Communication Middleware for Distributed Hard Real-Time Systems in Java

Distributed real-time embedded systems are becoming increasingly important to society. More demands will be made on them and greater reliance will be placed on the delivery of their services. A relevant subset of them is high-integrity or hard real-time systems, where failure can cause loss of life, environmental harm, or significant financial loss. Additionally, the evolution of communication networks and paradigms as well as the necessity of demanding processing power and fault tolerance, motivated the interconnection between electronic devices; many of the communications have the possibility of transferring data at a high speed. The concept of distributed systems emerged as systems where different parts are executed on several nodes that interact with each other via a communication network. Java’s popularity, facilities and platform independence have made it an interesting language for the real-time and embedded community. This was the motivation for the development of RTSJ (Real-Time Specification for Java), which is a language extension intended to allow the development of real-time systems. The use of Java in the development of high-integrity systems requires strict development and testing techniques. However, RTJS includes a number of language features that are forbidden in such systems. In the context of the HIJA project, the HRTJ (Hard Real-Time Java) profile was developed to define a robust subset of the language that is amenable to static analysis for high-integrity system certification. Currently, a specification under the Java community process (JSR- 302) is being developed. Its purpose is to define those capabilities needed to create safety critical applications with Java technology called Safety Critical Java (SCJ). However, neither RTSJ nor its profiles provide facilities to develop distributed realtime applications. This is an important issue, as most of the current and future systems will be distributed. The Distributed RTSJ (DRTSJ) Expert Group was created under the Java community process (JSR-50) in order to define appropriate abstractions to overcome this problem. Currently there is no formal specification. The aim of this thesis is to develop a communication middleware that is suitable for the development of distributed hard real-time systems in Java, based on the integration between the RMI (Remote Method Invocation) model and the HRTJ profile. It has been designed and implemented keeping in mind the main requirements such as the predictability and reliability in the timing behavior and the resource usage. iThe design starts with the definition of a computational model which identifies among other things: the communication model, most appropriate underlying network protocols, the analysis model, and a subset of Java for hard real-time systems. In the design, the remote references are the basic means for building distributed applications which are associated with all non-functional parameters and resources needed to implement synchronous or asynchronous remote invocations with real-time attributes. The proposed middleware separates the resource allocation from the execution itself by defining two phases and a specific threading mechanism that guarantees a suitable timing behavior. It also includes mechanisms to monitor the functional and the timing behavior. It provides independence from network protocol defining a network interface and modules. The JRMP protocol was modified to include two phases, non-functional parameters, and message size optimizations. Although serialization is one of the fundamental operations to ensure proper data transmission, current implementations are not suitable for hard real-time systems and there are no alternatives. This thesis proposes a predictable serialization that introduces a new compiler to generate optimized code according to the computational model. The proposed solution has the advantage of allowing us to schedule the communications and to adjust the memory usage at compilation time. In order to validate the design and the implementation a demanding validation process was carried out with emphasis in the functional behavior, the memory usage, the processor usage (the end-to-end response time and the response time in each functional block) and the network usage (real consumption according to the calculated consumption). The results obtained in an industrial application developed by Thales Avionics (a Flight Management System) and in exhaustive tests show that the design and the prototype are reliable for industrial applications with strict timing requirements. Los sistemas empotrados y distribuidos de tiempo real son cada vez más importantes para la sociedad. Su demanda aumenta y cada vez más dependemos de los