An Intercomparison of Modelling Approaches for Simulating the Atmospheric Dispersion of Ammonia Emitted by Agricultural Sources

RESUMEN La dispersión del amoniaco (NH3) emitido por fuentes agrícolas en medias distancias, y su posterior deposición en el suelo y la vegetación, pueden llevar a la degradación de ecosistemas vulnerables y a la acidificación de los suelos. La deposición de NH3 suele ser mayor junto a la fuente emisora, por lo que los impactos negativos de dichas emisiones son generalmente mayores en esas zonas. Bajo la legislación comunitaria, varios estados miembros emplean modelos de dispersión inversa para estimar los impactos de las emisiones en las proximidades de las zonas naturales de especial conservación. Una revisión reciente de métodos para evaluar impactos de NH3 en distancias medias recomendaba la comparación de diferentes modelos para identificar diferencias importantes entre los métodos empleados por los distintos países de la UE. En base a esta recomendación, esta tesis doctoral compara y evalúa las predicciones de las concentraciones atmosféricas de NH3 de varios modelos bajo condiciones, tanto reales como hipotéticas, que plantean un potencial impacto sobre ecosistemas (incluidos aquellos bajo condiciones de clima Mediterráneo). En este sentido, se procedió además a la comparación y evaluación de varias técnicas de modelización inversa para inferir emisiones de NH3. Finalmente, se ha desarrollado un modelo matemático simple para calcular las concentraciones de NH3 y la velocidad de deposición de NH3 en ecosistemas vulnerables cercanos a una fuente emisora. La comparativa de modelos supuso la evaluación de cuatro modelos de dispersión (ADMS 4.1; AERMOD v07026; OPS-st v3.0.3 y LADD v2010) en un amplio rango de casos hipotéticos (dispersión de NH3 procedente de distintos tipos de fuentes agrícolas de emisión). La menor diferencia entre las concentraciones medias estimadas por los distintos modelos se obtuvo para escenarios simples. La convergencia entre las predicciones de los modelos fue mínima para el escenario relativo a la dispersión de NH3 procedente de un establo ventilado mecánicamente. En este caso, el modelo ADMS predijo concentraciones significativamente menores que los otros modelos. Una explicación de estas diferencias podríamos encontrarla en la interacción de diferentes “penachos” y “capas límite” durante el proceso de parametrización. Los cuatro modelos de dispersión fueron empleados para dos casos reales de dispersión de NH3: una granja de cerdos en Falster (Dinamarca) y otra en Carolina del Norte (EEUU). Las concentraciones medias anuales estimadas por los modelos fueron similares para el caso americano (emisión de granjas ventiladas de forma natural y balsa de purines). La comparación de las predicciones de los modelos con concentraciones medias anuales medidas in situ, así como la aplicación de los criterios establecidos para la aceptación estadística de los modelos, permitió concluir que los cuatro modelos se comportaron aceptablemente para este escenario. No ocurrió lo mismo en el caso danés (nave ventilada mecánicamente), en donde el modelo LADD no dio buenos resultados debido a la ausencia de procesos de “sobreelevacion de penacho” (plume-rise). Los modelos de dispersión dan a menudo pobres resultados en condiciones de baja velocidad de viento debido a que la teoría de dispersión en la que se basan no es aplicable en estas condiciones. En situaciones de frecuente descenso en la velocidad del viento, la actual guía de modelización propone usar un modelo que sea eficaz bajo dichas condiciones, máxime cuando se realice una valoración que tenga como objeto establecer una política de regularización. Esto puede no ser siempre posible debido a datos meteorológicos insuficientes, en cuyo caso la única opción sería utilizar un modelo más común, como la versión avanzada de los modelos Gausianos ADMS o AERMOD. Con el objetivo de evaluar la idoneidad de estos modelos para condiciones de bajas velocidades de viento, ambos modelos fueron utilizados en un caso con condiciones Mediterráneas. Lo que supone sucesivos periodos de baja velocidad del viento. El estudio se centró en la dispersión de NH3 procedente de una granja de cerdos en Segovia (España central). Para ello la concentración de NH3 media mensual fue medida en 21 localizaciones en torno a la granja. Se realizaron también medidas de concentración de alta resolución en una única localización durante una campaña de una semana. En este caso, se evaluaron dos estrategias para mejorar la respuesta del modelo ante bajas velocidades del viento. La primera se basó en “no zero wind” (NZW), que sustituyó periodos de calma con el mínimo límite de velocidad del viento y “accumulated calm emissions” (ACE), que forzaban al modelo a calcular las emisiones totales en un periodo de calma y la siguiente hora de no-calma. Debido a las importantes incertidumbres en los datos de entrada del modelo (inputs) (tasa de emisión de NH3, velocidad de salida de la fuente, parámetros de la capa límite, etc.), se utilizó el mismo caso para evaluar la incertidumbre en la predicción del modelo y valorar como dicha incertidumbre puede ser considerada en evaluaciones del modelo. Un modelo dinámico de emisión, modificado para el caso de clima Mediterráneo, fue empleado para estimar la variabilidad temporal en las emisiones de NH3. Así mismo, se realizó una comparativa utilizando las emisiones dinámicas y la tasa constante de emisión. La incertidumbre predicha asociada a la incertidumbre de los inputs fue de 67-98% del valor medio para el modelo ADMS y entre 53-83% del valor medio para AERMOD. La mayoría de esta incertidumbre se debió a la incertidumbre del ratio de emisión en la fuente (50%), seguida por la de las condiciones meteorológicas (10-20%) y aquella asociada a las velocidades de salida (5-10%). El modelo AERMOD predijo mayores concentraciones que ADMS y existieron más simulaciones que alcanzaron los criterios de aceptabilidad cuando se compararon las predicciones con las concentraciones medias anuales medidas. Sin embargo, las predicciones del modelo ADMS se correlacionaron espacialmente mejor con las mediciones. El uso de valores dinámicos de emisión estimados mejoró el comportamiento de ADMS, haciendo empeorar el de AERMOD. La aplicación de estrategias destinadas a mejorar el comportamiento de este último tuvo efectos contradictorios similares. Con el objeto de comparar distintas técnicas de modelización inversa, varios modelos (ADMS, LADD y WindTrax) fueron empleados para un caso no agrícola, una colonia de pingüinos en la Antártida. Este caso fue empleado para el estudio debido a que suponía la oportunidad de obtener el primer factor de emisión experimental para una colonia de pingüinos antárticos. Además las condiciones eran propicias desde el punto de vista de la casi total ausencia de concentraciones ambiente (background). Tras el trabajo de modelización existió una concordancia suficiente entre las estimaciones obtenidas por los tres modelos. De este modo se pudo definir un factor de emisión de para la colonia de 1.23 g NH3 por pareja criadora por día (con un rango de incertidumbre de 0.8-2.54 g NH3 por pareja criadora por día). Posteriores aplicaciones de técnicas de modelización inversa para casos agrícolas mostraron también un buen compromiso estadístico entre las emisiones estimadas por los distintos modelos. Con todo ello, es posible concluir que la modelización inversa es una técnica robusta para estimar tasas de emisión de NH3. Modelos de selección (screening) permiten obtener una rápida y aproximada estimación de los impactos medioambientales, siendo una herramienta útil para evaluaciones de impactos en tanto que permite eliminar casos que presentan un riesgo potencial de daño bajo. De esta forma, lo recursos del modelo pueden Resumen (Castellano) destinarse a casos en donde la posibilidad de daño es mayor. El modelo de Cálculo Simple de los Límites de Impacto de Amoniaco (SCAIL) se desarrolló para obtener una estimación de la concentración media de NH3 y de la tasa de deposición seca asociadas a una fuente agrícola. Está técnica de selección, basada en el modelo LADD, fue evaluada y calibrada con diferentes bases de datos y, finalmente, validada utilizando medidas independientes de concentraciones realizadas cerca de las fuentes. En general SCAIL dio buenos resultados de acuerdo a los criterios estadísticos establecidos. Este trabajo ha permitido definir situaciones en las que las concentraciones predichas por modelos de dispersión son similares, frente a otras en las que las predicciones difieren notablemente entre modelos. Algunos modelos nos están diseñados para simular determinados escenarios en tanto que no incluyen procesos relevantes o están más allá de los límites de su aplicabilidad. Un ejemplo es el modelo LADD que no es aplicable en fuentes con velocidad de salida significativa debido a que no incluye una parametrización de sobreelevacion del penacho. La evaluación de un esquema simple combinando la sobreelevacion del penacho y una turbulencia aumentada en la fuente mejoró el comportamiento del modelo. Sin embargo más pruebas son necesarias para avanzar en este sentido. Incluso modelos que son aplicables y que incluyen los procesos relevantes no siempre dan similares predicciones. Siendo las razones de esto aún desconocidas. Por ejemplo, AERMOD predice mayores concentraciones que ADMS para dispersión de NH3 procedente de naves de ganado ventiladas mecánicamente. Existe evidencia que sugiere que el modelo ADMS infraestima concentraciones en estas situaciones debido a un elevado límite de velocidad de viento. Por el contrario, existen