Physiological drought responses improve predictions of live fuel moisture dynamics in a Mediterranean forest.

The moisture content of live fuels is an important determinant of forest flammability. Current approaches for modelling live fuel moisture content typically focus on the use of drought indices. However, these have mixed success partly because of species-specific differences in drought responses. Here we seek to understand the physiological mechanisms driving changes in live fuel moisture content, and to investigate the potential for incorporating plant physiological traits into live fuel moisture models. We measured the dynamics of leaf moisture content, access to water resources (through stable isotope analyses) and physiological traits (including leaf water potential, stomatal conductance, and cellular osmotic and elastic adjustments) across a fire season in a Mediterranean mixed forest in Catalonia, NE Spain. We found that differences in both seasonal variation and minimum values of live fuel moisture content were a function of access to water resources and plant physiological traits. Specifically, those species with the lowest minimum moisture content and largest seasonal variation in moisture (Cistus albidus: 49–137% and Rosmarinus officinalis: 47–144%) were most reliant on shallow soil water and had the lowest values of predawn leaf water potential. Species with the smallest variation in live fuel moisture content (Pinus nigra: 96–116% and Quercus ilex: 56–91%) exhibited isohydric behaviour (little variation in midday leaf water potential, and relatively tight regulation of stomata in response to soil drying). Of the traits measured, predawn leaf water potential provided the strongest predictor of live fuel moisture content (R2 = 0.63, AIC = 249), outperforming two commonly used drought indices (both with R2 = 0.49, AIC = 258). This is the first study to explicitly link fuel moisture with plant physiology and our findings demonstrate the potential and importance of incorporating ecophysiological plant traits to investigating seasonal changes in fuel moisture and, more broadly, forest flammability.This study was made possible thanks to the collaboration of and the staff from the Natural Park of Poblet, P Sopeña, and the technical staff from MedForLab. This study was funded by the Spanish Government (RYC-2012-10970, AGL2015-69151-R). R. H. Nolan was supported with funding from the New South Wales Office of Environment and Heritage, via the Bushfire Risk Management Research Hub. We benefitted from critical comments from J Voltas, JM Moreno and L Serrano and instrument loans from R Savín

