The Problem of Mutual Exclusion: A New Distributed Solution

In both centralized and distributed systems, processes cooperate and compete with each other to access the system resources. Some of these resources must be used exclusively. It is then required that only one process access the shared resource at a given time. This is referred to as the problem of mutual exclusion. Several synchronization mechanisms have been proposed to solve this problem. In this thesis, an effort has been made to compile most of the existing mutual exclusion solutions for both shared memory and message-passing based systems. A new distributed algorithm, which uses a dynamic information structure, is presented to solve the problem of mutual exclusion. It is proved to be free from both deadlock and starvation. This solution is shown to be economical in terms of the number of message exchanges required per critical section execution. Procedures for recovery from both site and link failures are also given

System support for object replication in distributed systems

Distributed systems are composed of a collection of cooperating but failure prone system components. The number of components in such systems is often large and, despite low probabilities of any particular component failing, the likelihood that there will be at least a small number of failures within the system at a given time is high. Therefore, distributed systems must be able to withstand partial failures. By being resilient to partial failures, a distributed system becomes more able to offer a dependable service and therefore more useful. Replication is a well known technique used to mask partial failures and increase reliability in distributed computer systems. However, replication management requires sophisticated distributed control algorithms, and is therefore a labour intensive and error prone task. Furthermore, replication is in most cases employed due to applications' non-functional requirements for reliability, as dependability is generally an orthogonal issue to the problem domain of the application. If system level support for replication is provided, the application developer can devote more effort to application specific issues. Distributed systems are inherently more complex than centralised systems. Encapsulation and abstraction of components and services can be of paramount importance in managing their complexity. The use of object oriented techniques and languages, providing support for encapsulation and abstraction, has made development of distributed systems more manageable. In systems where applications are being developed using object-oriented techniques, system support mechanisms must recognise this, and provide support for the object-oriented approach. The architecture presented exploits object-oriented techniques to improve transparency and to reduce the application programmer involvement required to use the replication mechanisms. This dissertation describes an approach to implementing system support for object replication, which is distinct from other approaches such as replicated objects in that objects are not specially designed for replication. Additionally, object replication, in contrast to data replication, is a function-shipping approach and deals with the replication of both operations and data. Object replication is complicated by objects' encapsulation of local state and the arbitrary interaction patterns that may exist among objects. Although fully transparent object replication has not been achieved, my thesis is that partial system support for replication of program-level objects is practicable and assists the development of certain classes of reliable distributed applications. I demonstrate the usefulness of this approach by describing a prototype implementation and showing how it supports the development of an example toy application. To increase their flexibility, the system support mechanisms described are tailorable. The approach adopted in this work is to provide partial support for object replication, relying on some assistance from the application developer to supply application dependent functionality within particular collators for dealing with processing of results from object replicas. Care is taken to make the programming model as simple and concise as possible

Byzantine state machine replication for the masses

Tese de doutoramento, Informática (Ciência da Computação), Universidade de Lisboa, Faculdade de Ciências, 2018The state machine replication technique is a popular approach for building Byzantine fault-tolerant services. However, despite the widespread adoption of this paradigm for crash fault-tolerant systems, there are still few examples of this paradigm for real Byzantine fault-tolerant systems. Our view of this situation is that there is a lack of robust implementations of Byzantine fault-tolerant state machine replication middleware, and that the performance penalty is too high, specially for geo-replication. These hindrances are tightly coupled to the distributed protocols used for enforcing such resilience. This thesis has the objective of finding methodologies for enhancing robustness and performance of state machine replication systems. The first contribution is Mod-SMaRt, a modular protocol that preserves optimal latency in terms of the communications steps exchanged among processes. By being a modular protocol, it becomes simpler to validate and implement, thus resulting in greater robustness; by also preserving optimal message-exchanges among processes, the protocol is capable of delivering desirable performance. The second contribution is concerned with implementing Mod-SMaRt into BFTSMART, a reliable and high-performance codebase that was maintained and improved over the entire course of the PhD that offers multicore-awareness, reconfiguration support, and a flexible API. The third contribution presents WHEAT, a protocol derived from Mod-SMaRt that uses optimizations shown to be effective in reducing latency via a practical evaluation conducted in a geo distributed environment. We additionally conducted an evaluation of both BFT-SMART and WHEAT applied to a relational database middleware and an ordering service for a permissioned blockchain platform. These evaluations revealed encouraging results for both systems and validated our work conducted in the geo-distributed context.A técnica de replicação máquina de estados é um paradigma popular usado em vários sistemas distribuídos modernos. No entanto, apesar da adoção deste paradigma em sistemas reais tolerantes a faltas por paragem, ainda existem poucos exemplos de sistemas reais tolerantes a faltas bizantinas. Segundo a nossa experiência nesta área de investigação, isto deve-se ao fato de existirem poucas concretizações robustas para replicação máquina de estados tolerante a faltas bizantinas, assim como uma perda de desempenho demasiado elevada, especialmente em ambientes geo-replicados. A razão fundamental para a existência destes obstáculos vem dos protocolos distribuídos necessários para assegurar este tipo de resiliência. Esta tese tem como objetivo explorar metodologias para a robustez e eficiência da replicação máquina de estados. A primeira contribuição da tese é o algoritmo Mod-SMaRt, um protocolo modular que preserva latência ótima em termos de passos de comunicação executados pelos processos. Sendo um protocolo modular, torna-se mais simples de validar e concretizar, o que resulta em maior robustez; ao preservar troca de mensagens ótima entre processos, também é capaz de entregar um desempenho desejável. A segunda contribuição consiste em concretizar o protocolo Mod SMaRt na ferramenta BFT-SMART, uma biblioteca fiável de alto desempenho, mantida e melhorada ao longo de todo o período correspondente ao doutoramento, capaz de suportar arquiteturas multi-núcleo, reconfiguração do grupo de réplicas, e uma API de programação flexível. A terceira contribuição consiste em um protocolo derivado do Mod-SMaRt designado WHEAT, que usa otimizações que demostraram serem eficientes na redução da latência segundo uma avaliação prática em ambiente geo-replicado. Adicionalmente, foram também realizadas avaliações de ambos os protocolos quando aplicados num middleware para base de dados relacionais, e num serviço de ordenação para uma plataforma blockchain. Ambas as avaliações revelam resultados encorajadores para ambos os sistemas e validam o trabalho realizado em contexto geo-distribuído.Projeto IRCoC (PTDC/EEI-SCR/6970/2014); Comissão Europeia, FP7 (Seventh Framework Programme for Research and Technological Development), projetos FP7/2007-2013, ICT-25724