servicios que proporcionan. Los sistemas de alta integridad constituyen un subconjunto de gran importancia. Se caracterizan por que un fallo en su funcionamiento puede causar pérdida de vidas humanas, daños en el medio ambiente o cuantiosas pérdidas económicas. La necesidad de satisfacer requisitos temporales estrictos, hace más complejo su desarrollo. Mientras que los sistemas empotrados se sigan expandiendo en nuestra sociedad, es necesario garantizar un coste de desarrollo ajustado mediante el uso técnicas adecuadas en su diseño, mantenimiento y certificación. En concreto, se requiere una tecnología flexible e independiente del hardware. La evolución de las redes y paradigmas de comunicación, así como la necesidad de mayor potencia de cómputo y de tolerancia a fallos, ha motivado la interconexión de dispositivos electrónicos. Los mecanismos de comunicación permiten la transferencia de datos con alta velocidad de transmisión. En este contexto, el concepto de sistema distribuido ha emergido como sistemas donde sus componentes se ejecutan en varios nodos en paralelo y que interactúan entre ellos mediante redes de comunicaciones. Un concepto interesante son los sistemas de tiempo real neutrales respecto a la plataforma de ejecución. Se caracterizan por la falta de conocimiento de esta plataforma durante su diseño. Esta propiedad es relevante, por que conviene que se ejecuten en la mayor variedad de arquitecturas, tienen una vida media mayor de diez anos y el lugar ˜ donde se ejecutan puede variar. El lenguaje de programación Java es una buena base para el desarrollo de este tipo de sistemas. Por este motivo se ha creado RTSJ (Real-Time Specification for Java), que es una extensión del lenguaje para permitir el desarrollo de sistemas de tiempo real. Sin embargo, RTSJ no proporciona facilidades para el desarrollo de aplicaciones distribuidas de tiempo real. Es una limitación importante dado que la mayoría de los actuales y futuros sistemas serán distribuidos. El grupo DRTSJ (DistributedRTSJ) fue creado bajo el proceso de la comunidad de Java (JSR-50) con el fin de definir las abstracciones que aborden dicha limitación, pero en la actualidad aun no existe una especificacion formal. El objetivo de esta tesis es desarrollar un middleware de comunicaciones para el desarrollo de sistemas distribuidos de tiempo real en Java, basado en la integración entre el modelo de RMI (Remote Method Invocation) y el perfil HRTJ. Ha sido diseñado e implementado teniendo en cuenta los requisitos principales, como la predecibilidad y la confiabilidad del comportamiento temporal y el uso de recursos. El diseño parte de la definición de un modelo computacional el cual identifica entre otras cosas: el modelo de comunicaciones, los protocolos de red subyacentes más adecuados, el modelo de análisis, y un subconjunto de Java para sistemas de tiempo real crítico. En el diseño, las referencias remotas son el medio básico para construcción de aplicaciones distribuidas las cuales son asociadas a todos los parámetros no funcionales y los recursos necesarios para la ejecución de invocaciones remotas síncronas o asíncronas con atributos de tiempo real. El middleware propuesto separa la asignación de recursos de la propia ejecución definiendo dos fases y un mecanismo de hebras especifico que garantiza un comportamiento temporal adecuado. Además se ha incluido mecanismos para supervisar el comportamiento funcional y temporal. Se ha buscado independencia del protocolo de red definiendo una interfaz de red y módulos específicos. También se ha modificado el protocolo JRMP para incluir diferentes fases, parámetros no funcionales y optimizaciones de los tamaños de los mensajes. Aunque la serialización es una de las operaciones fundamentales para asegurar la adecuada transmisión de datos, las actuales implementaciones no son adecuadas para sistemas críticos y no hay alternativas. Este trabajo propone una serialización predecible que ha implicado el desarrollo de un nuevo compilador para la generación de código optimizado acorde al modelo computacional. La solución propuesta tiene la ventaja que en tiempo de compilación nos permite planificar las comunicaciones y ajustar el uso de memoria. Con el objetivo de validar el diseño e implementación se ha llevado a cabo un exigente proceso de validación con énfasis en: el comportamiento funcional, el uso de memoria, el uso del procesador (tiempo de respuesta de extremo a extremo y en cada uno de los bloques funcionales) y el uso de la red (consumo real conforme al estimado). Los buenos resultados obtenidos en una aplicación industrial desarrollada por Thales Avionics (un sistema de gestión de vuelo) y en las pruebas exhaustivas han demostrado que el diseño y el prototipo son fiables para aplicaciones industriales con estrictos requisitos temporales.

