3D model reconstruction using neural gas accelerated on GPU

In this work, we propose the use of the neural gas (NG), a neural network that uses an unsupervised Competitive Hebbian Learning (CHL) rule, to develop a reverse engineering process. This is a simple and accurate method to reconstruct objects from point clouds obtained from multiple overlapping views using low-cost sensors. In contrast to other methods that may need several stages that include downsampling, noise filtering and many other tasks, the NG automatically obtains the 3D model of the scanned objects. To demonstrate the validity of our proposal we tested our method with several models and performed a study of the neural network parameterization computing the quality of representation and also comparing results with other neural methods like growing neural gas and Kohonen maps or classical methods like Voxel Grid. We also reconstructed models acquired by low cost sensors that can be used in virtual and augmented reality environments for redesign or manipulation purposes. Since the NG algorithm has a strong computational cost we propose its acceleration. We have redesigned and implemented the NG learning algorithm to fit it onto Graphics Processing Units using CUDA. A speed-up of 180× faster is obtained compared to the sequential CPU version.

Estudio y mejora de métodos de registro 3D: aceleración sobre unidades de procesamiento gráfico y caracterización del espacio de transformaciones iniciales

Durante los últimos años ha sido creciente el uso de las unidades de procesamiento gráfico, más conocidas como GPU (Graphic Processing Unit), en aplicaciones de propósito general, dejando a un lado el objetivo para el que fueron creadas y que no era otro que el renderizado de gráficos por computador. Este crecimiento se debe en parte a la evolución que han experimentado estos dispositivos durante este tiempo y que les ha dotado de gran potencia de cálculo, consiguiendo que su uso se extienda desde ordenadores personales a grandes cluster. Este hecho unido a la proliferación de sensores RGB-D de bajo coste ha hecho que crezca el número de aplicaciones de visión que hacen uso de esta tecnología para la resolución de problemas, así como también para el desarrollo de nuevas aplicaciones. Todas estas mejoras no solamente se han realizado en la parte hardware, es decir en los dispositivos, sino también en la parte software con la aparición de nuevas herramientas de desarrollo que facilitan la programación de estos dispositivos GPU. Este nuevo paradigma se acuñó como Computación de Propósito General sobre Unidades de Proceso Gráfico (General-Purpose computation on Graphics Processing Units, GPGPU). Los dispositivos GPU se clasifican en diferentes familias, en función de las distintas características hardware que poseen. Cada nueva familia que aparece incorpora nuevas mejoras tecnológicas que le permite conseguir mejor rendimiento que las anteriores. No obstante, para sacar un rendimiento óptimo a un dispositivo GPU es necesario configurarlo correctamente antes de usarlo. Esta configuración viene determinada por los valores asignados a una serie de parámetros del dispositivo. Por tanto, muchas de las implementaciones que hoy en día hacen uso de los dispositivos GPU para el registro denso de nubes de puntos 3D, podrían ver mejorado su rendimiento con una configuración óptima de dichos parámetros, en función del dispositivo utilizado. Es por ello que, ante la falta de un estudio detallado del grado de afectación de los parámetros GPU sobre el rendimiento final de una implementación, se consideró muy conveniente la realización de este estudio. Este estudio no sólo se realizó con distintas configuraciones de parámetros GPU, sino también con diferentes arquitecturas de dispositivos GPU. El objetivo de este estudio es proporcionar una herramienta de decisión que ayude a los desarrolladores a la hora implementar aplicaciones para dispositivos GPU. Uno de los campos de investigación en los que más prolifera el uso de estas tecnologías es el campo de la robótica ya que tradicionalmente en robótica, sobre todo en la robótica móvil, se utilizaban combinaciones de sensores de distinta naturaleza con un alto coste económico, como el láser, el sónar o el sensor de contacto, para obtener datos del entorno. Más tarde, estos datos eran utilizados en aplicaciones de visión por computador con un coste computacional muy alto. Todo este coste, tanto el económico de los sensores utilizados como el coste computacional, se ha visto reducido notablemente gracias a estas nuevas tecnologías. Dentro de las aplicaciones de visión por computador más utilizadas está el registro de nubes de puntos. Este proceso es, en general, la transformación de diferentes nubes de puntos a un sistema de coordenadas conocido. Los datos pueden proceder de fotografías, de diferentes sensores, etc. Se utiliza en diferentes campos como son la visión artificial, la imagen médica, el reconocimiento de objetos y el análisis de imágenes y datos de satélites. El registro se utiliza para poder comparar o integrar los datos obtenidos en diferentes mediciones. En este trabajo se realiza un repaso del estado del arte de los métodos de registro 3D. Al mismo tiempo, se presenta un profundo estudio sobre el método de registro 3D más utilizado, Iterative Closest Point (ICP), y una de sus variantes más conocidas, Expectation-Maximization ICP (EMICP). Este estudio contempla tanto su implementación secuencial como su implementación paralela en dispositivos GPU, centrándose en cómo afectan a su rendimiento las distintas configuraciones de parámetros GPU. Como consecuencia de este estudio, también se presenta una propuesta para mejorar el aprovechamiento de la memoria de los dispositivos GPU, permitiendo el trabajo con nubes de puntos más grandes, reduciendo el problema de la limitación de memoria impuesta por el dispositivo. El funcionamiento de los métodos de registro 3D utilizados en este trabajo depende en gran medida de la inicialización del problema. En este caso, esa inicialización del problema consiste en la correcta elección de la matriz de transformación con la que se iniciará el algoritmo. Debido a que este aspecto es muy importante en este tipo de algoritmos, ya que de él depende llegar antes o no a la solución o, incluso, no llegar nunca a la solución, en este trabajo se presenta un estudio sobre el espacio de transformaciones con el objetivo de caracterizarlo y facilitar la elección de la transformación inicial a utilizar en estos algoritmos.

