New strategies for the aerodynamic design optimization of aeronautical configurations through soft-computing techniques

Premio Extraordinario de Doctorado de la UAH en 2013Lozano Rodríguez, Carlos, codir.This thesis deals with the improvement of the optimization process in the aerodynamic design of aeronautical configurations. Nowadays, this topic is of great importance in order to allow the European aeronautical industry to reduce their development and operational costs, decrease the time-to-market for new aircraft, improve the quality of their products and therefore maintain their competitiveness. Within this thesis, a study of the state-of-the-art of the aerodynamic optimization tools has been performed, and several contributions have been proposed at different levels: -One of the main drawbacks for an industrial application of aerodynamic optimization tools is the huge requirement of computational resources, in particular, for complex optimization problems, current methodological approaches would need more than a year to obtain an optimized aircraft. For this reason, one proposed contribution of this work is focused on reducing the computational cost by the use of different techniques as surrogate modelling, control theory, as well as other more software-related techniques as code optimization and proper domain parallelization, all with the goal of decreasing the cost of the aerodynamic design process. -Other contribution is related to the consideration of the design process as a global optimization problem, and, more specifically, the use of evolutionary algorithms (EAs) to perform a preliminary broad exploration of the design space, due to their ability to obtain global optima. Regarding this, EAs have been hybridized with metamodels (or surrogate models), in order to substitute expensive CFD simulations. In this thesis, an innovative approach for the global aerodynamic optimization of aeronautical configurations is proposed, consisting of an Evolutionary Programming algorithm hybridized with a Support Vector regression algorithm (SVMr) as a metamodel. Specific issues as precision, dataset training size, geometry parameterization sensitivity and techniques for design of experiments are discussed and the potential of the proposed approach to achieve innovative shapes that would not be achieved with traditional methods is assessed. -Then, after a broad exploration of the design space, the optimization process is continued with local gradient-based optimization techniques for a finer improvement of the geometry. Here, an automated optimization framework is presented to address aerodynamic shape design problems. Key aspects of this framework include the use of the adjoint methodology to make the computational requirements independent of the number of design variables, and Computer Aided Design (CAD)-based shape parameterization, which uses the flexibility of Non-Uniform Rational B-Splines (NURBS) to handle complex configurations. The mentioned approach is applied to the optimization of several test cases and the improvements of the proposed strategy and its ability to achieve efficient shapes will complete this study

New strategies for the aerodynamic design optimization of aeronautical configurations through soft-computing techniques

Premio Extraordinario de Doctorado de la UAH en 2013Lozano Rodríguez, Carlos, codir.This thesis deals with the improvement of the optimization process in the aerodynamic design of aeronautical configurations. Nowadays, this topic is of great importance in order to allow the European aeronautical industry to reduce their development and operational costs, decrease the time-to-market for new aircraft, improve the quality of their products and therefore maintain their competitiveness. Within this thesis, a study of the state-of-the-art of the aerodynamic optimization tools has been performed, and several contributions have been proposed at different levels: -One of the main drawbacks for an industrial application of aerodynamic optimization tools is the huge requirement of computational resources, in particular, for complex optimization problems, current methodological approaches would need more than a year to obtain an optimized aircraft. For this reason, one proposed contribution of this work is focused on reducing the computational cost by the use of different techniques as surrogate modelling, control theory, as well as other more software-related techniques as code optimization and proper domain parallelization, all with the goal of decreasing the cost of the aerodynamic design process. -Other contribution is related to the consideration of the design process as a global optimization problem, and, more specifically, the use of evolutionary algorithms (EAs) to perform a preliminary broad exploration of the design space, due to their ability to obtain global optima. Regarding this, EAs have been hybridized with metamodels (or surrogate models), in order to substitute expensive CFD simulations. In this thesis, an innovative approach for the global aerodynamic optimization of aeronautical configurations is proposed, consisting of an Evolutionary Programming algorithm hybridized with a Support Vector regression algorithm (SVMr) as a metamodel. Specific issues as precision, dataset training size, geometry parameterization sensitivity and techniques for design of experiments are discussed and the potential of the proposed approach to achieve innovative shapes that would not be achieved with traditional methods is assessed. -Then, after a broad exploration of the design space, the optimization process is continued with local gradient-based optimization techniques for a finer improvement of the geometry. Here, an automated optimization framework is presented to address aerodynamic shape design problems. Key aspects of this framework include the use of the adjoint methodology to make the computational requirements independent of the number of design variables, and Computer Aided Design (CAD)-based shape parameterization, which uses the flexibility of Non-Uniform Rational B-Splines (NURBS) to handle complex configurations. The mentioned approach is applied to the optimization of several test cases and the improvements of the proposed strategy and its ability to achieve efficient shapes will complete this study