evidencias de que AERMOD sobreestima concentraciones debido a sobreestimaciones a bajas Resumen (Castellano) velocidades de viento. Sin embrago, una modificación simple del pre-procesador meteorológico parece mejorar notablemente el comportamiento del modelo. Es de gran importancia que estas diferencias entre las predicciones de los modelos sean consideradas en los procesos de evaluación regulada por los organismos competentes. Esto puede ser realizado mediante la aplicación del modelo más útil para cada caso o, mejor aún, mediante modelos múltiples o híbridos. ABSTRACT Short-range atmospheric dispersion of ammonia (NH3) emitted by agricultural sources and its subsequent deposition to soil and vegetation can lead to the degradation of sensitive ecosystems and acidification of the soil. Atmospheric concentrations and dry deposition rates of NH3 are generally highest near the emission source and so environmental impacts to sensitive ecosystems are often largest at these locations. Under European legislation, several member states use short-range atmospheric dispersion models to estimate the impact of ammonia emissions on nearby designated nature conservation sites. A recent review of assessment methods for short-range impacts of NH3 recommended an intercomparison of the different models to identify whether there are notable differences to the assessment approaches used in different European countries. Based on this recommendation, this thesis compares and evaluates the atmospheric concentration predictions of several models used in these impact assessments for various real and hypothetical scenarios, including Mediterranean meteorological conditions. In addition, various inverse dispersion modelling techniques for the estimation of NH3 emissions rates are also compared and evaluated and a simple screening model to calculate the NH3 concentration and dry deposition rate at a sensitive ecosystem located close to an NH3 source was developed. The model intercomparison evaluated four atmospheric dispersion models (ADMS 4.1; AERMOD v07026; OPS-st v3.0.3 and LADD v2010) for a range of hypothetical case studies representing the atmospheric dispersion from several agricultural NH3 source types. The best agreement between the mean annual concentration predictions of the models was found for simple scenarios with area and volume sources. The agreement between the predictions of the models was worst for the scenario representing the dispersion from a mechanically ventilated livestock house, for which ADMS predicted significantly smaller concentrations than the other models. The reason for these differences appears to be due to the interaction of different plume-rise and boundary layer parameterisations. All four dispersion models were applied to two real case studies of dispersion of NH3 from pig farms in Falster (Denmark) and North Carolina (USA). The mean annual concentration predictions of the models were similar for the USA case study (emissions from naturally ventilated pig houses and a slurry lagoon). The comparison of model predictions with mean annual measured concentrations and the application of established statistical model acceptability criteria concluded that all four models performed acceptably for this case study. This was not the case for the Danish case study (mechanically ventilated pig house) for which the LADD model did not perform acceptably due to the lack of plume-rise processes in the model. Regulatory dispersion models often perform poorly in low wind speed conditions due to the model dispersion theory being inapplicable at low wind speeds. For situations with frequent low wind speed periods, current modelling guidance for regulatory assessments is to use a model that can handle these conditions in an acceptable way. This may not always be possible due to insufficient meteorological data and so the only option may be to carry out the assessment using a more common regulatory model, such as the advanced Gaussian models ADMS or AERMOD. In order to assess the suitability of these models for low wind conditions, they were applied to a Mediterranean case study that included many periods of low wind speed. The case study was the dispersion of NH3 emitted by a pig farm in Segovia, Central Spain, for which mean monthly atmospheric NH3 concentration measurements were made at 21 locations surrounding the farm as well as high-temporal-resolution concentration measurements at one location during a one-week campaign. Two strategies to improve the model performance for low wind speed conditions were tested. These were ‘no zero wind’ (NZW), which replaced calm periods with the minimum threshold wind speed of the model and ‘accumulated calm emissions’ (ACE), which forced the model to emit the total emissions during a calm period during the first subsequent non-calm hour. Due to large uncertainties in the model input data (NH3 emission rates, source exit velocities, boundary layer parameters), the case study was also used to assess model prediction uncertainty and assess how this uncertainty can be taken into account in model evaluations. A dynamic emission model modified for the Mediterranean climate was used to estimate the temporal variability in NH3 emission rates and a comparison was made between the simulations using the dynamic emissions and a constant emission rate. Prediction uncertainty due to model input uncertainty was 67-98% of the mean value for ADMS and between 53-83% of the mean value for AERMOD. Most of this uncertainty was due to source emission rate uncertainty (~50%), followed by uncertainty in the meteorological conditions (~10-20%) and uncertainty in exit velocities (~5-10%). AERMOD predicted higher concentrations than ADMS and more of the simulations met the model acceptability criteria when compared with the annual mean measured concentrations. However, the ADMS predictions were better correlated spatially with the measurements. The use of dynamic emission estimates improved the performance of ADMS but worsened the performance of AERMOD and the application of strategies to improved model performance had similar contradictory effects. In order to compare different inverse modelling techniques, several models (ADMS, LADD and WindTrax) were applied to a non-agricultural case study of a penguin colony in Antarctica. This case study was used since it gave the opportunity to provide the first experimentally-derived emission factor for an Antarctic penguin colony and also had the advantage of negligible background concentrations. There was sufficient agreement between the emission estimates obtained from the three models to define an emission factor for the penguin colony (1.23 g NH3 per breeding pair per day with an uncertainty range of 0.8-2.54 g NH3 per breeding pair per day). This emission estimate compared favourably to the value obtained using a simple micrometeorological technique (aerodynamic gradient) of 0.98 g ammonia per breeding pair per day (95% confidence interval: 0.2-2.4 g ammonia per breeding pair per day). Further application of the inverse modelling techniques for a range of agricultural case studies also demonstrated good agreement between the emission estimates. It is concluded, therefore, that inverse dispersion modelling is a robust technique for estimating NH3 emission rates. Screening models that can provide a quick and approximate estimate of environmental impacts are a useful tool for impact assessments because they can be used to filter out cases that potentially have a minimal environmental impact allowing resources to be focussed on more potentially damaging cases. The Simple Calculation of Ammonia Impact Limits (SCAIL) model was developed as a screening model to provide an estimate of the mean NH3 concentration and dry deposition rate downwind of an agricultural source. This screening tool, based on the LADD model, was evaluated and calibrated with several experimental datasets and then validated using independent concentration measurements made near sources. Overall SCAIL performed acceptably according to established statistical criteria. This work has identified situations where the concentration predictions of dispersion models are similar and other situations where the predictions are significantly different. Some models are simply not designed to simulate certain scenarios since they do not include the relevant processes or are beyond the limits of their applicability. An example is the LADD model that is not applicable to sources with significant exit velocity since the model does not include a plume-rise parameterisation. The testing of a simple scheme combining a momentum-driven plume rise and increased turbulence at the source improved model performance, but more testing is required. Even models that are applicable and include the relevant process do not always give similar predictions and the reasons for this need to be investigated. AERMOD for example predicts higher concentrations than ADMS for dispersion from mechanically ventilated livestock housing. There is evidence to suggest that ADMS underestimates concentrations in these situations due to a high wind speed threshold. Conversely, there is also evidence that AERMOD overestimates concentrations in these situations due to overestimation at low wind speeds. However, a simple modification to the meteorological pre-processor appears to improve the performance of the model. It is important that these differences between the predictions of these models are taken into account in regulatory assessments. This can be done by applying the most suitable model for the assessment in question or, better still, using multiple or hybrid models.

