Simulating the behavior of the human brain on GPUS

The simulation of the behavior of the Human Brain is one of the most important challenges in computing today. The main problem consists of finding efficient ways to manipulate and compute the huge volume of data that this kind of simulations need, using the current technology. In this sense, this work is focused on one of the main steps of such simulation, which consists of computing the Voltage on neurons’ morphology. This is carried out using the Hines Algorithm and, although this algorithm is the optimum method in terms of number of operations, it is in need of non-trivial modifications to be efficiently parallelized on GPUs. We proposed several optimizations to accelerate this algorithm on GPU-based architectures, exploring the limitations of both, method and architecture, to be able to solve efficiently a high number of Hines systems (neurons). Each of the optimizations are deeply analyzed and described. Two different approaches are studied, one for mono-morphology simulations (batch of neurons with the same shape) and one for multi-morphology simulations (batch of neurons where every neuron has a different shape). In mono-morphology simulations we obtain a good performance using just a single kernel to compute all the neurons. However this turns out to be inefficient on multi-morphology simulations. Unlike the previous scenario, in multi-morphology simulations a much more complex implementation is necessary to obtain a good performance. In this case, we must execute more than one single GPU kernel. In every execution (kernel call) one specific part of the batch of the neurons is solved. These parts can be seen as multiple and independent tridiagonal systems. Although the present paper is focused on the simulation of the behavior of the Human Brain, some of these techniques, in particular those related to the solving of tridiagonal systems, can be also used for multiple oil and gas simulations. Our studies have proven that the optimizations proposed in the present work can achieve high performance on those computations with a high number of neurons, being our GPU implementations about 4× and 8× faster than the OpenMP multicore implementation (16 cores), using one and two NVIDIA K80 GPUs respectively. Also, it is important to highlight that these optimizations can continue scaling, even when dealing with a very high number of neurons.This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 720270 (HBP SGA1), from the Spanish Ministry of Economy and Competitiveness under the project Computación de Altas Prestaciones VII (TIN2015-65316-P), the Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programació i Entorns d’Execució Parallels (2014-SGR-1051). We thank the support of NVIDIA through the BSC/UPC NVIDIA GPU Center of Excellence, and the European Union’s Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie Grant Agreement No. 749516.Peer ReviewedPostprint (published version

Stability of the weighted splitting finite-difference scheme for a two-dimensional parabolic equation with two nonlocal integral conditions

AbstractNonlocal conditions arise in mathematical models of various physical, chemical or biological processes. Therefore, interest in developing computational techniques for the numerical solution of partial differential equations (PDEs) with various types of nonlocal conditions has been growing fast. We construct and analyse a weighted splitting finite-difference scheme for a two-dimensional parabolic equation with nonlocal integral conditions. The main attention is paid to the stability of the method. We apply the stability analysis technique which is based on the investigation of the spectral structure of the transition matrix of a finite-difference scheme. We demonstrate that depending on the parameters of the finite-difference scheme and nonlocal conditions the proposed method can be stable or unstable. The results of numerical experiments with several test problems are also presented and they validate theoretical results

Semantic model for mining e-learning usage with ontology and meaningful learning characteristics

The use of e-learning in higher education institutions is a necessity in the learning process. E-learning accumulates vast amount of usage data which could produce a new knowledge and useful for educators. The demand to gain knowledge from e-learning usage data requires a correct mechanism to extract exact information. Current models for mining e-learning usage have focused on the activities usage but ignored the actions usage. In addition, the models lack the ability to incorporate learning pedagogy, leading to a semantic gap to annotate mining data towards education domain. The other issue raised is the absence of usage recommendation that refers to result of data mining task. This research proposes a semantic model for mining e-learning usage with ontology and meaningful learning characteristics. The model starts by preparing data including activity and action hits. The next step is to calculate meaningful hits which categorized into five namely active, cooperative, constructive, authentic, and intentional. The process continues to apply K-means clustering analysis to group usage data into three clusters. Lastly, the usage data is mapped into ontology and the ontology manager generates the meaningful usage cluster and usage recommendation. The model was experimented with three datasets of distinct courses and evaluated by mapping against the student learning outcomes of the courses. The results showed that there is a positive relationship between meaningful hits and learning outcomes, and there is a positive relationship between meaningful usage cluster and learning outcomes. It can be concluded that the proposed semantic model is valid with 95% of confidence level. This model is capable to mine and gain insight into e-learning usage data and to provide usage recommendation