Scalability of Parallel Batch Pattern Neural Network Training Algorithm

The development of parallel batch pattern back propagation training algorithm of multilayer perceptron and its scalability research on general-purpose parallel computer are presented in this paper. The model of multilayer perceptron and batch pattern training algorithm are theoretically described. The algorithmic description of the parallel batch pattern training method is presented. The scalability research of the developed parallel algorithm is fulfilled at progressive increasing the dimension of the parallelized problem on general-purpose parallel computer NEC TX-7.Разработка параллельного группового алгоритма обучения обратного распространения ошибки многослойного персептрона и исследование его масштабированности на параллельном компьютере общего назначения представлены в этой статье. Модель многослойного персептрона и групповой алгоритм его обучения описаны формализованным образом. Параллельный групповой алгоритм обучения представлен в алгоритмическом виде. Исследование масштабированности разработанного параллельного алгоритма осуществлено для пропорционально увеличивающегося размера задачи параллелизации на параллельном компьютере общего назначения NEC TX-7.Розробка паралельного групового алгоритму навчання зворотного поширення помилки багатошарового персептрону та дослідження його масштабованості на паралельному комп’ютері загального призначення розглянуті в цій статті. Модель багатошарового персептрону та груповий алгоритм його навчання описані формалізованим чином. Паралельний груповий алгоритм навчання представлено в алгоритмічному вигляді. Дослідження масштабованості розробленого паралельного алгоритму здійснено для пропорційно збільшуваного розміру задачі паралелізації на паралельному комп’ютері загального призначення NEC TX-7

Parallel optimization algorithms for high performance computing : application to thermal systems