Cost and energy efficient reconfigurable embedded platform using Spartan-6 FPGAs

Modern FPGAs with run-time reconfiguration allow the implementation of complex systems offering both the flexibility of software-based solutions combined with the performance of hardware. This combination of characteristics, together with the development of new specific methodologies, make feasible to reach new points of the system design space, and make embedded systems built on these platforms acquire more and more importance. However, the practical exploitation of this technique in fields that traditionally have relied on resource restricted embedded systems, is mainly limited by strict power consumption requirements, the cost and the high dependence of DPR techniques with the specific features of the device technology underneath. In this work, we tackle the previously reported problems, designing a reconfigurable platform based on the low-cost and low-power consuming Spartan-6 FPGA family. The full process to develop the platform will be detailed in the paper from scratch. In addition, the implementation of the reconfiguration mechanism, including two profiles, is reported. The first profile is a low-area and low-speed reconfiguration engine based mainly on software functions running on the embedded processor, while the other one is a hardware version of the same engine, implemented in the FPGA logic. This reconfiguration hardware block has been originally designed to the Virtex-5 family, and its porting process will be also described in this work, facing the interoperability problem among different families.

High Performance Algorithms and Implementations Using Sparse and Parallelization Techniques on MBS

In this paper we will see how the efficiency of the MBS simulations can be improved in two different ways, by considering both an explicit and implicit semi-recursive formulation. The explicit method is based on a double velocity transformation that involves the solution of a redundant but compatible system of equations. The high computational cost of this operation has been drastically reduced by taking into account the sparsity pattern of the system. Regarding this, the goal of this method is the introduction of MA48, a high performance mathematical library provided by Harwell Subroutine Library. The second method proposed in this paper has the particularity that, depending on the case, between 70 and 85% of the computation time is devoted to the evaluation of forces derivatives with respect to the relative position and velocity vectors. Keeping in mind that evaluating these derivatives can be decomposed into concurrent tasks, the main goal of this paper lies on a successful and straightforward parallel implementation that have led to a substantial improvement with a speedup of 3.2 by keeping all the cores busy in a quad-core processor and distributing the workload between them, achieving on this way a huge time reduction by doing an ideal CPU usage

Integración MPlayer-OpenSVC en el procesador multinúcleo OMAP3530

La constante evolución de dispositivos portátiles multimedia que se ha producido en la última década ha provocado que hoy en día se disponga de una amplia variedad de dispositivos con capacidad para reproducir contenidos multimedia. En consecuencia, la reproducción de esos contenidos en dichos terminales lleva asociada disponer de procesadores que soporten una alta carga computacional, ya que las tareas de descodificación y presentación de video así lo requieren. Sin embargo, un procesador potente trabajando a elevadas frecuencias provoca un elevado consumo de la batería, y dado que se pretende trabajar con dispositivos portátiles, la vida útil de la batería se convierte en un asunto de especial importancia. La problemática que se plantea se ha convertido en una de las principales líneas de investigación del Grupo de Investigación GDEM (Grupo de Diseño Electrónico y Microelectrónico). En esta línea de trabajo, se persigue cómo optimizar el consumo de energía en terminales portables desde el punto de vista de la reducción de la calidad de experiencia del usuario a cambio de una mayor autonomía del terminal. Por tanto, para lograr esa reducción de la calidad de experiencia mencionada, se requiere un estándar de codificación de vídeo que así lo permita. El Grupo de Investigación GDEM cuenta con experiencia en el estándar de vídeo escalable H.264/SVC, el cual permite degradar la calidad de experiencia en función de las necesidades/características del dispositivo. Más concretamente, un video escalable contiene embebidas distintas versiones del video original que pueden ser descodificadas en diferentes resoluciones, tasas de cuadro y calidades (escalabilidades espacial, temporal y de calidad respectivamente), permitiendo una adaptación rápida y muy flexible. Seleccionado el estándar H.264/SVC para las tareas de vídeo, se propone trabajar con Mplayer, un reproductor de vídeos de código abierto (open source), al cual se le ha integrado un descodificador para vídeo escalable denominado OpenSVC. Por último, como dispositivo portable se trabajará con la plataforma de desarrollo BeagleBoard, un sistema embebido basado en el procesador OMAP3530 que permite modificar la frecuencia de reloj y la tensión de alimentación dinámicamente reduciendo de este modo el consumo del terminal. Este procesador a su vez contiene integrados un procesador de propósito general (ARM Cortex-A8) y un procesador digital de señal (DSP TMS320C64+TM). Debido a la alta carga computacional de la descodificación de vídeos escalables y la escasa optimización del ARM para procesamiento de datos, se propone llevar a cabo la ejecución de Mplayer en el ARM y encargar la tarea de descodificación al DSP, con la finalidad de reducir el consumo y por tanto aumentar la vida útil del sistema embebido sobre el cual se ejecutará la aplicación desarrollada. Una vez realizada esa integración, se llevará a cabo una caracterización del descodificador alojado en el DSP a través de una serie de medidas de rendimiento y se compararán los resultados con los obtenidos en el proceso de descodificación realizado únicamente en el ARM. ABSTRACT During the last years, the multimedia portable terminals have gradually evolved causing that nowadays a several range of devices with the ability of playing multimedia contents are easily available for everyone. Consequently, those multimedia terminals must have high-performance processors to play those contents because the coding and decoding tasks demand high computational load. However, a powerful processor performing to high frequencies implies higher battery consumption, and this issue has become one of the most important problems in the development cycle of a portable terminal. The power/energy consumption optimization on multimedia terminals has become in one the most significant work lines in the Electronic and Microelectronic Research Group of the Universidad Politécnica de Madrid. In particular, the group is researching how to reduce the user‟s Quality of Experience (QoE) quality in exchange for increased battery life. In order to reduce the Quality of Experience (QoE), a standard video coding that allows this operation is required. The H.264/SVC allows reducing the QoE according to the needs/characteristics of the terminal. Specifically, a scalable video contains different versions of original video embedded in an only one video stream, and each one of them can be decoded in different resolutions, frame rates and qualities (spatial, temporal and quality scalabilities respectively). Once the standard video coding is selected, a multimedia player with support for scalable video is needed. Mplayer has been proposed as a multimedia player, whose characteristics (open-source, enormous flexibility and scalable video decoder called OpenSVC) are the most suitable for the aims of this Master Thesis. Lastly, the embedded system BeagleBoard, based on the multi-core processor OMAP3530, will be the development platform used in this project. The multimedia terminal architecture is based on a commercial chip having a General Purpose Processor (GPP – ARM Cortex A8) and a Digital Signal Processor (DSP, TMS320C64+™). Moreover, the processor OMAP3530 has the ability to modify the operating frequency and the supply voltage in a dynamic way in order to reduce the power consumption of the embedded system. So, the main goal of this Master Thesis is the integration of the multimedia player, MPlayer, executed at the GPP, and scalable video decoder, OpenSVC, executed at the DSP in order to distribute the computational load associated with the scalable video decoding task and to reduce the power consumption of the terminal. Once the integration is accomplished, the performance of the OpenSVC decoder executed at the DSP will be measured using different combinations of scalability values. The obtained results will be compared with the scalable video decoding performed at the GPP in order to show the low optimization of this kind of architecture for decoding tasks in contrast to DSP architecture.