Integrating software testing and run-time checking in an assertion verification framework

We have designed and implemented a framework that unifies unit testing and run-time verification (as well as static verification and static debugging). A key contribution of our approach is that a unified assertion language is used for all of these tasks. We first propose methods for compiling runtime checks for (parts of) assertions which cannot be verified at compile-time via program transformation. This transformation allows checking preconditions and postconditions, including conditional postconditions, properties at arbitrary program points, and certain computational properties. The implemented transformation includes several optimizations to reduce run-time overhead. We also propose a minimal addition to the assertion language which allows defining unit tests to be run in order to detect possible violations of the (partial) specifications expressed by the assertions. This language can express for example the input data for performing the unit tests or the number of times that the unit tests should be repeated. We have implemented the framework within the Ciao/CiaoPP system and effectively applied it to the verification of ISO-prolog compliance and to the detection of different types of bugs in the Ciao system source code. Several experimental results are presented that ¡Ilústrate different trade-offs among program size, running time, or levéis of verbosity of the messages shown to the user.

Towards execution time estimation in abstract machine-based languages

Abstract machines provide a certain separation between platformdependent and platform-independent concerns in compilation. Many of the differences between architectures are encapsulated in the speciflc abstract machine implementation and the bytecode is left largely architecture independent. Taking advantage of this fact, we present a framework for estimating upper and lower bounds on the execution times of logic programs running on a bytecode-based abstract machine. Our approach includes a one-time, programindependent proflling stage which calculates constants or functions bounding the execution time of each abstract machine instruction. Then, a compile-time cost estimation phase, using the instruction timing information, infers expressions giving platform-dependent upper and lower bounds on actual execution time as functions of input data sizes for each program. Working at the abstract machine level makes it possible to take into account low-level issues in new architectures and platforms by just reexecuting the calibration stage instead of having to tailor the analysis for each architecture and platform. Applications of such predicted execution times include debugging/veriflcation of time properties, certiflcation of time properties in mobile code, granularity control in parallel/distributed computing, and resource-oriented specialization.

Integrating software testing and run-time checking in an assertion verification framework.

We have designed and implemented a framework that unifies unit testing and run-time verification (as well as static verification and static debugging). A key contribution of our approach is that a unified assertion language is used for all of these tasks. We first propose methods for compiling runtime checks for (parts of) assertions which cannot be verified at compile-time via program transformation. This transformation allows checking preconditions and postconditions, including conditional postconditions, properties at arbitrary program points, and certain computational properties. The implemented transformation includes several optimizations to reduce run-time overhead. We also propose a minimal addition to the assertion language which allows defining unit tests to be run in order to detect possible violations of the (partial) specifications expressed by the assertions. This language can express for example the input data for performing the unit tests or the number of times that the unit tests should be repeated. We have implemented the framework within the Ciao/CiaoPP system and effectively applied it to the verification of ISO-prolog compliance and to the detection of different types of bugs in the Ciao system source code. Several experimental results are presented that illustrate different trade-offs among program size, running time, or levels of verbosity of the messages shown to the user.

A new generation of real-time systems in the JET tokamak

Recently a new recipe for developing and deploying real-time systems has become increasingly adopted in the JET tokamak. Powered by the advent of x86 multi-core technology and the reliability of the JET’s well established Real-Time Data Network (RTDN) to handle all real-time I/O, an official Linux vanilla kernel has been demonstrated to be able to provide realtime performance to user-space applications that are required to meet stringent timing constraints. In particular, a careful rearrangement of the Interrupt ReQuests’ (IRQs) affinities together with the kernel’s CPU isolation mechanism allows to obtain either soft or hard real-time behavior depending on the synchronization mechanism adopted. Finally, the Multithreaded Application Real-Time executor (MARTe) framework is used for building applications particularly optimised for exploring multicore architectures. In the past year, four new systems based on this philosophy have been installed and are now part of the JET’s routine operation. The focus of the present work is on the configuration and interconnection of the ingredients that enable these new systems’ real-time capability and on the impact that JET’s distributed real-time architecture has on system engineering requirements, such as algorithm testing and plant commissioning. Details are given about the common real-time configuration and development path of these systems, followed by a brief description of each system together with results regarding their real-time performance. A cycle time jitter analysis of a user-space MARTe based application synchronising over a network is also presented. The goal is to compare its deterministic performance while running on a vanilla and on a Messaging Real time Grid (MRG) Linux kernel.

Unit Root Analysis of Traffic Time Series in Toll Highways

Concession contracts in highways often include some kind of clauses (for example, a minimum traffic guarantee) that allow for better management of the business risks. The value of these clauses may be important and should be added to the total value of the concession. However, in these cases, traditional valuation techniques, like the NPV (net present value) of the project, are insufficient. An alternative methodology for the valuation of highway concession is one based on the real options approach. This methodology is generally built on the assumption of the evolution of traffic volume as a GBM (geometric Brownian motion), which is the hypothesis analyzed in this paper. First, a description of the methodology used for the analysis of the existence of unit roots (i.e., the hypothesis of non-stationarity) is provided. The Dickey-Fuller approach has been used, which is the most common test for this kind of analysis. Then this methodology is applied to perform a statistical analysis of traffic series in Spanish toll highways. For this purpose, data on the AADT (annual average daily traffic) on a set of highways have been used. The period of analysis is around thirty years in most cases. The main outcome of the research is that the hypothesis that traffic volume follows a GBM process in Spanish toll highways cannot be rejected. This result is robust, and therefore it can be used as a starting point for the application of the real options theory to assess toll highway concessions.

