High available GNU/Linux systems

High availability goals and ways to reach them, from a GNU/Linux point of view.

Evaluation of performance analysis software for Linux computing cluster

Tietokonejärjestelmän osien ja ohjelmistojen suorituskykymittauksista saadaan tietoa,jota voidaan käyttää suorituskyvyn parantamiseen ja laitteistohankintojen päätöksen tukena. Tässä työssä tutustutaan suorituskyvyn mittaamiseen ja mittausohjelmiin eli ns. benchmark-ohjelmistoihin. Työssä etsittiin ja arvioitiin eri tyyppisiä vapaasti saatavilla olevia benchmark-ohjelmia, jotka soveltuvat Linux-laskentaklusterin suorituskyvynanalysointiin. Benchmarkit ryhmiteltiin ja arvioitiin testaamalla niiden ominaisuuksia Linux-klusterissa. Työssä käsitellään myös mittausten tekemisen ja rinnakkaislaskennan haasteita. Benchmarkkeja löytyi moneen tarkoitukseen ja ne osoittautuivat laadultaan ja laajuudeltaan vaihteleviksi. Niitä on myös koottu ohjelmistopaketeiksi, jotta laitteiston suorituskyvystä saisi laajemman kuvan kuin mitä yhdellä ohjelmalla on mahdollista saada. Olennaista on ymmärtää nopeus, jolla dataa saadaan siirretyä prosessorille keskusmuistista, levyjärjestelmistä ja toisista laskentasolmuista. Tyypillinen benchmark-ohjelma sisältää paljon laskentaa tarvitsevan matemaattisen algoritmin, jota käytetään tieteellisissä ohjelmistoissa. Benchmarkista riippuen tulosten ymmärtäminen ja hyödyntäminen voi olla haasteellista.

Käyttöliittymä verkonhallintaan sulautetussa Linux-käyttöjärjestelmässä

During the project we get familiar with Linksys WRT54GL wireless router and its network managing methods. Operating system is OpenWRT which is Linux-based distribution for embedded devices. OpenWRT uses two kind of approach for its network administration. The first one is web-based user interface and the second one is command line based. Both methods are working but do not solve all problems that competent network administrator can need for secured network managing. The goal of the project was design an NCurses-based user interface for network administration that can be run from command line. The user interface can be use for example from terminal via SSH which is yet faster and also light to use. The idea is to combine the user friendly of WWW-interface and the advanced options that command line based network managing can offer. Linux-based open source OpenWRT offers good development tools. There exist also a compact development community if there is need for further development of software in future. So far user interface for command line based network administrator is not available.

Multilayer switch hardware support for Linux

VDSL on teknologia, joka mahdollistaa nopeat Internet-yhteydet tavallista puhelinlinjaa käyttäen. Tätä varten käyttäjä tarvitsee VDSL-modeemin ja Internet-operaattori reitittimen, johon VDSL-linjat kytketään. Reitittimen on oltava suorituskykyinen, jotta kaikki VDSL-liikenne voidaan reittittää eteenpäin. Tehokkuutta haetaan tekemällä suuri osa reitityksestä erityisillä reititinpiireillä. Tässä diplomityössä käsitellään reititinpiirien teoriaa ja niiden hallintaa. Lisäksi vertailtiin kolmen suuren valmistajan tuotteita. Tuotteiden tarjoamat ominaisuudet vaikuttivat hyvin yhteneväisiltä. Ominaisuuksien hallinta ja toteutus olivat erilaisia. Työn tavoitteena oli löytää ohjelmistoarkkitehtuuri piirien ohjaamiseen niin, että Linux-käyttöjärjestelmän ytimen palveluja voitaisiin käyttää mahdollisimman hyödyllisesti. Työssä havaittiin, että ohjelmistoarkkitehtuurin voi määritellä monella eri tavalla riippuen siitä, miten piiri on kytketty prosessoriin, mitä piirin ominaisuuksia halutaan käyttää ja miten arkkitehtuuria halutaan jatkossa laajentaa.

Maladie des griffes du chat et autres bartonelloses [Cat scratch disease and other human infections caused by Bartonella species].