B-LOG: A branch and bound methodology for the parallel execution of logic programs

We propose a computational methodology -"B-LOG"-, which offers the potential for an effective implementation of Logic Programming in a parallel computer. We also propose a weighting scheme to guide the search process through the graph and we apply the concepts of parallel "branch and bound" algorithms in order to perform a "best-first" search using an information theoretic bound. The concept of "session" is used to speed up the search process in a succession of similar queries. Within a session, we strongly modify the bounds in a local database, while bounds kept in a global database are weakly modified to provide a better initial condition for other sessions. We also propose an implementation scheme based on a database machine using "semantic paging", and the "B-LOG processor" based on a scoreboard driven controller.

IDRA (IDeal Resource Allocation): A tool for computing ideal speedups

Performance studies of actual parallel systems usually tend to concéntrate on the effectiveness of a given implementation. This is often done in the absolute, without quantitave reference to the potential parallelism contained in the programs from the point of view of the execution paradigm. We feel that studying the parallelism inherent to the programs is interesting, as it gives information about the best possible behavior of any implementation and thus allows contrasting the results obtained. We propose a method for obtaining ideal speedups for programs through a combination of sequential or parallel execution and simulation, and the algorithms that allow implementing the method. Our approach is novel and, we argüe, more accurate than previously proposed methods, in that a crucial part of the data - the execution times of tasks - is obtained from actual executions, while speedup is computed by simulation. This allows obtaining speedup (and other) data under controlled and ideal assumptions regarding issues such as number of processor, scheduling algorithm and overheads, etc. The results obtained can be used for example to evalúate the ideal parallelism that a program contains for a given model of execution and to compare such "perfect" parallelism to that obtained by a given implementation of that model. We also present a tool, IDRA, which implements the proposed method, and results obtained with IDRA for benchmark programs, which are then compared with those obtained in actual executions on real parallel systems.

On-Chip Thermal Monitoring: Design, Placement and Interconnection of Temperature Sensors