Time derivatives in air temperature and enthalpy as non-invasive welfare indicators during long distance animal transport in Spain and Portugal.

High temperatures and relative humidity can compromise animal welfare on the farm level, but less is known about those changes during long distance transport of domestic animals to slaughter. Although upper temperature limits have been established to transport pigs in Europe, few indices include relative or absolute humidity maxima or mention appropriate enthalpy ranges.

The time variable in the calculation of building structures. How to extend the working life until the 100 years?

The idea that a building and consequently its structure is for a lifetime has stopped being a reference. CTE establishes that the life utility of a normal construction structure should be of 50years. If the time variable is introduced in the calculation of actions on structures, seems evident thatdifferent values can be used for a standard building, for a provisional structure with ≤ 10 years of life utility or for a monumental building with a life utility of 100 years. The present presentation follows at all moment, the directives and formulations given in the different structural Eurocodes, till the moment not included in the CTE. Finally the values of the actions that must be used to extend the life utility of a building until. 100 years will be deduced, also it suitability and e conomic feasibility will be discuss.

Test Analysis Tool (TATo). A new tool for standardization of time series in maritime and port environment

During the last decades, Puertos del Estado and research groups have developed a huge effort on numerical an physical monitoring. This effort has led to the necessity to implement a tool to standardize, store and process all gathered data. The Test Analysis Tool (TATo) is described in the paper.

Time scales in cognitive neuroscience

Cognitive neuroscience boils down to describing the ways in which cognitive function results from brain activity. In turn, brain activity shows complex fluctuations, with structure at many spatio-temporal scales. Exactly how cognitive function inherits the physical dimensions of neural activity, though, is highly non-trivial, and so are generally the corresponding dimensions of cognitive phenomena. As for any physical phenomenon, when studying cognitive function, the first conceptual step should be that of establishing its dimensions. Here, we provide a systematic presentation of the temporal aspects of task-related brain activity, from the smallest scale of the brain imaging technique's resolution, to the observation time of a given experiment, through the characteristic time scales of the process under study. We first review some standard assumptions on the temporal scales of cognitive function. In spite of their general use, these assumptions hold true to a high degree of approximation for many cognitive (viz. fast perceptual) processes, but have their limitations for other ones (e.g., thinking or reasoning). We define in a rigorous way the temporal quantifiers of cognition at all scales, and illustrate how they qualitatively vary as a function of the properties of the cognitive process under study. We propose that each phenomenon should be approached with its own set of theoretical, methodological and analytical tools. In particular, we show that when treating cognitive processes such as thinking or reasoning, complex properties of ongoing brain activity, which can be drastically simplified when considering fast (e.g., perceptual) processes, start playing a major role, and not only characterize the temporal properties of task-related brain activity, but also determine the conditions for proper observation of the phenomena. Finally, some implications on the design of experiments, data analyses, and the choice of recording parameters are discussed.

Contradictio in terminis: dialéctica de la ambigüedad en la arquitectura contemporánea

