Development of Embedded Linux Applications Using ZedBoard

The purpose of this document is to create a modest integration guide for embedding a Linux Operating System on ZedBoard development platform, based on Xilinx’s Zynq-7000 All Programmable System on Chip which contains a dual core ARM Cortex-A9 and a 7 Series FPGA Artix-7. The integration process has been structured in four chapters according to the logic generation of the different parts that compose the embedded system. With the intention of automating the generation process of a complete Linux distribution specific for ZedBoard platform, BuildRoot development platform it is used. Once the embedding process finished, it was decided to add to the system the required functionalities for adding support for IEEE1588 Standard for Precision Clock Synchronization Protocol for Networked Measurement and Control Systems, through a user space Linux program which implements the protocol. That PTP user space implementation program has been cross-compiled, executed on target and tested for evaluating the functionalities added. RESUMEN El propósito de este documento es crear una modesta guía de integración de un sistema operativo Linux para la plataforma de desarrollo ZedBoard, basada en un System on Chip del fabricante Xilinx llamado Zynq-7000. Este System on Chip está compuesto por un procesador de doble núcleo ARM Cortex-A9 y una FPGA de la Serie 7 equiparable a una Artix-7. El proceso de integración se ha estructurado en cuatro grandes capítulos que se rigen según el orden lógico de generación de las distintas partes por las que el sistema empotrado está compuesto. Con el ánimo de automatizar el proceso de creación de una distribución de Linux específica para la plataforma ZedBoard, se ha utilizado la plataforma de desarrollo BuildRoot. Una vez terminado el proceso de integración del sistema empotrado, se procedió a dar dotar al sistema de las funcionalidades necesarias para dar soporte al estándar de sincronización de relojes en redes de área local, PTP IEEE1588, a través de una implementación del mismo en un programa de lado de usuario el cual ha sido compilado, ejecutado y testeado para evaluar el correcto funcionamiento de las funcionalidades añadidas.

Synchronization waves in geometric networks

We report synchronization of networked excitable nodes embedded in a metric space, where the connectivity properties are mostly determined by the distance between units. Such a high clustered structure, combined with the lack of long-range connections, prevents full synchronization and yields instead the emergence of synchronization waves. We show that this regime is optimal for information transmission through the system, as it enhances the options of reconstructing the topology from the dynamics. Measurements of topological and functional centralities reveal that the wave-synchronization state allows detection of the most structurally relevant nodes from a single observation of the dynamics, without any a priori information on the model equations ruling the evolution of the ensemble

Reduced synchronization persistence in neural networks derived from atm-deficient mice

Many neurodegenerative diseases are characterized by malfunction of the DNA damage response. Therefore, it is important to understand the connection between system level neural network behavior and DNA. Neural networks drawn from genetically engineered animals, interfaced with micro-electrode arrays allowed us to unveil connections between networks’ system level activity properties and such genome instability. We discovered that Atm protein deficiency, which in humans leads to progressive motor impairment, leads to a reduced synchronization persistence compared to wild type synchronization, after chemically imposed DNA damage. Not only do these results suggest a role for DNA stability in neural network activity, they also establish an experimental paradigm for empirically determining the role a gene plays on the behavior of a neural network.

Assortative and modular networks are shaped by adaptive synchronization processes

Modular organization and degree-degree correlations are ubiquitous in the connectivity structure of biological, technological, and social interacting systems. So far most studies have concentrated on unveiling both features in real world networks, but a model that succeeds in generating them simultaneously is needed. We consider a network of interacting phase oscillators, and an adaptation mechanism for the coupling that promotes the connection strengths between those elements that are dynamically correlated. We show that, under these circumstances, the dynamical organization of the oscillators shapes the topology of the graph in such a way that modularity and assortativity features emerge spontaneously and simultaneously. In turn, we prove that such an emergent structure is associated with an asymptotic arrangement of the collective dynamical state of the network into cluster synchronization.