The need of optimization is present in every field of engineering. Moreover, applications requiring a multidisciplinary approach in order to make a step forward are increasing. This leads to the need of solving complex optimization problems that exceed the capacity of human brain or intuition. A standard way of proceeding is to use evolutionary algorithms, among which genetic algorithms hold a prominent place. These are characterized by their robustness and versatility, as well as their high computational cost and low convergence speed. Many optimization packages are available under free software licenses and are representative of the current state of the art in optimization technology. However, the ability of optimization algorithms to adapt to massively parallel computers reaching satisfactory efficiency levels is still an open issue. Even packages suited for multilevel parallelism encounter difficulties when dealing with objective functions involving long and variable simulation times. This variability is common in Computational Fluid Dynamics and Heat Transfer (CFD & HT), nonlinear mechanics, etc. and is nowadays a dominant concern for large scale applications. Current research in improving the performance of evolutionary algorithms is mainly focused on developing new search algorithms. Nevertheless, there is a vast knowledge of sequential well-performing algorithmic suitable for being implemented in parallel computers. The gap to be covered is efficient parallelization. Moreover, advances in the research of both new search algorithms and efficient parallelization are additive, so that the enhancement of current state of the art optimization software can be accelerated if both fronts are tackled simultaneously. The motivation of this Doctoral Thesis is to make a step forward towards the successful integration of Optimization and High Performance Computing capabilities, which has the potential to boost technological development by providing better designs, shortening product development times and minimizing the required resources. After conducting a thorough state of the art study of the mathematical optimization techniques available to date, a generic mathematical optimization tool has been developed putting a special focus on the application of the library to the field of Computational Fluid Dynamics and Heat Transfer (CFD & HT). Then the main shortcomings of the standard parallelization strategies available for genetic algorithms and similar population-based optimization methods have been analyzed. Computational load imbalance has been identified to be the key point causing the degradation of the optimization algorithm¿s scalability (i.e. parallel efficiency) in case the average makespan of the batch of individuals is greater than the average time required by the optimizer for performing inter-processor communications. It occurs because processors are often unable to finish the evaluation of their queue of individuals simultaneously and need to be synchronized before the next batch of individuals is created. Consequently, the computational load imbalance is translated into idle time in some processors. Several load balancing algorithms have been proposed and exhaustively tested, being extendable to any other population-based optimization method that needs to synchronize all processors after the evaluation of each batch of individuals. Finally, a real-world engineering application that consists on optimizing the refrigeration system of a power electronic device has been presented as an illustrative example in which the use of the proposed load balancing algorithms is able to reduce the simulation time required by the optimization tool.El aumento de las aplicaciones que requieren de una aproximación multidisciplinar para poder avanzar se constata en todos los campos de la ingeniería, lo cual conlleva la necesidad de resolver problemas de optimización complejos que exceden la capacidad del cerebro humano o de la intuición. En estos casos es habitual el uso de algoritmos evolutivos, principalmente de los algoritmos genéticos, caracterizados por su robustez y versatilidad, así como por su gran coste computacional y baja velocidad de convergencia. La multitud de paquetes de optimización disponibles con licencias de software libre representan el estado del arte actual en tecnología de optimización. Sin embargo, la capacidad de adaptación de los algoritmos de optimización a ordenadores masivamente paralelos alcanzando niveles de eficiencia satisfactorios es todavía una tarea pendiente. Incluso los paquetes adaptados al paralelismo multinivel tienen dificultades para gestionar funciones objetivo que requieren de tiempos de simulación largos y variables. Esta variabilidad es común en la Dinámica de Fluidos Computacional y la Transferencia de Calor (CFD & HT), mecánica no lineal, etc. y es una de las principales preocupaciones en aplicaciones a gran escala a día de hoy. La investigación actual que tiene por objetivo la mejora del rendimiento de los algoritmos evolutivos está enfocada principalmente al desarrollo de nuevos algoritmos de búsqueda. Sin embargo, ya se conoce una gran variedad de algoritmos secuenciales apropiados para su implementación en ordenadores paralelos. La tarea pendiente es conseguir una paralelización eficiente. Además, los avances en la investigación de nuevos algoritmos de búsqueda y la paralelización son aditivos, por lo que el proceso de mejora del software de optimización actual se verá incrementada si se atacan ambos frentes simultáneamente. La motivación de esta Tesis Doctoral es avanzar hacia una integración completa de las capacidades de Optimización y Computación de Alto Rendimiento para así impulsar el desarrollo tecnológico proporcionando mejores diseños, acortando los tiempos de desarrollo del producto y minimizando los recursos necesarios. Tras un exhaustivo estudio del estado del arte de las técnicas de optimización matemática disponibles a día de hoy, se ha diseñado una librería de optimización orientada al campo de la Dinámica de Fluidos Computacional y la Transferencia de Calor (CFD & HT). A continuación se han analizado las principales limitaciones de las estrategias de paralelización disponibles para algoritmos genéticos y otros métodos de optimización basados en poblaciones. En el caso en que el tiempo de evaluación medio de la tanda de individuos sea mayor que el tiempo medio que necesita el optimizador para llevar a cabo comunicaciones entre procesadores, se ha detectado que la causa principal de la degradación de la escalabilidad o eficiencia paralela del algoritmo de optimización es el desequilibrio de la carga computacional. El motivo es que a menudo los procesadores no terminan de evaluar su cola de individuos simultáneamente y deben sincronizarse antes de que se cree la siguiente tanda de individuos. Por consiguiente, el desequilibrio de la carga computacional se convierte en tiempo de inactividad en algunos procesadores. Se han propuesto y testado exhaustivamente varios algoritmos de equilibrado de carga aplicables a cualquier método de optimización basado en una población que necesite sincronizar los procesadores tras cada tanda de evaluaciones. Finalmente, se ha presentado como ejemplo ilustrativo un caso real de ingeniería que consiste en optimizar el sistema de refrigeración de un dispositivo de electrónica de potencia. En él queda demostrado que el uso de los algoritmos de equilibrado de carga computacional propuestos es capaz de reducir el tiempo de simulación que necesita la herramienta de optimización

Accelerate Microstructure Evolution Simulation Using Graph Neural Networks with Adaptive Spatiotemporal Resolution