Configuration Analysis for Large Scale Feature Models: Towards Speculative-Based Solutions

Los sistemas de alta variabilidad son sistemas de software en los que la gestión de la variabilidad es una actividad central. Algunos ejemplos actuales de sistemas de alta variabilidad son el sistema web de gesión de contenidos Drupal, el núcleo de Linux, y las distribuciones Debian de Linux. La configuración en sistemas de alta variabilidad es la selección de opciones de configuración según sus restricciones de configuración y los requerimientos de usuario. Los modelos de características son un estándar “de facto” para modelar las funcionalidades comunes y variables de sistemas de alta variabilidad. No obstante, el elevado número de componentes y configuraciones que un modelo de características puede contener hacen que el análisis manual de estos modelos sea una tarea muy costosa y propensa a errores. Así nace el análisis automatizado de modelos de características con mecanismos y herramientas asistidas por computadora para extraer información de estos modelos. Las soluciones tradicionales de análisis automatizado de modelos de características siguen un enfoque de computación secuencial para utilizar una unidad central de procesamiento y memoria. Estas soluciones son adecuadas para trabajar con sistemas de baja escala. Sin embargo, dichas soluciones demandan altos costos de computación para trabajar con sistemas de gran escala y alta variabilidad. Aunque existan recusos informáticos para mejorar el rendimiento de soluciones de computación, todas las soluciones con un enfoque de computación secuencial necesitan ser adaptadas para el uso eficiente de estos recursos y optimizar su rendimiento computacional. Ejemplos de estos recursos son la tecnología de múltiples núcleos para computación paralela y la tecnología de red para computación distribuida. Esta tesis explora la adaptación y escalabilidad de soluciones para el analisis automatizado de modelos de características de gran escala. En primer lugar, nosotros presentamos el uso de programación especulativa para la paralelización de soluciones. Además, nosotros apreciamos un problema de configuración desde otra perspectiva, para su solución mediante la adaptación y aplicación de una solución no tradicional. Más tarde, nosotros validamos la escalabilidad y mejoras de rendimiento computacional de estas soluciones para el análisis automatizado de modelos de características de gran escala. Concretamente, las principales contribuciones de esta tesis son: • Programación especulativa para la detección de un conflicto mínimo y 1 2 preferente. Los algoritmos de detección de conflictos mínimos determinan el conjunto mínimo de restricciones en conflicto que son responsables de comportamiento defectuoso en el modelo en análisis. Nosotros proponemos una solución para, mediante programación especulativa, ejecutar en paralelo y reducir el tiempo de ejecución de operaciones de alto costo computacional que determinan el flujo de acción en la detección de conflicto mínimo y preferente en modelos de características de gran escala. • Programación especulativa para un diagnóstico mínimo y preferente. Los algoritmos de diagnóstico mínimo determinan un conjunto mínimo de restricciones que, por una adecuada adaptación de su estado, permiten conseguir un modelo consistente o libre de conflictos. Este trabajo presenta una solución para el diagnóstico mínimo y preferente en modelos de características de gran escala mediante la ejecución especulativa y paralela de operaciones de alto costo computacional que determinan el flujo de acción, y entonces disminuir el tiempo de ejecución de la solución. • Completar de forma mínima y preferente una configuración de modelo por diagnóstico. Las soluciones para completar una configuración parcial determinan un conjunto no necesariamente mínimo ni preferente de opciones para obtener una completa configuración. Esta tesis soluciona el completar de forma mínima y preferente una configuración de modelo mediante técnicas previamente usadas en contexto de diagnóstico de modelos de características. Esta tesis evalua que todas nuestras soluciones preservan los valores de salida esperados, y también presentan mejoras de rendimiento en el análisis automatizado de modelos de características con modelos de gran escala en las operaciones descrita