The different Bartonella species can cause various human infections such as cat scratch disease, chronic bacteremia (homeless patient with nonspecific symptom), endocarditis, bacillary angiomatosis, peliosis, and Carrion's disease. Diagnostic approaches include serology, culture and molecular approaches. PCR is especially useful on lymph nodes biopsies from patients with cat-scratch disease and on valvular samples taken from culture-negative endocarditis. Serology exhibits a very high sensitivity in the latter situation. The treatment should be chosen according to the clinical presentation.

XSOFT: estudo de reconhecimento, exploração e prevenção de vulnerabilidades de software através de uma distribuição LINUX

This work aims to give greater visibility to the issue of software security, due to people talk a lot in security conferences, that much of both IT (Information Technology) staff and, more specifically, IS (Information Security) staff does not know this, and, thanks to the spread of the mobile computing and of the cloud computing, this lack of deeper knowledge on this subject is increasingly becoming worrisome. It aims too, make applications to be developed in a security manner, priorizing the security of the information processed. It attempts to demonstrate the secure coding techniques, the principles of software security, the means to identify software vulnerabilities, the cutting-edge software exploitation techniques and the mechanisms of mitigation. Nowadays, the security guys are in charge of the most of the security tests in applications, audits and pentests, and it is undeniable that the so-called security experts, most often come from computer network field, having few experience in software development and programming. Therefore, the development process does not consider the security issue, thanks to the lack of knowledge on the subject by the developer, and the security tests could be improved whether security experts had a greater know-how on application development. Given this problem, the goal here is to integrate information security with software development, spreading out the process of secure software development. To achieve this, a Linux distribution with proof of concept applicati... (Complete abstract click electronic access below)

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Governance of Massive Multiauthor Collaboration – Linux, Wikipedia, and Other Networks: Governed by Bilateral Contracts, Partnerships, or Something in Between?

Open collaborative projects are moving to the foreground of knowledge production. Some online user communities develop into longterm projects that generate a highly valuable and at the same time freely accessible output. Traditional copyright law that is organized around the idea of a single creative entity is not well equipped to accommodate the needs of these forms of collaboration. In order to enable a peculiar network-type of interaction participants instead draw on public licensing models that determine the freedoms to use individual contributions. With the help of these access rules the operational logic of the project can be implemented successfully. However, as the case of the Wikipedia GFDL-CC license transition demonstrates, the adaptation of access rules in networks to new circumstances raises collective action problems and suffers from pitfalls caused by the fact that public licensing is grounded in individual copyright. Legal governance of open collaboration projects is a largely unexplored field. The article argues that the license steward of a public license assumes the position of a fiduciary of the knowledge commons generated under the license regime. Ultimately, the governance of decentralized networks translates into a composite of organizational and contractual elements. It is concluded that the production of global knowledge commons relies on rules of transnational private law.

Accelerated wound closure in vitro by fibroblasts from a subgroup of cleft lip/palate patients: role of transforming growth factor-α.

In a fraction of patients surgically treated for cleft lip/palate, excessive scarring disturbs maxillary growth and dento-alveolar development. Since certain genes are involved in craniofacial morphogenesis as well as tissue repair, a primary defect causing cleft lip/palate could lead to altered wound healing. We performed in vitro wound healing assays with primary lip fibroblasts from 16 cleft lip/palate patients. Nine foreskin fibroblast strains were included for comparison. Cells were grown to confluency and scratch wounds were applied; wound closure was monitored morphometrically over time. Wound closure rate showed highly significant differences between fibroblast strains. Statistically, fibroblast strains from the 25 individuals could be divided into three migratory groups, namely "fast", "intermediate", and "slow". Most cleft lip/palate fibroblasts were distributed between the "fast" (5 strains) and the "intermediate" group (10 strains). These phenotypes were stable over different cell passages from the same individual. Expression of genes involved in cleft lip/palate and wound repair was determined by quantitative PCR. Transforming growth factor-α mRNA was significantly up-regulated in the "fast" group. 5 ng/ml transforming growth factor-α added to the culture medium increased the wound closure rate of cleft lip/palate strains from the "intermediate" migratory group to the level of the "fast", but had no effect on the latter group. Conversely, antibody to transforming growth factor-α or a specific inhibitor of its receptor most effectively reduced the wound closure rate of "fast" cleft lip/palate strains. Thus, fibroblasts from a distinct subgroup of cleft lip/palate patients exhibit an increased migration rate into wounds in vitro, which is linked to higher transforming growth factor-α expression and attenuated by interfering with its signaling.