La temperatura es una preocupación que juega un papel protagonista en el diseño de circuitos integrados modernos. El importante aumento de las densidades de potencia que conllevan las últimas generaciones tecnológicas ha producido la aparición de gradientes térmicos y puntos calientes durante el funcionamiento normal de los chips. La temperatura tiene un impacto negativo en varios parámetros del circuito integrado como el retardo de las puertas, los gastos de disipación de calor, la fiabilidad, el consumo de energía, etc. Con el fin de luchar contra estos efectos nocivos, la técnicas de gestión dinámica de la temperatura (DTM) adaptan el comportamiento del chip en función en la información que proporciona un sistema de monitorización que mide en tiempo de ejecución la información térmica de la superficie del dado. El campo de la monitorización de la temperatura en el chip ha llamado la atención de la comunidad científica en los últimos años y es el objeto de estudio de esta tesis. Esta tesis aborda la temática de control de la temperatura en el chip desde diferentes perspectivas y niveles, ofreciendo soluciones a algunos de los temas más importantes. Los niveles físico y circuital se cubren con el diseño y la caracterización de dos nuevos sensores de temperatura especialmente diseñados para los propósitos de las técnicas DTM. El primer sensor está basado en un mecanismo que obtiene un pulso de anchura variable dependiente de la relación de las corrientes de fuga con la temperatura. De manera resumida, se carga un nodo del circuito y posteriormente se deja flotando de tal manera que se descarga a través de las corrientes de fugas de un transistor; el tiempo de descarga del nodo es la anchura del pulso. Dado que la anchura del pulso muestra una dependencia exponencial con la temperatura, la conversión a una palabra digital se realiza por medio de un contador logarítmico que realiza tanto la conversión tiempo a digital como la linealización de la salida. La estructura resultante de esta combinación de elementos se implementa en una tecnología de 0,35 _m. El sensor ocupa un área muy reducida, 10.250 nm2, y consume muy poca energía, 1.05-65.5nW a 5 muestras/s, estas cifras superaron todos los trabajos previos en el momento en que se publicó por primera vez y en el momento de la publicación de esta tesis, superan a todas las implementaciones anteriores fabricadas en el mismo nodo tecnológico. En cuanto a la precisión, el sensor ofrece una buena linealidad, incluso sin calibrar; se obtiene un error 3_ de 1,97oC, adecuado para tratar con las aplicaciones de DTM. Como se ha explicado, el sensor es completamente compatible con los procesos de fabricación CMOS, este hecho, junto con sus valores reducidos de área y consumo, lo hacen especialmente adecuado para la integración en un sistema de monitorización de DTM con un conjunto de monitores empotrados distribuidos a través del chip. Las crecientes incertidumbres de proceso asociadas a los últimos nodos tecnológicos comprometen las características de linealidad de nuestra primera propuesta de sensor. Con el objetivo de superar estos problemas, proponemos una nueva técnica para obtener la temperatura. La nueva técnica también está basada en las dependencias térmicas de las corrientes de fuga que se utilizan para descargar un nodo flotante. La novedad es que ahora la medida viene dada por el cociente de dos medidas diferentes, en una de las cuales se altera una característica del transistor de descarga |la tensión de puerta. Este cociente resulta ser muy robusto frente a variaciones de proceso y, además, la linealidad obtenida cumple ampliamente los requisitos impuestos por las políticas DTM |error 3_ de 1,17oC considerando variaciones del proceso y calibrando en dos puntos. La implementación de la parte sensora de esta nueva técnica implica varias consideraciones de diseño, tales como la generación de una referencia de tensión independiente de variaciones de proceso, que se analizan en profundidad en la tesis. Para la conversión tiempo-a-digital, se emplea la misma estructura de digitalización que en el primer sensor. Para la implementación física de la parte de digitalización, se ha construido una biblioteca de células estándar completamente nueva orientada a la reducción de área y consumo. El sensor resultante de la unión de todos los bloques se caracteriza por una energía por muestra ultra baja (48-640 pJ) y un área diminuta de 0,0016 mm2, esta cifra mejora todos los trabajos previos. Para probar esta afirmación, se realiza una comparación exhaustiva con más de 40 propuestas de sensores en la literatura científica. Subiendo el nivel de abstracción al sistema, la tercera contribución se centra en el modelado de un sistema de monitorización que consiste de un conjunto de sensores distribuidos por la superficie del chip. Todos los trabajos anteriores de la literatura tienen como objetivo maximizar la precisión del sistema con el mínimo número de monitores. Como novedad, en nuestra propuesta se introducen nuevos parámetros de calidad aparte del número de sensores, también se considera el consumo de energía, la frecuencia de muestreo, los costes de interconexión y la posibilidad de elegir diferentes tipos de monitores. El modelo se introduce en un algoritmo de recocido simulado que recibe la información térmica de un sistema, sus propiedades físicas, limitaciones de área, potencia e interconexión y una colección de tipos de monitor; el algoritmo proporciona el tipo seleccionado de monitor, el número de monitores, su posición y la velocidad de muestreo _optima. Para probar la validez del algoritmo, se presentan varios casos de estudio para el procesador Alpha 21364 considerando distintas restricciones. En comparación con otros trabajos previos en la literatura, el modelo que aquí se presenta es el más completo. Finalmente, la última contribución se dirige al nivel de red, partiendo de un conjunto de monitores de temperatura de posiciones conocidas, nos concentramos en resolver el problema de la conexión de los sensores de una forma eficiente en área y consumo. Nuestra primera propuesta en este campo es la introducción de un nuevo nivel en la jerarquía de interconexión, el nivel de trillado (o threshing en inglés), entre los monitores y los buses tradicionales de periféricos. En este nuevo nivel se aplica selectividad de datos para reducir la cantidad de información que se envía al controlador central. La idea detrás de este nuevo nivel es que en este tipo de redes la mayoría de los datos es inútil, porque desde el punto de vista del controlador sólo una pequeña cantidad de datos |normalmente sólo los valores extremos| es de interés. Para cubrir el nuevo nivel, proponemos una red de monitorización mono-conexión que se basa en un esquema de señalización en el dominio de tiempo. Este esquema reduce significativamente tanto la actividad de conmutación sobre la conexión como el consumo de energía de la red. Otra ventaja de este esquema es que los datos de los monitores llegan