Run-time support for multi-level disjoint memory address spaces

High Performance Computing (HPC) systems have become widely used tools in many industry areas and research fields. Research to produce more powerful and efficient systems has grown in par with their popularity. As a consequence, the complexity of modern HPC architectures has increased in order to provide systems with the highest levels of performance. This increased complexity has also affected the way HPC systems are programmed. HPC users have to deal with new devices, languages and tools, and this is can be a significant access barrier to people that do not have a deep knowledge in computer science. On par with the evolution of HPC systems, programming models have also evolved to ease the task of developing applications for these machines. Two well-known examples are OpenMP and MPI. The former can be used in shared memory systems and is praised for offering an easy methodology of software development. The latter is more popular because it targets distributed environments but it is considered burdensome to use. Besides these two, many programming models have emerged to propose new methodologies or to handle new hardware devices. One of these models is OmpSs. OmpSs is a programming model for modern HPC systems that is based on OpenMP and StarSs. Developed by the Programming Models group at the Barcelona Supercomputing Center, it targets the latest generation of HPC systems while benefiting from the ease of use of OpenMP. OmpSs offers asynchronous parallelism with the concept of tasks with data dependencies. These tasks allow the specification of sections of code that can be executed in parallel while the dependencies specify the restrictions about the order in which the tasks can be executed. With this, OmpSs programs can adapt to a many different system configurations while fundamentally still being sequential programs with annotations. This thesis explores the benefits of providing OmpSs the capability to target architectures with complex memory hierarchies. An example of such systems can be the new generation of clusters that use accelerators to power their computing capabilities. The memory hierarchy of these machines is composed of a first level of distributed memory formed by the memory of each individual node, and a second level formed by the private memory of each accelerator devices. Our first contribution shows the implementation of the support of cluster of multi-cores for the OmpSs programming model. We also present two optimizations to boost the performance of applications running on top of cluster systems: a specific task scheduling policy and the addition of slave-to-slave transfers. We evaluate our implementation using a set of benchmarks coded in OmpSs and we also compare them against the same applications implemented using MPI, the most widely used programming model for these systems. We extend our initial implementation in our second contribution, which provides OmpSs with support for clusters of GPUs. We show that OmpSs programs targeting these complex systems are capable of achieving a good performance when compared against MPI+CUDA implementations. The third contribution of this thesis presents an implementation and evaluation of the performance and programmability impact of supporting non-contiguous memory regions. Offering this feature allows applications with complex data accesses to be easily annotated with OmpSs. This is important to widen the spectrum of applications that can be handled by the programming model.Els sistemes de computació d'altes prestacions (CAP) han esdevingut eines importants en diferents sectors industrials i camps de recerca. La recerca per produir sistemes més potents i eficients ha crescut proporcionalment a aquesta popularitat. Com a conseqüència, la complexitat d'aquest tipus de sistemes s'ha incrementat per tal de dotar-los d'altes prestacions. Aquest increment en la complexitat també ha afectat la manera de programar aquest tipus de sistemes. Els usuaris de sistemes CAP han de treballar amb nous dispositius, llenguatges i eines, i això pot convertir-se en una barrera d'entrada significativa per aquelles persones que no tinguin uns alts coneixements informàtics. Seguin l'evolució dels sistemes CAP, els models de programació també han evolucionat per tal de facilitar la tasca de desenvolupar aplicacions per aquests sistemes. Dos exemples ben coneguts son OpenMP i MPI. El primer es pot utilitzar en sistemes de memòria compartida i es reconegut per oferir una metodologia de desenvolupament senzilla. El segon és més popular perquè està dissenyat per sistemes distribuïts, però està considerat difícil d'utilitzar. A part d'aquests dos, altres models de programació han sorgit per proposar noves metodologies o per suportar nous components hardware. Un d'aquests nous models és OmpSs. OmpSs és un model de programació per sistemes CAP moderns que està basat en OpenMP i StarSs. Desenvolupat pel grup de Models de Programació del Barcelona Supercomputing Center, està dissenyat per suportar la darrera generació de sistemes CAP i alhora oferir la facilitat d'us d'OpenMP. OmpSs ofereix paral·lelisme asíncron mitjançant el concepte de tasques amb dependències de dades. Aquestes tasques permeten especificar regions de codi que poden ser executades en paral·lel, mentre que les dependències especifiquen les restriccions sobre l'ordre en que aquestes tasques poden ser executades. Amb això, els programes fets amb OmpSs poden adaptar-se a sistemes amb diferents configuracions tot i ser fonamentalment programes seqüencials amb anotacions. Aquesta tesi explora els beneficis de proveir a OmpSs amb la capacitat de funcionar sobre arquitectures amb jerarquies de memòria complexes. Un exemple d'un sistema així pot ser un dels clústers de nova generació que utilitzen acceleradors per tal d'oferir més capacitat de càlcul. La jerarquia de memòria en aquestes màquines està composada per un primer nivell de memòria distribuïda formada per la memòria de cada node individual, i el segon nivell està format per la memòria privada de cada accelerador. La primera contribució d'aquesta tesi mostra la implementació del suport de clústers de multi-cores pel model de programació OmpSs. També presentem dos optimitzacions per millorar el rendiment de les aplicacions quan s'executen en sistemes clúster: una política de planificació de tasques específica i la incorporació dels missatges entre nodes esclaus. Avaluem la nostra implementació usant un conjunt d'aplicacions programades en OmpSs i també les comparem amb les mateixes aplicacions implementades usant MPI, el model de programació més estès per aquest tipus de sistemes. En la segona contribució estenem la nostra implementació inicial per tal de dotar OmpSs de suport per clústers de GPUs. Mostrem que els programes OmpSs son capaços d'obtenir un bon rendiment sobre aquests tipus de sistemes, fins i tot quan els comparem amb versions implementades usant MPI+CUDA. La tercera contribució descriu la implementació i avaluació del rendiment i de l'impacte de suportar regions de memòria no contigües. Oferir aquesta funcionalitat permet implementar fàcilment amb OmpSs aplicacions amb accessos complexes a memòria, cosa que és important de cara a ampliar l'espectre d'aplicacions que poden ser tractades pel model de programació

Measuring TCP bandwidth on top of a Gigabit and Myrinet network

In this article we measure the bandwidth achieved by the TCP protocol on top of a Gigabit and Myrinet network. We have created a synthetic benchmark, consisting on a server and a client that both produce and consume data, to measure bandwidth. Four different versions of this benchmark are evaluated: (a) a simple one-threaded version; (b) a version that can consume data if the producer is unable to produce data; (c) a version with the Nagle algorithm disabled; and (d) a version where producers and consumers are threads on their owns. The results shows that on both networks: (1) it is necessary to drain the network to avoid deadlocks; (2) the Nagle algorithm is useful and gets smaller variation in results; and (3) adding an extra thread for reading reduces the maximum bandwidth achievable and it gets better bandwidth for bigger messages and worse for smaller ones when a great number of messages are sent.Preprin

A trade-off between embolism resistance and bark thickness in conifers: Are drought and fire adaptations antagonistic?