Multibeam Converter - a tool to create Ocean Data View import files from multibeam files

The software Multibeam Converter is a tool to convert files or folders of files (ascii/tab-separated data files with or without metaheader), downloaded from PANGAEA via the search engine or the data warehouse to the ODV import format, e.g. for visualization or further processing. MultibeamConverter is distributed as freeware for the operating systems Microsoft Windows, Apple OS X and Linux.

LatLong Converter - converts positions from geodetic system to Gauss-Krüger or UTM coordinates

LatLongConverter converts positions from geodetic system to Gauss-Krüger or UTM coordinates. This program is distributed as freeware for the operating systems Microsoft Windows, Apple OS X and Linux.

Aplicación de representación gráfica de datos y/o señales en entorno GNU/LINUX

El contenido de este PFC supone el desarrollo de una aplicación gráfica en el entorno GNU/LINUX. La aplicación debe representar en la pantalla gráficos procedentes de una fuente externa (un fichero, una tarjeta de adquisición de datos, otra aplicación, etc.) Debe permitir las siguientes funcionalidades: Representar la señal uniendo puntos o marcándolos como símbolos. Debe gestionar de forma adecuada el zoom. Debe permitir exportar la gráfica a formatos SVG y PDF. Debe permitir mostrar varias señales superpuestas para poder compararlas. Opcionalmente debe permitir arrastrar y soltar (“drag and drop”). ABSTRACT The content of the thesis is the development of a graphical application in GNU / Linux environment. The application must render graphics on the screen from an external source (a file, a data acquisition card, other applications, etc..) It must allow the following functionality: Joining dots represent the signal or marking them as symbols. Must properly manage the zoom. Allow export the graph to SVG and PDF formats. Allow display multiple signals superimposed for comparison. Optionally should allow drag and drop.

Desarrollo de aplicaciones basadas en Linux Embedded en una arquitectura basada en Cyclone V SoC (System on Chip) de Altera

We attempt to integrate and start up the set of necessary tools to deploy the design cycle of embedded systems based on Embedded Linux on a "Cyclone V SoC" made by Altera. First, we will analyze the available tools for designing the hardware system of the SoCkit development kit, made by Arrow, which has a "Cyclone V SoC" system (based on a "ARM Cortex-A9 MP Core" architecture). When designing the SoCkit board hardware, we will create a new peripheral to integrate it into the hardware system, so it can be used as any other existent resource of the SoCkit board previously configured. Next, we will analyze the tools to generate an Embedded Linux distribution adapted to the SoCkit board. In order to generate the Linux distribution we will use, on the one hand, a software package from Yocto recommended by Altera; on the other hand, the programs and tools of Altera, Embedded Development Suite. We will integrate all the components needed to build the Embedded Linux distribution, creating a complete and functional system which can be used for developing software applications. Finally, we will study the programs for developing and debugging applications in C or C++ language that will be executed in this hardware platform, then we will program a Linux application as an example to illustrate the use of SoCkit board resources. RESUMEN Se pretende integrar y poner en funcionamiento el conjunto de herramientas necesarias para desplegar el ciclo de diseño de sistemas embebidos basados en "Embedded Linux" sobre una "Cyclone V SoC" de Altera. En primer lugar, se analizarán las diversas herramientas disponibles para diseñar el sistema hardware de la tarjeta de desarrollo SoCkit, fabricada por Arrow, que dispone de un sistema "Cyclone V SoC" (basado en una arquitectura "ARM Cortex A9 MP Core"). En el diseño hardware de la SoCkit se creará un periférico propio y se integrará en el sistema, pudiendo ser utilizado como cualquier otro recurso de la tarjeta ya existente y configurado. A continuación, también se analizarán las herramientas para generar una distribución de "Embedded Linux" adaptado a la placa SoCkit. Para generar la distribución de Linux se utilizará, por una parte, un paquete software de Yocto recomendado por Altera y, por otra parte, las propias herramientas y programas de Altera. Se integrarán todos los componentes necesarios para construir la distribución Linux, creando un sistema completo y funcional que se pueda utilizar para el desarrollo de aplicaciones software. Por último, se estudiarán las herramientas para el diseño y depuración de aplicaciones en lenguaje C ó C++ que se ejecutarán en esta plataforma hardware. Se pretende desarrollar una aplicación de ejemplo para ilustrar el uso de los recursos más utilizados de la SoCkit.