Low-complexity timing synchronization scheme for MB-OFDM UWB receiver based on sign-bit

A unified low complexity sign-bit correlation based symbol timing synchronization scheme for Multiband Orthogonal Frequency Division Multiplexing (MB-OFDM) Ultra Wideband (UWB) receiver system is proposed. By using the time domain sequence of the packet/frame synchronization preamble, the proposed scheme is in charge of detecting the upcoming MB-OFDM symbol and it estimates the exact boundary of the start of Fast Fourier Transform (FFT) window. The proposed algorithm is implemented by using an efficient Hardware-Software co-simulation methodology. The effectiveness of the proposed synchronization scheme and the optimization criteria is confirmed by hardware implementation results.

Digital chaos synchronization in optical networks

A new method to obtain digital chaos synchronization between two systems is reported. It is based on the use of Optically Programmable Logic Cells as chaos generators. When these cells are feedbacked, periodic and chaotic behaviours are obtained. They depend on the ratio between internal and external delay times. Chaos synchronization is obtained if a common driving signal feeds both systems. A control to impose the same boundary conditions to both systems is added to the emitter. New techniques to analyse digital chaos are presented. The main application of these structures is to obtain secure communications in optical networks.

Chaos synchronization in optically programmable logic cells

A possible approach to the synchronization of chaotic circuits is reported. It is based on an Optically Programmable Logic Cell and the signals are fully digital. A method to study the characteristics of the obtained chaos is reported as well as a new technique to compare the obtained chaos from an emitter and a receiver. This technique allows the synchronization of chaotic signals. The signals received at the receiver, composed by the addition of information and chaotic signals, are compared with the chaos generated there and a pure information signal can be detected. Its application to cryptography in Optical Communications comes directly from these properties. The model here presented is based on a computer simulation.

Wireless measurement system for structural health monitoring with high time synchronization accuracy

Structural health monitoring (SHM) systems have excellent potential to improve the regular operation and maintenance of structures. Wireless networks (WNs) have been used to avoid the high cost of traditional generic wired systems. The most important limitation of SHM wireless systems is time-synchronization accuracy, scalability, and reliability. A complete wireless system for structural identification under environmental load is designed, implemented, deployed, and tested on three different real bridges. Our contribution ranges from the hardware to the graphical front end. System goal is to avoid the main limitations of WNs for SHM particularly in regard to reliability, scalability, and synchronization. We reduce spatial jitter to 125 ns, far below the 120 μs required for high-precision acquisition systems and much better than the 10-μs current solutions, without adding complexity. The system is scalable to a large number of nodes to allow for dense sensor coverage of real-world structures, only limited by a compromise between measurement length and mandatory time to obtain the final result. The system addresses a myriad of problems encountered in a real deployment under difficult conditions, rather than a simulation or laboratory test bed.

Optically programmable logic cells as basic units for transmission and synchronization of chaotic signals

We proposed an optical communications system, based on a digital chaotic signal where the synchronization of chaos was the main objective, in some previous papers. In this paper we will extend this work. A way to add the digital data signal to be transmitted onto the chaotic signal and its correct reception, is the main objective. We report some methods to study the main characteristics of the resulting signal. The main problem with any real system is the presence of some retard between the times than the signal is generated at the emitter at the time when this signal is received. Any system using chaotic signals as a method to encrypt need to have the same characteristics in emitter and receiver. It is because that, this control of time is needed. A method to control, in real time the chaotic signals, is reported.

Uncovering cold disruption of the circadian clock in poplar

Dormancy is an adaptive mechanism that allows woody plants to survive at low temperatures during the winter. Disruption of circadian clock genes in winter or under low temperatures, both in long days as in short days, were described in our group few years ago (Ramos et al., 2005). Basic mechanisms of the circadian clock function are similar in herbaceous as well as in woody plants although there are differences in their response to low temperatures (Bieniawska et al., 2008). Woody plants growing in daylight conditions should have a specific transcriptional control above the circadian clock genes, which is responsible of their constitutive transcriptional activation observed under low temperatures conditions. In order to understand this regulatory process, we are analyzing the behavior of a circadian clock gene in poplar. To this aim, we have isolated its promoter region and fused to the luciferase reporter gene. This construct has been transformed into Populus tremula x P. alba 717-1B4 INRA clone. Here we present the characterization of these transgenic lines under different conditions of light and temperature.