Multi-Tenant Virtual GPUs for Optimising Performance of a Financial Risk Application

Graphics Processing Units (GPUs) are becoming popular accelerators in modern High-Performance Computing (HPC) clusters. Installing GPUs on each node of the cluster is not efficient resulting in high costs and power consumption as well as underutilisation of the accelerator. The research reported in this paper is motivated towards the use of few physical GPUs by providing cluster nodes access to remote GPUs on-demand for a financial risk application. We hypothesise that sharing GPUs between several nodes, referred to as multi-tenancy, reduces the execution time and energy consumed by an application. Two data transfer modes between the CPU and the GPUs, namely concurrent and sequential, are explored. The key result from the experiments is that multi-tenancy with few physical GPUs using sequential data transfers lowers the execution time and the energy consumed, thereby improving the overall performance of the application.

A fast parallel hyperspectral coded aperture algorithm for compressive sensing using OpenCL

In this paper, we develop a fast implementation of an hyperspectral coded aperture (HYCA) algorithm on different platforms using OpenCL, an open standard for parallel programing on heterogeneous systems, which includes a wide variety of devices, from dense multicore systems from major manufactures such as Intel or ARM to new accelerators such as graphics processing units (GPUs), field programmable gate arrays (FPGAs), the Intel Xeon Phi and other custom devices. Our proposed implementation of HYCA significantly reduces its computational cost. Our experiments have been conducted using simulated data and reveal considerable acceleration factors. This kind of implementations with the same descriptive language on different architectures are very important in order to really calibrate the possibility of using heterogeneous platforms for efficient hyperspectral imaging processing in real remote sensing missions.

A three-dimensional representation method for noisy point clouds based on growing self-organizing maps accelerated on GPUs

The research described in this thesis was motivated by the need of a robust model capable of representing 3D data obtained with 3D sensors, which are inherently noisy. In addition, time constraints have to be considered as these sensors are capable of providing a 3D data stream in real time. This thesis proposed the use of Self-Organizing Maps (SOMs) as a 3D representation model. In particular, we proposed the use of the Growing Neural Gas (GNG) network, which has been successfully used for clustering, pattern recognition and topology representation of multi-dimensional data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models, without considering time constraints. It is proposed a hardware implementation leveraging the computing power of modern GPUs, which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). The proposed methods were applied to different problem and applications in the area of computer vision such as the recognition and localization of objects, visual surveillance or 3D reconstruction.