directamente ordenados al controlador. Si este tipo de señalización se aplica a sensores que realizan conversión tiempo-a-digital, se puede obtener compartición de recursos de digitalización tanto en tiempo como en espacio, lo que supone un importante ahorro de área y consumo. Finalmente, se presentan dos prototipos de sistemas de monitorización completos que de manera significativa superan la características de trabajos anteriores en términos de área y, especialmente, consumo de energía. Abstract Temperature is a first class design concern in modern integrated circuits. The important increase in power densities associated to recent technology evolutions has lead to the apparition of thermal gradients and hot spots during run time operation. Temperature impacts several circuit parameters such as speed, cooling budgets, reliability, power consumption, etc. In order to fight against these negative effects, dynamic thermal management (DTM) techniques adapt the behavior of the chip relying on the information of a monitoring system that provides run-time thermal information of the die surface. The field of on-chip temperature monitoring has drawn the attention of the scientific community in the recent years and is the object of study of this thesis. This thesis approaches the matter of on-chip temperature monitoring from different perspectives and levels, providing solutions to some of the most important issues. The physical and circuital levels are covered with the design and characterization of two novel temperature sensors specially tailored for DTM purposes. The first sensor is based upon a mechanism that obtains a pulse with a varying width based on the variations of the leakage currents on the temperature. In a nutshell, a circuit node is charged and subsequently left floating so that it discharges away through the subthreshold currents of a transistor; the time the node takes to discharge is the width of the pulse. Since the width of the pulse displays an exponential dependence on the temperature, the conversion into a digital word is realized by means of a logarithmic counter that performs both the timeto- digital conversion and the linearization of the output. The structure resulting from this combination of elements is implemented in a 0.35_m technology and is characterized by very reduced area, 10250 nm2, and power consumption, 1.05-65.5 nW at 5 samples/s, these figures outperformed all previous works by the time it was first published and still, by the time of the publication of this thesis, they outnumber all previous implementations in the same technology node. Concerning the accuracy, the sensor exhibits good linearity, even without calibration it displays a 3_ error of 1.97oC, appropriate to deal with DTM applications. As explained, the sensor is completely compatible with standard CMOS processes, this fact, along with its tiny area and power overhead, makes it specially suitable for the integration in a DTM monitoring system with a collection of on-chip monitors distributed across the chip. The exacerbated process fluctuations carried along with recent technology nodes jeop-ardize the linearity characteristics of the first sensor. In order to overcome these problems, a new temperature inferring technique is proposed. In this case, we also rely on the thermal dependencies of leakage currents that are used to discharge a floating node, but now, the result comes from the ratio of two different measures, in one of which we alter a characteristic of the discharging transistor |the gate voltage. This ratio proves to be very robust against process variations and displays a more than suficient linearity on the temperature |1.17oC 3_ error considering process variations and performing two-point calibration. The implementation of the sensing part based on this new technique implies several issues, such as the generation of process variations independent voltage reference, that are analyzed in depth in the thesis. In order to perform the time-to-digital conversion, we employ the same digitization structure the former sensor used. A completely new standard cell library targeting low area and power overhead is built from scratch to implement the digitization part. Putting all the pieces together, we achieve a complete sensor system that is characterized by ultra low energy per conversion of 48-640pJ and area of 0.0016mm2, this figure outperforms all previous works. To prove this statement, we perform a thorough comparison with over 40 works from the scientific literature. Moving up to the system level, the third contribution is centered on the modeling of a monitoring system consisting of set of thermal sensors distributed across the chip. All previous works from the literature target maximizing the accuracy of the system with the minimum number of monitors. In contrast, we introduce new metrics of quality apart form just the number of sensors; we consider the power consumption, the sampling frequency, the possibility to consider different types of monitors and the interconnection costs. The model is introduced in a simulated annealing algorithm that receives the thermal information of a system, its physical properties, area, power and interconnection constraints and a collection of monitor types; the algorithm yields the selected type of monitor, the number of monitors, their position and the optimum sampling rate. We test the algorithm with the Alpha 21364 processor under several constraint configurations to prove its validity. When compared to other previous works in the literature, the modeling presented here is the most complete. Finally, the last contribution targets the networking level, given an allocated set of temperature monitors, we focused on solving the problem of connecting them in an efficient way from the area and power perspectives. Our first proposal in this area is the introduction of a new interconnection hierarchy level, the threshing level, in between the monitors and the traditional peripheral buses that applies data selectivity to reduce the amount of information that is sent to the central controller. The idea behind this new level is that in this kind of networks most data are useless because from the controller viewpoint just a small amount of data |normally extreme values| is of interest. To cover the new interconnection level, we propose a single-wire monitoring network based on a time-domain signaling scheme that significantly reduces both the switching activity over the wire and the power consumption of the network. This scheme codes the information in the time domain and allows a straightforward obtention of an ordered list of values from the maximum to the minimum. If the scheme is applied to monitors that employ TDC, digitization resource sharing is achieved, producing an important saving in area and power consumption. Two prototypes of complete monitoring systems are presented, they significantly overcome previous works in terms of area and, specially, power consumption.