Antimicrobial activity and mode of action - Examples from natural products, peptides, and peptidomimetics

Infections caused by bacteria are the third leading cause of death worldwide. Antimicrobials are used to treat and prevent those infections and enabled the development of the modern healthcare system as we know it. However, those achievements are threatened by the global emergence of antimicrobial-resistant bacteria. There is an obvious need for developing new antimicrobials. Natural environments, like the Arctic Ocean, offer largely underexplored biodiversity with promising natural antimicrobial products. This thesis investigates marine and marine-inspired molecules for their antibacterial properties and potential applications

Service management for multi-domain Active Networks

The Internet is an example of a multi-agent system. In our context, an agent is synonymous with network operators, Internet service providers (ISPs) and content providers. ISPs mutually interact for connectivity's sake, but the fact remains that two peering agents are inevitably self-interested. Egoistic behaviour manifests itself in two ways. Firstly, the ISPs are able to act in an environment where different ISPs would have different spheres of influence, in the sense that they will have control and management responsibilities over different parts of the environment. On the other hand, contention occurs when an ISP intends to sell resources to another, which gives rise to at least two of its customers sharing (hence contending for) a common transport medium. The multi-agent interaction was analysed by simulating a game theoretic approach and the alignment of dominant strategies adopted by agents with evolving traits were abstracted. In particular, the contention for network resources is arbitrated such that a self-policing environment may emerge from a congested bottleneck. Over the past 5 years, larger ISPs have simply peddled as fast as they could to meet the growing demand for bandwidth by throwing bandwidth at congestion problems. Today, the dire financial positions of Worldcom and Global Crossing illustrate, to a certain degree, the fallacies of over-provisioning network resources. The proposed framework in this thesis enables subscribers of an ISP to monitor and police each other's traffic in order to establish a well-behaved norm in utilising limited resources. This framework can be expanded to other inter-domain bottlenecks within the Internet. One of the main objectives of this thesis is also to investigate the impact on multi-domain service management in the future Internet, where active nodes could potentially be located amongst traditional passive routers. The advent of Active Networking technology necessitates node-level computational resource allocations, in addition to prevailing resource reservation approaches for communication bandwidth. Our motivation is to ensure that a service negotiation protocol takes account of these resources so that the response to a specific service deployment request from the end-user is consistent and predictable. To promote the acceleration of service deployment by means of Active Networking technology, a pricing model is also evaluated for computational resources (e.g., CPU time and memory). Previous work in these areas of research only concentrate on bandwidth (i.e., communication) - related resources. Our pricing approach takes account of both guaranteed and best-effort service by adapting the arbitrage theorem from financial theory. The central tenet for our approach is to synthesise insights from different disciplines to address problems in data networks. The greater parts of research experience have been obtained during direct and indirect participation in the 1ST-10561 project known as FAIN (Future Active IP Networks) and ACTS-AC338 project called MIAMI (Mobile Intelligent Agent for Managing the Information Infrastructure). The Inter-domain Manager (IDM) component was integrated as an integral part of the FAIN policy-based network management systems (PBNM). Its monitoring component (developed during the MIAMI project) learns about routing changes that occur within a domain so that the management system and the managed nodes have the same topological view of the network. This enabled our reservation mechanism to reserve resources along the existing route set up by whichever underlying routing protocol is in place