Improving drug discovery using a neural networks based parallel scoring function

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface to find new hotspots, where ligands might potentially interact with, and which is implemented in massively parallel Graphics Processing Units, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to solve this problem, we propose a novel approach where neural networks are trained with databases of known active (drugs) and inactive compounds, and later used to improve VS predictions.

Contributions to 3D Data Registration and Representation

Nowadays, new computers generation provides a high performance that enables to build computationally expensive computer vision applications applied to mobile robotics. Building a map of the environment is a common task of a robot and is an essential part to allow the robots to move through these environments. Traditionally, mobile robots used a combination of several sensors from different technologies. Lasers, sonars and contact sensors have been typically used in any mobile robotic architecture, however color cameras are an important sensor due to we want the robots to use the same information that humans to sense and move through the different environments. Color cameras are cheap and flexible but a lot of work need to be done to give robots enough visual understanding of the scenes. Computer vision algorithms are computational complex problems but nowadays robots have access to different and powerful architectures that can be used for mobile robotics purposes. The advent of low-cost RGB-D sensors like Microsoft Kinect which provide 3D colored point clouds at high frame rates made the computer vision even more relevant in the mobile robotics field. The combination of visual and 3D data allows the systems to use both computer vision and 3D processing and therefore to be aware of more details of the surrounding environment. The research described in this thesis was motivated by the need of scene mapping. Being aware of the surrounding environment is a key feature in many mobile robotics applications from simple robotic navigation to complex surveillance applications. In addition, the acquisition of a 3D model of the scenes is useful in many areas as video games scene modeling where well-known places are reconstructed and added to game systems or advertising where once you get the 3D model of one room the system can add furniture pieces using augmented reality techniques. In this thesis we perform an experimental study of the state-of-the-art registration methods to find which one fits better to our scene mapping purposes. Different methods are tested and analyzed on different scene distributions of visual and geometry appearance. In addition, this thesis proposes two methods for 3d data compression and representation of 3D maps. Our 3D representation proposal is based on the use of Growing Neural Gas (GNG) method. This Self-Organizing Maps (SOMs) has been successfully used for clustering, pattern recognition and topology representation of various kind of data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models without considering time constraints. Self-organising neural models have the ability to provide a good representation of the input space. In particular, the Growing Neural Gas (GNG) is a suitable model because of its flexibility, rapid adaptation and excellent quality of representation. However, this type of learning is time consuming, specially for high-dimensional input data. Since real applications often work under time constraints, it is necessary to adapt the learning process in order to complete it in a predefined time. This thesis proposes a hardware implementation leveraging the computing power of modern GPUs which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). Our proposed geometrical 3D compression method seeks to reduce the 3D information using plane detection as basic structure to compress the data. This is due to our target environments are man-made and therefore there are a lot of points that belong to a plane surface. Our proposed method is able to get good compression results in those man-made scenarios. The detected and compressed planes can be also used in other applications as surface reconstruction or plane-based registration algorithms. Finally, we have also demonstrated the goodness of the GPU technologies getting a high performance implementation of a CAD/CAM common technique called Virtual Digitizing.

Algoritmo paralelo para determinação de autovalores de matrizes hermitianas

Dissertação (mestrado)–Universidade de Brasília, Universidade UnB de Planaltina, Programa de Pós-Graduação em Ciência de Materiais, 2015.

Load balancing for constraint solving with GPUs

Solving a complex Constraint Satisfaction Problem (CSP) is a computationally hard task which may require a considerable amount of time. Parallelism has been applied successfully to the job and there are already many applications capable of harnessing the parallel power of modern CPUs to speed up the solving process. Current Graphics Processing Units (GPUs), containing from a few hundred to a few thousand cores, possess a level of parallelism that surpasses that of CPUs and there are much less applications capable of solving CSPs on GPUs, leaving space for further improvement. This paper describes work in progress in the solving of CSPs on GPUs, CPUs and other devices, such as Intel Many Integrated Cores (MICs), in parallel. It presents the gains obtained when applying more devices to solve some problems and the main challenges that must be faced when using devices with as different architectures as CPUs and GPUs, with a greater focus on how to effectively achieve good load balancing between such heterogeneous devices.