Background: Understanding the mechanisms that explain the spatial distribution of conifers across biogeographical gradients is important for anticipating potential range shifts owing to global change. Classical explanations have involved trade-offs between shade and drought tolerances, but more recent studies observed that trade-offs between fire and drought tolerances could also be important. Aims: Here we propose that a contributing mechanism to explain how conifer species are distributed across productivity gradients – with marked variation in the incidence of fire – involves a trade-off between allocation to bark, which serves to protect against fire, or to embolism resistance, which serves to protect against drought. Methods: We compiled information from different datasets and performed regression analyses. Results: We observed a trade-off between bark thickness and embolism resistance in conifer species such that species show either large investments of carbon to the bark or have thinner barks but xylem resistant to embolism; we did not observe conifer species concomitantly showing high fire tolerance and embolism resistance. Conclusions: This study serves as a starting point for a novel framework on how fire and drought adaptations affect conifer biogeography. Additional studies will be necessary to discover the generality of our findings by including other species of conifers, for example those in the Southern Hemisphere.This work was supported by the Ministerio de Economía y Competitividad [RYC-2012-10970, AGL2015-69151-R, AGL2015-68274-C3-]

The AXIOM software layers

AXIOM project aims at developing a heterogeneous computing board (SMP-FPGA).The Software Layers developed at the AXIOM project are explained.OmpSs provides an easy way to execute heterogeneous codes in multiple cores. People and objects will soon share the same digital network for information exchange in a world named as the age of the cyber-physical systems. The general expectation is that people and systems will interact in real-time. This poses pressure onto systems design to support increasing demands on computational power, while keeping a low power envelop. Additionally, modular scaling and easy programmability are also important to ensure these systems to become widespread. The whole set of expectations impose scientific and technological challenges that need to be properly addressed.The AXIOM project (Agile, eXtensible, fast I/O Module) will research new hardware/software architectures for cyber-physical systems to meet such expectations. The technical approach aims at solving fundamental problems to enable easy programmability of heterogeneous multi-core multi-board systems. AXIOM proposes the use of the task-based OmpSs programming model, leveraging low-level communication interfaces provided by the hardware. Modular scalability will be possible thanks to a fast interconnect embedded into each module. To this aim, an innovative ARM and FPGA-based board will be designed, with enhanced capabilities for interfacing with the physical world. Its effectiveness will be demonstrated with key scenarios such as Smart Video-Surveillance and Smart Living/Home (domotics).Peer ReviewedPostprint (author's final draft

The AXIOM platform for next-generation cyber physical systems

Cyber-Physical Systems (CPSs) are widely used in many applications that require interactions between humans and their physical environment. These systems usually integrate a set of hardware-software components for optimal application execution in terms of performance and energy consumption. The AXIOM project (Agile, eXtensible, fast I/O Module), presented in this paper, proposes a hardware-software platform for CPS coupled with an easy parallel programming model and sufficient connectivity so that the performance can scale-up by adding multiple boards. AXIOM supports a task-based programming model based on OmpSs and leverages a high-speed, inexpensive communication interface called AXIOM-Link. The board also tightly couples the CPU with reconfigurable resources to accelerate portions of the applications. As case studies, AXIOM uses smart video surveillance, and smart home living applicationsThis work is partially supported by the European Union H2020 program through the AXIOM project (grant ICT-01-2014 GA 645496) and HiPEAC (GA 687698), by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project, and by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272). We also thank the Xilinx University Program for its hardware and software donations.Peer ReviewedPostprint (author's final draft

Epidemiología básica. Material docente para prácticas en ciencias de la salud

Material docente teórico práctico para apoyar la enseñanza de la epidemiología. Consta de 4 unidades, cada una de ellas con una introducción teórica y unos ejercicios basados en artículos publicados en inglés en revistas científicas

Utilización de los medios de comunicación como herramienta de aprendizaje y consolidación de conocimientos en epidemiología y salud pública

Reforzar conceptos de salud pública mediante análisis de información publicada por los medios. Se seleccionarán informaciones que traten temas de salud pública. Se realizará un análisis evaluando qué conceptos se manejan, y si están bien utilizados

Efecto de tratamiento selvícolas post-incendio y sequía inducida sobre el suelo y diversidad vegetal en regenerados de pino carrasco (Pinus halepensis Mill.)