The twentieth century brought a new sensibility characterized by the discredit of cartesian rationality and the weakening of universal truths, related with aesthetic values as order, proportion and harmony. In the middle of the century, theorists such as Theodor Adorno, Rudolf Arnheim and Anton Ehrenzweig warned about the transformation developed by the artistic field. Contemporary aesthetics seemed to have a new goal: to deny the idea of art as an organized, finished and coherent structure. The order had lost its privileged position. Disorder, probability, arbitrariness, accidentality, randomness, chaos, fragmentation, indeterminacy... Gradually new terms were coined by aesthetic criticism to explain what had been happening since the beginning of the century. The first essays on the matter sought to provide new interpretative models based on, among other arguments, the phenomenology of perception, the recent discoveries of quantum mechanics, the deeper layers of the psyche or the information theories. Overall, were worthy attempts to give theoretical content to a situation as obvious as devoid of founding charter. Finally, in 1962, Umberto Eco brought together all this efforts by proposing a single theoretical frame in his book Opera Aperta. According to his point of view, all of the aesthetic production of twentieth century had a characteristic in common: its capacity to express multiplicity. For this reason, he considered that the nature of contemporary art was, above all, ambiguous. The aim of this research is to clarify the consequences of the incorporation of ambiguity in architectural theoretical discourse. We should start making an accurate analysis of this concept. However, this task is quite difficult because ambiguity does not allow itself to be clearly defined. This concept has the disadvantage that its signifier is as imprecise as its signified. In addition, the negative connotations that ambiguity still has outside the aesthetic field, stigmatizes this term and makes its use problematic. Another problem of ambiguity is that the contemporary subject is able to locate it in all situations. This means that in addition to distinguish ambiguity in contemporary productions, so does in works belonging to remote ages and styles. For that reason, it could be said that everything is ambiguous. And that’s correct, because somehow ambiguity is present in any creation of the imperfect human being. However, as Eco, Arnheim and Ehrenzweig pointed out, there are two major differences between current and past contexts. One affects the subject and the other the object. First, it’s the contemporary subject, and no other, who has acquired the ability to value and assimilate ambiguity. Secondly, ambiguity was an unexpected aesthetic result in former periods, while in contemporary object it has been codified and is deliberately present. In any case, as Eco did, we consider appropriate the use of the term ambiguity to refer to the contemporary aesthetic field. Any other term with more specific meaning would only show partial and limited aspects of a situation quite complex and difficult to diagnose. Opposed to what normally might be expected, in this case ambiguity is the term that fits better due to its particular lack of specificity. In fact, this lack of specificity is what allows to assign a dynamic condition to the idea of ambiguity that in other terms would hardly be operative. Thus, instead of trying to define the idea of ambiguity, we will analyze how it has evolved and its consequences in architectural discipline. Instead of trying to define what it is, we will examine what its presence has supposed in each moment. We will deal with ambiguity as a constant presence that has always been latent in architectural production but whose nature has been modified over time. Eco, in the mid-twentieth century, discerned between classical ambiguity and contemporary ambiguity. Currently, half a century later, the challenge is to discern whether the idea of ambiguity has remained unchanged or have suffered a new transformation. What this research will demonstrate is that it’s possible to detect a new transformation that has much to do with the cultural and aesthetic context of last decades: the transition from modernism to postmodernism. This assumption leads us to establish two different levels of contemporary ambiguity: each one related to one these periods. The first level of ambiguity is widely well-known since many years. Its main characteristics are a codified multiplicity, an interpretative freedom and an active subject who gives conclusion to an object that is incomplete or indefinite. This level of ambiguity is related to the idea of indeterminacy, concept successfully introduced into contemporary aesthetic language. The second level of ambiguity has been almost unnoticed for architectural criticism, although it has been identified and studied in other theoretical disciplines. Much of the work of Fredric Jameson and François Lyotard shows reasonable evidences that the aesthetic production of postmodernism has transcended modern ambiguity to reach a new level in which, despite of the existence of multiplicity, the interpretative freedom and the active subject have been questioned, and at last denied. In this period ambiguity seems to have reached a new level in which it’s no longer possible to obtain a conclusive and complete interpretation of the object because it has became an unreadable device. The postmodern production offers a kind of inaccessible multiplicity and its nature is deeply contradictory. This hypothetical transformation of the idea of ambiguity has an outstanding analogy with that shown in the poetic analysis made by William Empson, published in 1936 in his Seven Types of Ambiguity. Empson established