Towards a Multi-device Constraints Solver

To reduce the amount of time needed to solve the most complex Constraint Satisfaction Problems (CSPs) usually multi-core CPUs are used. There are already many applications capable of harnessing the parallel power of these devices to speed up the CSPs solving process. Nowadays, the Graphics Processing Units (GPUs) possess a level of parallelism that surpass the CPUs, containing from a few hundred to a few thousand cores and there are much less applications capable of solving CSPs on GPUs, leaving space for possible improvements. This article describes the work in progress for solving CSPs on GPUs and CPUs and compares results with some state-of-the-art solvers, presenting already some good results on GPUs.

Parallel implementation of vertex component analysis for hyperspectral endmember extraction

International Conference with Peer Review 2012 IEEE International Conference in Geoscience and Remote Sensing Symposium (IGARSS), 22-27 July 2012, Munich, Germany

Parallel programming in biomedical signal processing

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Aceleración de Algoritmos en Procesadores Multicore, GPGPU y FPGA. Algorithm Acceleration with Multicore, GPGPU and FPGA Processors.

El avance en la potencia de cómputo en nuestros días viene dado por la paralelización del procesamiento, dadas las características que disponen las nuevas arquitecturas de hardware. Utilizar convenientemente este hardware impacta en la aceleración de los algoritmos en ejecución (programas). Sin embargo, convertir de forma adecuada el algoritmo en su forma paralela es complejo, y a su vez, esta forma, es específica para cada tipo de hardware paralelo. En la actualidad los procesadores de uso general más comunes son los multicore, procesadores paralelos, también denominados Symmetric Multi-Processors (SMP). Hoy en día es difícil hallar un procesador para computadoras de escritorio que no tengan algún tipo de paralelismo del caracterizado por los SMP, siendo la tendencia de desarrollo, que cada día nos encontremos con procesadores con mayor numero de cores disponibles. Por otro lado, los dispositivos de procesamiento de video (Graphics Processor Units - GPU), a su vez, han ido desarrollando su potencia de cómputo por medio de disponer de múltiples unidades de procesamiento dentro de su composición electrónica, a tal punto que en la actualidad no es difícil encontrar placas de GPU con capacidad de 200 a 400 hilos de procesamiento paralelo. Estos procesadores son muy veloces y específicos para la tarea que fueron desarrollados, principalmente el procesamiento de video. Sin embargo, como este tipo de procesadores tiene muchos puntos en común con el procesamiento científico, estos dispositivos han ido reorientándose con el nombre de General Processing Graphics Processor Unit (GPGPU). A diferencia de los procesadores SMP señalados anteriormente, las GPGPU no son de propósito general y tienen sus complicaciones para uso general debido al límite en la cantidad de memoria que cada placa puede disponer y al tipo de procesamiento paralelo que debe realizar para poder ser productiva su utilización. Los dispositivos de lógica programable, FPGA, son dispositivos capaces de realizar grandes cantidades de operaciones en paralelo, por lo que pueden ser usados para la implementación de algoritmos específicos, aprovechando el paralelismo que estas ofrecen. Su inconveniente viene derivado de la complejidad para la programación y el testing del algoritmo instanciado en el dispositivo. Ante esta diversidad de procesadores paralelos, el objetivo de nuestro trabajo está enfocado en analizar las características especificas que cada uno de estos tienen, y su impacto en la estructura de los algoritmos para que su utilización pueda obtener rendimientos de procesamiento acordes al número de recursos utilizados y combinarlos de forma tal que su complementación sea benéfica. Específicamente, partiendo desde las características del hardware, determinar las propiedades que el algoritmo paralelo debe tener para poder ser acelerado. Las características de los algoritmos paralelos determinará a su vez cuál de estos nuevos tipos de hardware son los mas adecuados para su instanciación. En particular serán tenidos en cuenta el nivel de dependencia de datos, la necesidad de realizar sincronizaciones durante el procesamiento paralelo, el tamaño de datos a procesar y la complejidad de la programación paralela en cada tipo de hardware. Today´s advances in high-performance computing are driven by parallel processing capabilities of available hardware architectures. These architectures enable the acceleration of algorithms when thes ealgorithms are properly parallelized and exploit the specific processing power of the underneath architecture. Most current processors are targeted for general pruposes and integrate several processor cores on a single chip, resulting in what is known as a Symmetric Multiprocessing (SMP) unit. Nowadays even desktop computers make use of multicore processors. Meanwhile, the industry trend is to increase the number of integrated rocessor cores as technology matures. On the other hand, Graphics Processor Units (GPU), originally designed to handle only video processing, have emerged as interesting alternatives to implement algorithm acceleration. Current available GPUs are able to implement from 200 to 400 threads for parallel processing. Scientific computing can be implemented in these hardware thanks to the programability of new GPUs that have been denoted as General Processing Graphics Processor Units (GPGPU).However, GPGPU offer little memory with respect to that available for general-prupose processors; thus, the implementation of algorithms need to be addressed carefully. Finally, Field Programmable Gate Arrays (FPGA) are programmable devices which can implement hardware logic with low latency, high parallelism and deep pipelines. Thes devices can be used to implement specific algorithms that need to run at very high speeds. However, their programmability is harder that software approaches and debugging is typically time-consuming. In this context where several alternatives for speeding up algorithms are available, our work aims at determining the main features of thes architectures and developing the required know-how to accelerate algorithm execution on them. We look at identifying those algorithms that may fit better on a given architecture as well as compleme