Embedded Linux integration using Linuxlink tool and peripheral driver development for Zedboard

This project is divided into two main parts: The first part shows the integration of an Embedded Linux operating system on a development hardware platform named Zedboard. This platform contains a Zynq-7000 System on Chip (Soc) which is composed by two dual core ARM Cortex-A9 processors and a FPGA Artix-7. The Embedded Linux is built with Linuxlink, a Timesys tool. Meanwhile, the platform hardware configuration is done with Xilinx Vivado. The system is loaded with an SD card which requires to have every files needed for the booting process and for the operation. Some of these files are generated with Xilinx SDK software. The second part starts up from the system already built to integrate a peripheral in the Zynq-7000 FPGA. Also the drivers for controlling the peripheral from the operating system are developed. Finally, a user space program is created to test both of them. RESUMEN. Este proyecto consta de dos partes: La primera muestra la integración de un sistema operativo Linux embebido en una plataforma de desarrollo hardware llamada Zedboard. Esta plataforma utiliza un System on Chip (SoC) Zynq-7000 que está formado por dos procesadores ARM Cortex-A9 de doble núcleo y una FPGA Artix-7. El Linux embebido se construye utilizando la herramienta Linuxlink de Timesys, mientras que el hardware de la plataforma de desarrollo se configura con Vivado de Xilinx. El sistema se carga en una tarjeta SD que debe tener todos los archivos necesarios para completar el arranque y hacer funcionar el sistema. Algunos de esos archivos se generan con la herramienta SDK de Xilinx. En la segunda parte se utiliza el sistema construido para integrar un periférico en la FPGA del Zynq-7000, haciendo uso de Vivado, y se desarrollan los drivers necesarios para utilizarlo mediante el sistema operativo. Para probar esta última parte se desarrolla un programa de espacio de usuario.