Generalized synchronization in relay systems with instantaneous coupling

We demonstrate the existence of generalized synchronization in systems that act as mediators between two dynamical units that, in turn, show complete synchronization with each other. These are the so-called relay systems. Specifically, we analyze the Lyapunov spectrum of the full system to elucidate when complete and generalized synchronization appear. We show that once a critical coupling strength is achieved, complete synchronization emerges between the systems to be synchronized, and at the same point, generalized synchronization with the relay system also arises. Next, we use two nonlinear measures based on the distance between phase-space neighbors to quantify the generalized synchronization in discretized time series. Finally, we experimentally show the robustness of the phenomenon and of the theoretical tools here proposed to characterize it.

Temporal task allocation in periodic environments. An approach based on synchronization

In this paper, we study a robot swarm that has to perform task allocation in an environment that features periodic properties. In this environment, tasks appear in different areas following periodic temporal patterns. The swarm has to reallocate its workforce periodically, performing a temporal task allocation that must be synchronized with the environment to be effective. We tackle temporal task allocation using methods and concepts that we borrow from the signal processing literature. In particular, we propose a distributed temporal task allocation algorithm that synchronizes robots of the swarm with the environment and with each other. In this algorithm, robots use only local information and a simple visual communication protocol based on light blinking. Our results show that a robot swarm that uses the proposed temporal task allocation algorithm performs considerably more tasks than a swarm that uses a greedy algorithm.

Modelización e integración de sistemas de adquisición de datos inteligentes en sistemas de instrumentación para dispositivos de fusión

La obtención de energía a partir de la fusión nuclear por confinamiento magnético del plasma, es uno de los principales objetivos dentro de la comunidad científica dedicada a la energía nuclear. Desde la construcción del primer dispositivo de fusión, hasta la actualidad, se han llevado a cabo multitud de experimentos, que hoy en día, gran parte de ellos dan soporte al proyecto International Thermonuclear Experimental Reactor (ITER). El principal problema al que se enfrenta ITER, se basa en la monitorización y el control del plasma. Gracias a las nuevas tecnologías, los sistemas de instrumentación y control permiten acercarse más a la solución del problema, pero a su vez, es más complicado estandarizar los sistemas de adquisición de datos que se usan, no solo en ITER, sino en otros proyectos de igual complejidad. Desarrollar nuevas implementaciones hardware y software bajo los requisitos de los diagnósticos definidos por los científicos, supone una gran inversión de tiempo, retrasando la ejecución de nuevos experimentos. Por ello, la solución que plantea esta tesis, consiste en la definición de una metodología de diseño que permite implementar sistemas de adquisición de datos inteligentes y su fácil integración en entornos de fusión para la implementación de diagnósticos. Esta metodología requiere del uso de los dispositivos Reconfigurable Input/Output (RIO) y Flexible RIO (FlexRIO), que son sistemas embebidos basados en tecnología Field-Programmable Gate Array (FPGA). Para completar la metodología de diseño, estos dispositivos van a ser soportados por un software basado en EPICS Device Support utilizando la tecnología EPICS software asynDriver. Esta metodología se ha evaluado implementando prototipos para los controladores rápidos de planta de ITER, tanto para casos prácticos de ámbito general como adquisición de datos e imágenes, como para casos concretos como el diagnóstico del fission chamber, implementando pre-procesado en tiempo real. Además de casos prácticos, esta metodología se ha utilizado para implementar casos reales, como el Ion Source Hydrogen Positive (ISHP), desarrollada por el European Spallation Source (ESS Bilbao) y la Universidad del País Vasco. Finalmente, atendiendo a las necesidades que los experimentos en los entornos de fusión requieren, se ha diseñado un mecanismo mediante el cual los sistemas de adquisición de datos, que pueden ser implementados mediante la metodología de diseño propuesta, pueden integrar un reloj hardware capaz de sincronizarse con el protocolo IEEE1588-V2, permitiendo a estos, obtener los TimeStamps de las muestras adquiridas con una exactitud y precisión de decenas de nanosegundos y realizar streaming de datos con TimeStamps. ABSTRACT Fusion energy reaching by means of nuclear fusion plasma confinement is one of the main goals inside nuclear energy scientific community. Since the first fusion device was built, many experiments have been carried out and now, most of them give support to the International Thermonuclear Experimental Reactor (ITER) project. The main difficulty that ITER has to overcome is the plasma monitoring and control. Due to new technologies, the instrumentation and control systems allow an approaching to the solution, but in turn, the standardization of the used data acquisition systems, not only in ITER but also in other similar projects, is more complex. To develop new hardware and software implementations under scientific diagnostics requirements, entail time costs, delaying new experiments execution. Thus, this thesis presents a solution that consists in a design methodology definition, that permits the implementation of intelligent data acquisition systems and their easy integration into fusion environments for diagnostic purposes. This methodology requires the use of Reconfigurable Input/Output (RIO) and Flexible RIO (FlexRIO) devices, based on Field-Programmable Gate Array (FPGA) embedded technology. In order to complete the design methodology, these devices are going to be supported by an EPICS Device Support software, using asynDriver technology. This methodology has been evaluated implementing ITER PXIe fast controllers prototypes, as well as data and image acquisition, so as for concrete solutions like the fission chamber diagnostic use case, using real time preprocessing. Besides of these prototypes solutions, this methodology has been applied for the implementation of real experiments like the Ion Source Hydrogen Positive (ISHP), developed by the European Spallation Source and the Basque country University. Finally, a hardware mechanism has been designed to integrate a hardware clock into RIO/FlexRIO devices, to get synchronization with the IEEE1588-V2 precision time protocol. This implementation permits to data acquisition systems implemented under the defined methodology, to timestamp all data acquired with nanoseconds accuracy, permitting high throughput timestamped data streaming.