different levels of ambiguity and classified them according to their poetic effect. This layout had an ascendant logic towards incoherence. In seventh level, where ambiguity is higher, he located the contradiction between irreconcilable opposites. It could be said that contradiction, once it undermines the coherence of the object, was the better way that contemporary aesthetics found to confirm the Hegelian judgment, according to which art would ultimately reject its capacity to express truth. Much of the transformation of architecture throughout last century is related to the active involvement of ambiguity in its theoretical discourse. In modern architecture ambiguity is present afterwards, in its critical review made by theoreticians like Colin Rowe, Manfredo Tafuri and Bruno Zevi. The publication of several studies about Mannerism in the forties and fifties rescued certain virtues of an historical style that had been undervalued due to its deviation from Renacentist canon. Rowe, Tafuri and Zevi, among others, pointed out the similarities between Mannerism and certain qualities of modern architecture, both devoted to break previous dogmas. The recovery of Mannerism allowed joining ambiguity and modernity for first time in the same sentence. In postmodernism, on the other hand, ambiguity is present ex-professo, developing a prominent role in the theoretical discourse of this period. The distance between its analytical identification and its operational use quickly disappeared because of structuralism, an analytical methodology with the aspiration of becoming a modus operandi. Under its influence, architecture began to be identified and studied as a language. Thus, postmodern theoretical project discerned between the components of architectural language and developed them separately. Consequently, there is not only one, but three projects related to postmodern contradiction: semantic project, syntactic project and pragmatic project. Leading these projects are those prominent architects whose work manifested an especial interest in exploring and developing the potential of the use of contradiction in architecture. Thus, Robert Venturi, Peter Eisenman and Rem Koolhaas were who established the main features through which architecture developed the dialectics of ambiguity, in its last and extreme level, as a theoretical project in each component of architectural language. Robert Venturi developed a new interpretation of architecture based on its semantic component, Peter Eisenman did the same with its syntactic component, and also did Rem Koolhaas with its pragmatic component. With this approach this research aims to establish a new reflection on the architectural transformation from modernity to postmodernity. Also, it can serve to light certain aspects still unaware that have shaped the architectural heritage of past decades, consequence of a fruitful relationship between architecture and ambiguity and its provocative consummation in a contradictio in terminis. Esta investigación centra su atención fundamentalmente sobre las repercusiones de la incorporación de la ambigüedad en forma de contradicción en el discurso arquitectónico postmoderno, a través de cada uno de sus tres proyectos teóricos. Está estructurada, por tanto, en torno a un capítulo principal titulado Dialéctica de la ambigüedad como proyecto teórico postmoderno, que se desglosa en tres, de títulos: Proyecto semántico. Robert Venturi; Proyecto sintáctico. Peter Eisenman; y Proyecto pragmático. Rem Koolhaas. El capítulo central se complementa con otros dos situados al inicio. El primero, titulado Dialéctica de la ambigüedad contemporánea. Una aproximación realiza un análisis cronológico de la evolución que ha experimentado la idea de la ambigüedad en la teoría estética del siglo XX, sin entrar aún en cuestiones arquitectónicas. El segundo, titulado Dialéctica de la ambigüedad como crítica del proyecto moderno se ocupa de examinar la paulatina incorporación de la ambigüedad en la revisión crítica de la modernidad, que sería de vital importancia para posibilitar su posterior introducción operativa en la postmodernidad. Un último capítulo, situado al final del texto, propone una serie de Proyecciones que, a tenor de lo analizado en los capítulos anteriores, tratan de establecer una relectura del contexto arquitectónico actual y su evolución posible, considerando, en todo momento, que la reflexión en torno a la ambigüedad todavía hoy permite vislumbrar nuevos horizontes discursivos. Cada doble página de la Tesis sintetiza la estructura tripartita del capítulo central y, a grandes rasgos, la principal herramienta metodológica utilizada en la investigación. De este modo, la triple vertiente semántica, sintáctica y pragmática con que se ha identificado al proyecto teórico postmoderno se reproduce aquí en una distribución específica de imágenes, notas a pie de página y cuerpo principal del texto. En la columna de la izquierda están colocadas las imágenes que acompañan al texto principal. Su distribución atiende a criterios estéticos y compositivos, cualificando, en la medida de lo posible, su condición semántica. A continuación, a su derecha, están colocadas las notas a pie de página. Su disposición es en columna y cada nota está colocada a la misma altura que su correspondiente llamada en el texto principal. Su distribución reglada, su valor como notación y su posible equiparación con una estructura profunda aluden a su condición sintáctica. Finalmente, el cuerpo principal del texto ocupa por completo la mitad derecha de cada doble página. Concebido como un relato continuo, sin apenas interrupciones, su papel como responsable de satisfacer las demandas discursivas que plantea una investigación doctoral está en correspondencia con su condición pragmática.

