster and 35.83% better than first order methods) while having only a single hyperparameter. B-SDLM also supports mini-batch learning mode for high parallelism. Based on known previous works, this is among the first successful attempts of mapping a stochastic second order learning algorithm to be deployed in distributed ML platforms. Running the distributed B-SDLM on a 16- core cluster achieves up to 12.08x and 8.72x faster to reach a certain convergence state and accuracy on the Mixed National Institute of Standards and Technology (MNIST) data set. All three complex case studies tested with the proposed algorithms give comparable or better classification accuracies compared to those provided in previous works, but with better efficiency. As an example, the proposed solutions achieved 99.14% classification accuracy for the MNIST case study, and 100% for face recognition using AR Purdue data set, which proves the feasibility of proposed algorithms in visual pattern recognition tasks