Digital chaos synchronization in optical networks

A possible approach to the synchronization of chaotic circuits is reported. It is based on an Optically Programmable Logic Cell and as a consequence its output is digital, its application to cryptography in Optical Communications comes directly from its properties. The model here presented is based on a computer simulation.

Hardware timestamping for image acquisition system based on FlexRIO and IEEE 1588 v2 Standard

Current fusion devices consist of multiple diagnostics and hundreds or even thousands of signals. This situation forces on multiple occasions to use distributed data acquisition systems as the best approach. In this type of distributed systems, one of the most important issues is the synchronization between signals, so that it is possible to have a temporal correlation as accurate as possible between the acquired samples of all channels. In last decades, many fusion devices use different types of video cameras to provide inside views of the vessel during operations and to monitor plasma behavior. The synchronization between each video frame and the rest of the different signals acquired from any other diagnostics is essential in order to know correctly the plasma evolution, since it is possible to analyze jointly all the information having accurate knowledge of their temporal correlation. The developed system described in this paper allows timestamping image frames in a real-time acquisition and processing system using 1588 clock distribution. The system has been implemented using FPGA based devices together with a 1588 synchronized timing card (see Fig.1). The solution is based on a previous system [1] that allows image acquisition and real-time image processing based on PXIe technology. This architecture is fully compatible with the ITER Fast Controllers [2] and offers integration with EPICS to control and monitor the entire system. However, this set-up is not able to timestamp the frames acquired since the frame grabber module does not present any type of timing input (IRIG-B, GPS, PTP). To solve this lack, an IEEE1588 PXI timing device its used to provide an accurate way to synchronize distributed data acquisition systems using the Precision Time Protocol (PTP) IEEE 1588 2008 standard. This local timing device can be connected to a master clock device for global synchronization. The timing device has a buffer timestamp for each PXI trigger line and requires tha- a software application assigns each frame the corresponding timestamp. The previous action is critical and cannot be achieved if the frame rate is high. To solve this problem, it has been designed a solution that distributes the clock from the IEEE 1588 timing card to all FlexRIO devices [3]. This solution uses two PXI trigger lines that provide the capacity to assign timestamps to every frame acquired and register events by hardware in a deterministic way. The system provides a solution for timestamping frames to synchronize them with the rest of the different signals.