Modelling seed germination in forest tree species through survival analysis. The Pinus pinea L. case study

The direct application of existing models for seed germination may often be inadequate in the context of ecology and forestry germination experiments. This is because basic model assumptions are violated and variables available to forest managers are rarely used. In this paper, we present a method which addresses the aforementioned shortcomings. The approach is illustrated through a case study of Pinus pinea L. Our findings will also shed light on the role of germination in the general failure of natural regeneration in managed forests of this species. The presented technique consists of a mixed regression model based on survival analysis. Climate and stand covariates were tested. Data for fitting the model were gathered from a 5-year germination experiment in a mature, managed P. pinea stand in the Northern Plateau of Spain in which two different stand densities can be found. The model predictions proved to be unbiased and highly accurate when compared with the training data. Germination in P. pinea was controlled through thermal variables at stand level. At microsite level, low densities negatively affected the probability of germination. A time-lag in the response was also detected. Overall, the proposed technique provides a reliable alternative to germination modelling in ecology/forestry studies by using accessible/ suitable variables. The P. pinea case study highlights the importance of producing unbiased predictions. In this species, the occurrence and timing of germination suggest a very different regeneration strategy from that understood by forest managers until now, which may explain the high failure rate of natural regeneration in managed stands. In addition, these findings provide valuable information for the management of P. pinea under climate-change conditions.

Order 10 4 speedup in global linear instability analysis using matrix formation

A unified solution framework is presented for one-, two- or three-dimensional complex non-symmetric eigenvalue problems, respectively governing linear modal instability of incompressible fluid flows in rectangular domains having two, one or no homogeneous spatial directions. The solution algorithm is based on subspace iteration in which the spatial discretization matrix is formed, stored and inverted serially. Results delivered by spectral collocation based on the Chebyshev-Gauss-Lobatto (CGL) points and a suite of high-order finite-difference methods comprising the previously employed for this type of work Dispersion-Relation-Preserving (DRP) and Padé finite-difference schemes, as well as the Summationby- parts (SBP) and the new high-order finite-difference scheme of order q (FD-q) have been compared from the point of view of accuracy and efficiency in standard validation cases of temporal local and BiGlobal linear instability. The FD-q method has been found to significantly outperform all other finite difference schemes in solving classic linear local, BiGlobal, and TriGlobal eigenvalue problems, as regards both memory and CPU time requirements. Results shown in the present study disprove the paradigm that spectral methods are superior to finite difference methods in terms of computational cost, at equal accuracy, FD-q spatial discretization delivering a speedup of ð (10 4). Consequently, accurate solutions of the three-dimensional (TriGlobal) eigenvalue problems may be solved on typical desktop computers with modest computational effort.

A method for revealing phase space structures of general time dependent dynamical systems

In this paper we develop new techniques for revealing geometrical structures in phase space that are valid for aperiodically time dependent dynamical systems, which we refer to as Lagrangian descriptors. These quantities are based on the integration, for a finite time, along trajectories of an intrinsic bounded, positive geometrical and/or physical property of the trajectory itself. We discuss a general methodology for constructing Lagrangian descriptors, and we discuss a “heuristic argument” that explains why this method is successful for revealing geometrical structures in the phase space of a dynamical system. We support this argument by explicit calculations on a benchmark problem having a hyperbolic fixed point with stable and unstable manifolds that are known analytically. Several other benchmark examples are considered that allow us the assess the performance of Lagrangian descriptors in revealing invariant tori and regions of shear. Throughout the paper “side-by-side” comparisons of the performance of Lagrangian descriptors with both finite time Lyapunov exponents (FTLEs) and finite time averages of certain components of the vector field (“time averages”) are carried out and discussed. In all cases Lagrangian descriptors are shown to be both more accurate and computationally efficient than these methods. We also perform computations for an explicitly three dimensional, aperiodically time-dependent vector field and an aperiodically time dependent vector field defined as a data set. Comparisons with FTLEs and time averages for these examples are also carried out, with similar conclusions as for the benchmark examples.

Phase transitions in number theory: from the birthday problem to Sidon sets

In this work, we show how number theoretical problems can be fruitfully approached with the tools of statistical physics. We focus on g-Sidon sets, which describe sequences of integers whose pairwise sums are different, and propose a random decision problem which addresses the probability of a random set of k integers to be g-Sidon. First, we provide numerical evidence showing that there is a crossover between satisfiable and unsatisfiable phases which converts to an abrupt phase transition in a properly defined thermodynamic limit. Initially assuming independence, we then develop a mean-field theory for the g-Sidon decision problem. We further improve the mean-field theory, which is only qualitatively correct, by incorporating deviations from independence, yielding results in good quantitative agreement with the numerics for both finite systems and in the thermodynamic limit. Connections between the generalized birthday problem in probability theory, the number theory of Sidon sets and the properties of q-Potts models in condensed matter physics are briefly discussed