El cambio global, definido como el conjunto de cambios ambientales de origen antrópico sobre el funcionamiento del sistema Tierra, modifica ciertos regímenes de perturbaciones naturales. Las variaciones de los usos del suelo así como el cambio climático, ambos componentes del cambio global, modifican el régimen de incendios y de sequías, pudiendo afectar notablemente a los ecosistemas forestales. De este modo, se pueden producir efectos de inadaptación de ciertas masas forestales más vulnerables, dando lugar a la pseudo-estabilización de estadios regresivos o una degradación irreversible. Tras la ocurrencia de un incendio, otra perturbación añadida al cambio global y al incendio, puede ser en algunos casos el manejo selvícola post-incendio necesario para mejorar la masa forestal. Por otra parte, estos tratamientos selvícolas post-incendio tradicionalmente han prestado una mayor atención a la vegetación que a los suelos, cuando éstos últimos son la base de todos los ecosistemas terrestres. Por ello, esta tesis se ha centrado principalmente en el estudio de los efectos de las tres perturbaciones mencionadas (incendios, cambio global y manejo selvícola post-incendio) sobre los suelos. Así como también se ha presentado un estudio del efecto del manejo selvícola post-incendio y de los efectos del cambio climático sobre la diversidad vegetal. En el verano de 1994, en España se quemaron cerca de 250.000 ha de superficie arbolada. Este estudio se ha realizado en dos grandes incendios acontecidos en este año en el sureste de la Península Ibérica: en Yeste (provincia de Albacete) y en Calasparra (provincia de Murcia) en dónde el pino carrasco (Pinus halepensis Mill.) ocupaba una gran parte del área forestal. El incendio de Yeste quemó 14.000 ha mientras que el de Calasparra quemó 30.000 ha. El objetivo principal de la presente tesis es observar, en primer lugar, en qué medida los tratamientos selvícolas tempranos efectuados en regenerados naturales post-incendio de pino carrasco afectan a las propiedades microbiológicas y enzimáticas del suelo estudiadas; en segundo lugar, determinar la influencia que pudiera tener una reducción de la precipitación, atendiendo a las predicciones del IPCC, sobre parámetros edáficos y sobre la diversidad vegetal. En tercer lugar, estudiar también el efecto de la estacionalidad y la diferente cubierta vegetal sobre las propiedades del suelo. En ambos casos se han considerado dos ombroclimas, seco (Yeste) y semiárido (Calasparra), con el objeto de determinar posibles diferencias en la influencia de tratamientos y reducción de la precipitación (sequía) sobre los suelos y la diversidad vegetal. Para ello, dado que medir la calidad del suelo es una tarea muy complicada y no existe un consenso por parte de la comunidad científica, se han elegido diferentes indicadores del suelo que puedan representar ciertas características o funciones del suelo mediante su medición, como son parámetros físico-químicos (pH, carbonatos totales, nitrógeno total, conductividad eléctrica, fósforo disponible, materia orgánica, etc.) así como parámetros microbiológicos (respiración basal del suelo y carbono de la biomasa microbiana) y actividades enzimáticas (deshidrogenasa, ureasa, fosfatasa y beta-glucosidasa). Por otra parte, se han realizado transectos mediante el método de muestreo de la intersección lineal para caracterizar la diversidad vegetal de la vegetación de la zona estudiada. Como conclusiones principales de este trabajo, se han obtenido: ¿ El ombroclima (la localidad) ejerce una influencia significativa tanto en las propiedades del suelo que nos permiten caracterizar la calidad del suelo, con en los parámetros medidos de biodiversidad. Sitios más húmedos y más fríos, dentro del rango mediterráneo, generan mayor actividad microbiológica. ¿ El incendio no ejerce ninguna influencia pasados 17 años después de su ocurrencia sobre las propiedades del suelo, por lo que se concluye que los suelos estudiados son resilientes a estas perturbaciones, es decir, se recuperan de la perturbación llegando a alcanzar niveles similares a los que tenía en momentos previos a ésta. ¿ Los clareos realizados no mostraron diferencias significativas por lo que podemos concluir que el suelo se ha recuperado de dicha perturbación artificial. Por otro lado, los clareos ejercieron un efecto positivo en la biodiversidad vegetal. ¿ La estacionalidad ejerce un efecto significativo en las propiedades microbiológicas y actividades enzimáticas de los suelos. ¿ La cobertura del pino frente a zonas de suelo desnudo no genera diferencias en los parámetros medidos, lo cual puede explicarse por la calidad de la hojarasca más resistente a la degradación por su contenido de lignina. ¿ Las propiedades del suelo no mostraron diferencias frente a una reducción del 15% en la precipitación media anual. Menor variabilidad en cuanto a la sequía inducida en Calasparra que en Yeste

Measuring TCP bandwidth on top of a Gigabit and Myrinet network

In this article we measure the bandwidth achieved by the TCP protocol on top of a Gigabit and Myrinet network. We have created a synthetic benchmark, consisting on a server and a client that both produce and consume data, to measure bandwidth. Four different versions of this benchmark are evaluated: (a) a simple one-threaded version; (b) a version that can consume data if the producer is unable to produce data; (c) a version with the Nagle algorithm disabled; and (d) a version where producers and consumers are threads on their owns. The results shows that on both networks: (1) it is necessary to drain the network to avoid deadlocks; (2) the Nagle algorithm is useful and gets smaller variation in results; and (3) adding an extra thread for reading reduces the maximum bandwidth achievable and it gets better bandwidth for bigger messages and worse for smaller ones when a great number of messages are sent