A Feasibility Study of a Pelleting Plant as an Option for By Product Upgrading in Wood-Processing Industry

Tämän kannattavuustutkimuksen lähtökohtana oli se, että Yhtyneet Sahat Oy:n Kaukaan sahalla ja Luumäen jatkojalostuslaitoksella haluttiin selvittää pellettitehtaan kannattavuus nykyisessä markkinatilanteessa. Tämä työon luonteeltaan teknis-taloudellinen selvitys eli ns. feasibility study. Pelletöintiprosessi on tekniikaltaan yksinkertainen eikä edellytä korkea teknologian laitteita. Toimiala on maailmanlaajuisesti varsin uusi. Suomessa pellettimarkkinat ovat vielä pienet ja kehittymättömät, mutta kasvua on viime vuosina tapahtunut. Valtaosa kotimaan tuotannosta menee vientiin. Investoinnin laskentaprosessissa saadut tuotannon alkuarvot sekä kustannusrakenteen määrittelyt ovat perustana varsinaisille kannattavuuslaskelmille. Laskelmista on selvitetty investointeihin liittyvät yleisimmät taloudelliset tunnusluvut ja herkimpiä muuttujia on tutkittu ja pohdittu herkkyysanalyysiä apuna käyttäen.

RR3D: Uma solução para renderização remota de imagens médicas tridimensionais

The visualization of three-dimensional(3D)images is increasigly being sed in the area of medicine, helping physicians diagnose desease. the advances achived in scaners esed for acquisition of these 3d exames, such as computerized tumography(CT) and Magnetic Resonance imaging (MRI), enable the generation of images with higher resolutions, thus, generating files with much larger sizes. Currently, the images of computationally expensive one, and demanding the use of a righ and computer for such task. The direct remote acess of these images thruogh the internet is not efficient also, since all images have to be trasferred to the user´s equipment before the 3D visualization process ca start. with these problems in mind, this work proposes and analyses a solution for the remote redering of 3D medical images, called Remote Rendering (RR3D). In RR3D, the whole hedering process is pefomed a server or a cluster of servers, with high computational power, and only the resulting image is tranferred to the client, still allowing the client to peform operations such as rotations, zoom, etc. the solution was developed using web services written in java and an architecture that uses the scientific visualization packcage paraview, the framework paraviewWeb and the PACS server DCM4CHEE.The solution was tested with two scenarios where the rendering process was performed by a sever with graphics hadwere (GPU) and by a server without GPUs. In the scenarios without GPUs, the soluction was executed in parallel with several number of cores (processing units)dedicated to it. In order to compare our solution to order medical visualization application, a third scenario was esed in the rendering process, was done locally. In all tree scenarios, the solution was tested for different network speeds. The solution solved satisfactorily the problem with the delay in the transfer of the DICOM files, while alowing the use of low and computers as client for visualizing the exams even, tablets and smart phones