Using Buildroot for building Embedded Linux Systems

This document describes the basic steps to developed and embedded Linux-based system using the BeagleBoard. The document has been specifically written to use a BeagleBoard development system based on the OMAP `processor.

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

Ontology-based access to sensor data streams

Sensor networks are increasingly becoming one of the main sources of Big Data on the Web. However, the observations that they produce are made available with heterogeneous schemas, vocabularies and data formats, making it difficult to share and reuse these data for other purposes than those for which they were originally set up. In this thesis we address these challenges, considering how we can transform streaming raw data to rich ontology-based information that is accessible through continuous queries for streaming data. Our main contribution is an ontology-based approach for providing data access and query capabilities to streaming data sources, allowing users to express their needs at a conceptual level, independent of implementation and language-specific details. We introduce novel query rewriting and data translation techniques that rely on mapping definitions relating streaming data models to ontological concepts. Specific contributions include: • The syntax and semantics of the SPARQLStream query language for ontologybased data access, and a query rewriting approach for transforming SPARQLStream queries into streaming algebra expressions. • The design of an ontology-based streaming data access engine that can internally reuse an existing data stream engine, complex event processor or sensor middleware, using R2RML mappings for defining relationships between streaming data models and ontology concepts. Concerning the sensor metadata of such streaming data sources, we have investigated how we can use raw measurements to characterize streaming data, producing enriched data descriptions in terms of ontological models. Our specific contributions are: • A representation of sensor data time series that captures gradient information that is useful to characterize types of sensor data. • A method for classifying sensor data time series and determining the type of data, using data mining techniques, and a method for extracting semantic sensor metadata features from the time series.