Phobos eclipse detection on Mars : theory and practice

We present a general approach to study solar eclipses by Phobos on Mars: its parameterization and prediction.The validation of the model and the involved parameters is made with the already observed eclipses by previous Mars missions. Eclipse prediction is applied for the past Mars lander missions: Viking, Pathfinder and Phoenix, as well as for the future Mars MetNet Precursor Mission. A successful detection of eclipses could be used for the localization of landers and to study atmospheric properties. We also consider the data analysis, with special emphasis in the tomographic method to identify events which are very localized in space and time. Large computation requirements are needed for the implemented methods. To this propose an efficient Cloud Computing Network Infrastructure has been used.Esittelemme yleisen lähestymistavan Phoboksen auringonpimennysten tutkimiseen, parametrisointiin ja ennustamiseen. Mallin ja sen parametrien validointi tehdään menneiden ja nykyisten Mars-missioiden havaitsemien pimennysten avulla. Pimennysten ennustamista käytetään menneisiin Viking-, Pathfinder- ja Phoenix-laskeutujiin, samoin kuin tulevaan Mars MetNet Precursor missioon. Pimennysten onnistuneita havaintoja voitaisiin käyttää laskeutujien paikantamiseen ja kaasukehän ominaisuuksien tutkimiseen. Käsittelemme myös data-analyysiä, painottaen erityisesti tomografiamenetelmää, havaitaksemme tapahtumia jotka ovat paikallisia ajan ja sijainnin suhteen. Menetelmien toteuttamiseen vaaditaan suuri laskentakapasiteetti. Tämän toteuttamiseen on käytetty pilvilaskentaa

A Map-algebra-inspired Approach for Interacting With Wireless Sensor Networks, Cyber-physical Systems or Internet of Things

The typical approach for consuming data from wireless sensor networks (WSN) and Internet of Things (IoT) has been to send data back to central servers for processing and analysis. This thesis develops an alternative strategy for processing and acting on data directly in the environment referred to as Active embedded Map Algebra (AeMA). Active refers to the near real time production of data, and embedded refers to the architecture of distributed embedded sensor nodes. Network macroprogramming, a style of programming adopted for wireless sensor networks and IoT, addresses the challenges of coordinating the behavior of multiple connected devices through a high-level programming model. Several macroprogramming models have been proposed, but none to date has adopted a comprehensive spatial model. This thesis takes the unique approach of adapting the well-known Map Algebra model from Geographic Information Science to extend the functionality of WSN/IoT and the opportunities for user interaction with WSN/IoT. As an inherently spatial model, the Map Algebra-inspired metaphor supports the types of computation desired from a network of geographically dispersed WSN nodes. The AeMA data model aligns with the conceptual model of GIS layers and specific layer operations from Map Algebra. A declarative query and network tasking language, based on Map Algebra operations, provides the basis for operations and interactions. The model adds functionality to calculate and store time series and specific temporal summary-type composite objects as an extension to traditional Map Algebra. The AeMA encodes Map Algebra-inspired operations into an extensible Virtual Machine Runtime system, called MARS (Map Algebra Runtime System) that supports Map Algebra in an efficient and extensible way. Map algebra-like operations are performed in a distributed manner. Data do not leave the network but are analyzed and consumed in place. As a consequence, collected information is available in-situ to drive local actions. The conceptual model and tasking language are designed to direct nodes as active entities, able to perform some actions on their environment. This Map Algebra inspired network macroprogramming model has many potential applications for spatially deployed WSN/IoT networks. In particular the thesis notes its utility for precision agriculture applications

Computational intelligence approaches to robotics, automation, and control [Volume guest editors]

No abstract available

Improving the Perfomance of a Pointer-Based, Speculative Parallelization Scheme

La paralelización especulativa es una técnica que intenta extraer paralelismo de los bucles no paralelizables en tiempo de compilación. La idea subyacente es ejecutar el código de forma optimista mientras un subsistema comprueba que no se viole la semántica secuencial. Han sido muchos los trabajos realizados en este campo, sin embargo, no conocemos ninguno que fuese capaz de paralelizar aplicaciones que utilizasen aritmética de punteros. En un trabajo previo del autor de esta memoria, se desarrolló una librería software capaz de soportar este tipo de aplicaciones. No obstante, el software desarrollado sufría de una limitación muy importante: el tiempo de ejecución de las versiones paralelas era mayor que el de las versiones secuenciales. A lo largo de este Trabajo de Fin de Máster, se aborda esta limitación, encontrando y corrigiendo las razones de esta falta de eficiencia, y situando el trabajo realizado en perspectiva, dentro de las contribuciones mundiales en este ámbito. Los resultados experimentales obtenidos con aplicaciones reales nos permiten afirmar que estas limitaciones han sido solventadas, ya que obtenemos speedups de hasta de un 1.61 . Así, con la nueva versión de la librería se han llegado a obtener mejoras de hasta el 421.4% respecto al tiempo de ejecución generado por la versión original de la librería especulativa.InformáticaMáster en Investigación en Tecnologías de la Información y las Comunicacione