Study of OLSR protocol with Network Simulator 2 over Linux

Until a few years ago, most of the network communications were based in the wire as the physical media, but due to the advances and the maturity of the wireless communications, this is changing. Nowadays wireless communications offers fast, secure, efficient and reliable connections. Mobile communications are in expansion, clearly driven by the use of smart phones and other mobile devices, the use of laptops, etc… Besides that point, the inversion in the installation and maintenance of the physical medium is much lower than in wired communications, not only because the air has no cost, but because the installation and maintenance of the wire require a high economic cost. Besides the economic cost we find that wire is a more vulnerable medium to external threats such as noise, sabotages, etc… There are two different types of wireless networks: those which the structure is part of the network itself and those which have a lack of structure or any centralization, in a way that the devices that form part of the network can connect themselves in a dynamic and random way, handling also the routing of every control and information messages, this kind of networks is known as Ad-hoc. In the present work we will proceed to study one of the multiple wireless protocols that allows mobile communications, it is Optimized Link State Routing, from now on, OLSR, it is an pro-active routing, standard mechanism that works in a distributed in order to stablish the connections among the different nodes that belong to a wireless network. Thanks to this protocol it is possible to get all the routing tables in all the devices correctly updated every moment through the periodical transmission of control messages and on this way allow a complete connectivity among the devices that are part of the network and also, allow access to other external networks such as virtual private networks o Internet. This protocol could be perfectly used in environments such as airports, malls, etc… The update of the routing tables in all the devices is got thanks to the periodical transmission of control messages and finally it will offer connectivity among all the devices and the corresponding external networks. For the study of OLSR protocol we will have the help of the network simulator “Network Simulator 2”, a freeware network simulator programmed in C++ based in discrete events. This simulator is used mainly in educational and research environments and allows a very extensive range of protocols, both, wired networks protocols and wireless network protocols, what is going to be really useful to proceed to the simulation of different configurations of networks and protocols. In the present work we will also study different simulations with Network Simulator 2, in different scenarios with different configurations, wired networks, and Ad-hoc networks, where we will study OLSR Protocol. RESUMEN. Hasta hace pocos años, la mayoría de las comunicaciones de red estaban basadas en el cable como medio físico pero debido al avance y madurez alcanzados en el campo de las comunicaciones inalámbricas esto está cambiando. Hoy día las comunicaciones inalámbricas nos ofrecen conexiones veloces, seguras, eficientes y fiables. Las comunicaciones móviles se encuentran en su momento de máxima expansión, claramente impulsadas por el uso de teléfonos y demás dispositivos móviles, el uso de portátiles, etc… Además la inversión a realizar en la instalación y el mantenimiento del medio físico en las comunicaciones móviles es muchísimo menor que en comunicaciones por cable, ya no sólo porque el aire no tenga coste alguno, sino porque la instalación y mantenimiento del cable precisan de un elevado coste económico por norma. Además del coste económico nos encontramos con que es un medio más vulnerable a amenazas externas tales como el ruido, escuchas no autorizadas, sabotajes, etc… Existen dos tipos de redes inalámbricas: las constituidas por una infraestructura que forma parte más o menos de la misma y las que carecen de estructura o centralización alguna, de modo que los dispositivos que forman parte de ella pueden conectarse de manera dinámica y arbitraria entre ellos, encargándose además del encaminamiento de todos los mensajes de control e información, a este tipo de redes se las conoce como redes Ad-hoc. En el presente Proyecto de Fin de Carrera se procederá al estudio de uno de los múltiples protocolos inalámbricos que permiten comunicaciones móviles, se trata del protocolo inalámbrico Optimized Link State Routing, de ahora en adelante OLSR, un mecanismo estándar de enrutamiento pro-activo, que trabaja de manera distribuida para establecer las conexiones entre los nodos que formen parte de las redes inalámbricas Ad-hoc, las cuales carecen de un nodo central y de una infraestructura pre-existente. Gracias a este protocolo es posible conseguir que todos los equipos mantengan en todo momento las tablas de ruta actualizadas correctamente mediante la transmisión periódica de mensajes de control y así permitir una completa conectividad entre todos los equipos que formen parte de la red y, a su vez, también permitir el acceso a otras redes externas tales como redes privadas virtuales o Internet. Este protocolo sería usado en entornos tales como aeropuertos La actualización de las tablas de enrutamiento de todos los equipos se conseguirá mediante la transmisión periódica de mensajes de control y así finalmente se podrá permitir conectividad entre todos los equipos y con las correspondientes redes externas. Para el estudio del protocolo OLSR contaremos con el simulador de redes Network Simulator 2, un simulador de redes freeware programado en C++ basado en eventos discretos. Este simulador es usado principalmente en ambientes educativos y de investigación y permite la simulación tanto de protocolos unicast como multicast. El campo donde más se utiliza es precisamente en el de la investigación de redes móviles Ad-hoc. El simulador Network Simulator 2 no sólo implementa el protocolo OLSR, sino que éste implementa una amplia gama de protocolos, tanto de redes cableadas como de redes inalámbricas, lo cual va a sernos de gran utilidad para proceder a la simulación de distintas configuraciones de redes y protocolos. En el presente Proyecto de Fin de Carrera se estudiarán también diversas simulaciones con el simulador NS2 en diferentes escenarios con diversas configuraciones; redes cableadas, redes inalámbricas Ad-hoc, donde se estudiará el protocolo antes mencionado: OLSR. Este Proyecto de Fin de Carrera consta de cuatro apartados distintos: Primeramente se realizará el estudio completo del protocolo OLSR, se verán los beneficios y contrapartidas que ofrece este protocolo inalámbrico. También se verán los distintos tipos de mensajes existentes en este protocolo y unos pequeños ejemplos del funcionamiento del protocolo OLSR. Seguidamente se hará una pequeña introducción al simulador de redes Network Simulator 2, veremos la historia de este simulador, y también se hará referencia a la herramienta extra NAM, la cual nos permitirá visualizar el intercambio de paquetes que se produce entre los diferentes dispositivos de nuestras simulaciones de forma intuitiva y amigable. Se hará mención a la plataforma MASIMUM, encargada de facilitar en un entorno académico software y documentación a sus alumnos con el fin de facilitarles la investigación y la simulación de redes y sensores Ad-hoc. Finalmente se verán dos ejemplos, uno en el que se realizará una simulación entre dos PCs en un entorno Ethernet y otro ejemplo en el que se realizará una simulación inalámbrica entre cinco dispositivos móviles mediante el protocolo a estudiar, OLSR.