A Web Implementation of A Generalized NEP

The Networks of Evolutionary Processors (NEPs) are computing mechanisms directly inspired from the behavior of cell populations more specifically the point mutations in DNA strands. These mechanisms are been used for solving NP-complete problems by means of a parallel computation postulation. This paper describes an implementation of the basic model of NEP using Web technologies and includes the possibility of designing some of the most common variants of it by means the use of the web page design which eases the configuration of a given problem. It is a system intended to be used in a multicore processor in order to benefit from the multi thread use.

A dual-band priority assignment algorithm for dynamic QoS resource management

Future high-quality consumer electronics will contain a number of applications running in a highly dynamic environment, and their execution will need to be efficiently arbitrated by the underlying platform software. The multimedia applications that currently execute in such similar contexts face frequent run-time variations in their resource demands, originated by the greedy nature of the multimedia processing itself. Changes in resource demands are triggered by numerous reasons (e.g. a switch in the input media compression format). Such situations require real-time adaptation mechanisms to adjust the system operation to the new requirements, and this must be done seamlessly to satisfy the user experience. One solution for efficiently managing application execution is to apply quality of service resource management techniques, based on assigning and enforcing resource contracts to applications. Most resource management solutions provide temporal isolation by enforcing resource assignments and avoiding any resource overruns. However, this has a clear limitation over the cost-effective resource usage. This paper presents a simple priority assignment scheme based on uniform priority bands to allow that greedy multimedia tasks incur in safe overruns that increase resource usage and do not threaten the timely execution of non-overrunning tasks. Experimental results show that the proposed priority assignment scheme in combination with a resource accounting mechanism preserves timely multimedia execution and delivery, achieves a higher cost-effective processor usage, and guarantees the execution isolation of non-overrunning tasks.

Performance assessment of a kinetically-powered network for herd localization

Developing a herd localization system capable to operate unattended in communication-challenged areas arises from the necessity of improving current systems in terms of cost, autonomy or any other facilities that a certain target group (or overall users) may demand. A network architecture of herd localization is proposed with its corresponding hardware and a methodology to assess performance in different operating conditions. The system is designed taking into account an eventual environmental impact hence most nodes are simple, cheap and kinetically powered from animal movements-neither batteries nor sophisticated processor chips are needed. Other network elements integrating GPS and batteries operate with selectable duty cycles, thus reducing maintenance duties. Equipment has been tested on Scandinavian reindeer in Lapland and its element modeling is integrated into a simulator to analyze such localization network applicability for different use cases. Performance indicators (detection frequency, localization accuracy and delay) are fitted to assess the overall performance; system relative costs are enclosed also for a range of deployments.

An Interleaved EPE-Immune PA-DPL Structure for Resisting Concentrated EM Side Channel Attacks on FPGA Implementation

Early propagation effect (EPE) is a critical problem in conventional dual-rail logic implementations against Side Channel Attacks (SCAs). Among previous EPE-resistant architectures, PA-DPL logic offers EPE-free capability at relatively low cost. However, its separate dual core structure is a weakness when facing concentrated EM attacks where a tiny EM probe can be precisely positioned closer to one of the two cores. In this paper, we present an PA-DPL dual-core interleaved structure to strengthen resistance against sophisticated EM attacks on Xilinx FPGA implementations. The main merit of the proposed structure is that every two routing in each signal pair are kept identical even the dual cores are interleaved together. By minimizing the distance between the complementary routings and instances of both cores, even the concentrated EM measurement cannot easily distinguish the minor EM field unbalance. In PA- DPL, EPE is avoided by compressing the evaluation phase to a small portion of the clock period, therefore, the speed is inevitably limited. Regarding this, we made an improvement to extend the duty cycle of evaluation phase to more than 40 percent, yielding a larger maximum working frequency. The detailed design flow is also presented. We validate the security improvement against EM attack by implementing a simplified AES co-processor in Virtex-5 FPGA.

Quantity and degree assessment in an RDF.based semantic language

This paper introduces a semantic language developed with the objective to be used in a semantic analyzer based on linguistic and world knowledge. Linguistic knowledge is provided by a Combinatorial Dictionary and several sets of rules. Extra-linguistic information is stored in an Ontology. The meaning of the text is represented by means of a series of RDF-type triples of the form predicate (subject, object). Semantic analyzer is one of the options of the multifunctional ETAP-3 linguistic processor. The analyzer can be used for Information Extraction and Question Answering. We describe semantic representation of expressions that provide an assessment of the number of objects involved and/or give a quantitative evaluation of different types of attributes. We focus on the following aspects: 1) parametric and non-parametric attributes; 2) gradable and non-gradable attributes; 3) ontological representation of different classes of attributes; 4) absolute and relative quantitative assessment; 5) punctual and interval quantitative assessment; 6) intervals with precise and fuzzy boundaries