Surrogate models driven by sizeable datasets and scientific machine-learning methods have emerged as an attractive microstructure simulation tool with the potential to deliver predictive microstructure evolution dynamics with huge savings in computational costs. Taking 2D and 3D grain growth simulations as an example, we present a completely overhauled computational framework based on graph neural networks with not only excellent agreement to both the ground truth phase-field methods and theoretical predictions, but enhanced accuracy and efficiency compared to previous works based on convolutional neural networks. These improvements can be attributed to the graph representation, both improved predictive power and a more flexible data structure amenable to adaptive mesh refinement. As the simulated microstructures coarsen, our method can adaptively adopt remeshed grids and larger timesteps to achieve further speedup. The data-to-model pipeline with training procedures together with the source codes are provided.Comment: 28 pages, 11 figure

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

Learning for Optimization with Virtual Savant

Optimization problems arising in multiple fields of study demand efficient algorithms that can exploit modern parallel computing platforms. The remarkable development of machine learning offers an opportunity to incorporate learning into optimization algorithms to efficiently solve large and complex problems. This thesis explores Virtual Savant, a paradigm that combines machine learning and parallel computing to solve optimization problems. Virtual Savant is inspired in the Savant Syndrome, a mental condition where patients excel at a specific ability far above the average. In analogy to the Savant Syndrome, Virtual Savant extracts patterns from previously-solved instances to learn how to solve a given optimization problem in a massively-parallel fashion. In this thesis, Virtual Savant is applied to three optimization problems related to software engineering, task scheduling, and public transportation. The efficacy of Virtual Savant is evaluated in different computing platforms and the experimental results are compared against exact and approximate solutions for both synthetic and realistic instances of the studied problems. Results show that Virtual Savant can find accurate solutions, effectively scale in the problem dimension, and take advantage of the availability of multiple computing resources.Los problemas de optimización que surgen en múltiples campos de estudio demandan algoritmos eficientes que puedan explotar las plataformas modernas de computación paralela. El notable desarrollo del aprendizaje automático ofrece la oportunidad de incorporar el aprendizaje en algoritmos de optimización para resolver problemas complejos y de grandes dimensiones de manera eficiente. Esta tesis explora Savant Virtual, un paradigma que combina aprendizaje automático y computación paralela para resolver problemas de optimización. Savant Virtual está inspirado en el Sı́ndrome de Savant, una condición mental en la que los pacientes se destacan en una habilidad especı́fica muy por encima del promedio. En analogı́a con el sı́ndrome de Savant, Savant Virtual extrae patrones de instancias previamente resueltas para aprender a resolver un determinado problema de optimización de forma masivamente paralela. En esta tesis, Savant Virtual se aplica a tres problemas de optimización relacionados con la ingenierı́a de software, la planificación de tareas y el transporte público. La eficacia de Savant Virtual se evalúa en diferentes plataformas informáticas y los resultados se comparan con soluciones exactas y aproximadas para instancias tanto sintéticas como realistas de los problemas estudiados. Los resultados muestran que Savant Virtual puede encontrar soluciones precisas, escalar eficazmente en la dimensión del problema y aprovechar la disponibilidad de múltiples recursos de cómputo.Fundación Carolina Agencia Nacional de Investigación e Innovación (ANII, Uruguay) Universidad de Cádiz Universidad de la Repúblic

Parallel ant colony optimization for the training of cell signaling networks

[Abstract]: Acquiring a functional comprehension of the deregulation of cell signaling networks in disease allows progress in the development of new therapies and drugs. Computational models are becoming increasingly popular as a systematic tool to analyze the functioning of complex biochemical networks, such as those involved in cell signaling. CellNOpt is a framework to build predictive logic-based models of signaling pathways by training a prior knowledge network to biochemical data obtained from perturbation experiments. This training can be formulated as an optimization problem that can be solved using metaheuristics. However, the genetic algorithm used so far in CellNOpt presents limitations in terms of execution time and quality of solutions when applied to large instances. Thus, in order to overcome those issues, in this paper we propose the use of a method based on ant colony optimization, adapted to the problem at hand and parallelized using a hybrid approach. The performance of this novel method is illustrated with several challenging benchmark problems in the study of new therapies for liver cancer