Partial replication in the database state machine

Tese de Doutoramento em Informática - Ramo do Conhecimento em Tecnologias da ProgramaçãoEnterprise information systems are nowadays commonly structured as multi-tier architectures and invariably built on top of database management systems responsible for the storage and provision of the entire business data. Database management systems therefore play a vital role in today’s organizations, from their reliability and availability directly depends the overall system dependability. Replication is a well known technique to improve dependability. By maintaining consistent replicas of a database one can increase its fault tolerance and simultaneously improve system’s performance by splitting the workload among the replicas. In this thesis we address these issues by exploiting the partial replication of databases. We target large scale systems where replicas are distributed across wide area networks aiming at both fault tolerance and fast local access to data. In particular, we envision information systems of multinational organizations presenting strong access locality in which fully replicated data should be kept to a minimum and a judicious placement of replicas should be able to allow the full recovery of any site in case of failure. Our research departs from work on database replication algorithms based on group communication protocols, in detail, multi-master certification-based protocols. At the core of these protocols resides a total order multicast primitive responsible for establishing a total order of transaction execution. A well known performance optimization in local area networks exploits the fact that often the definitive total order of messages closely following the spontaneous network order, thus making it possible to optimistically proceed in parallel with the ordering protocol. Unfortunately, this optimization is invalidated in wide area networks, precisely when the increased latency would make it more useful. To overcome this we present a novel total order protocol with optimistic delivery for wide area networks. Our protocol uses local statistic estimates to independently order messages closely matching the definitive one thus allowing optimistic execution in real wide area networks. Handling partial replication within a certification based protocol is also particularly challenging as it directly impacts the certification procedure itself. Depending on the approach, the added complexity may actually defeat the purpose of partial replication. We devise, implement and evaluate two variations of the Database State Machine protocol discussing their benefits and adequacy with the workload of the standard TPC-C benchmark.Os sistemas de informação empresariais actuais estruturam-se normalmente em arquitecturas de software multi-nível, e apoiam-se invariavelmente sobre um sistema de gestão de bases de dados para o armazenamento e aprovisionamento de todos os dados do negócio. A base de dado desempenha assim um papel vital, sendo a confiabilidade do sistema directamente dependente da sua fiabilidade e disponibilidade. A replicação é uma das formas de melhorar a confiabilidade. Garantindo a coerência de um conjunto de réplicas da base de dados, é possível aumentar simultaneamente a sua tolerância a faltas e o seu desempenho, ao distribuir as tarefas a realizar pelas várias réplicas não sobrecarregando apenas uma delas. Nesta tese, propomos soluções para estes problemas utilizando a replicação parcial das bases de dados. Nos sistemas considerados, as réplicas encontram-se distribuídas numa rede de larga escala, almejando-se simultaneamente obter tolerância a faltas e garantir um acesso local rápido aos dados. Os sistemas propostos têm como objectivo adequarem-se às exigências dos sistemas de informação de multinacionais em que em cada réplica existe uma elevada localidade dos dados acedidos. Nestes sistemas, os dados replicados em todas as réplicas devem ser apenas os absolutamente indispensáveis, e a selecção criteriosa dos dados a colocar em cada réplica, deve permitir em caso de falha a reconstrução completa da base de dados. Esta investigação tem como ponto de partida os protocolos de replicação de bases de dados utilizando comunicação em grupo, em particular os baseados em certificação e execução optimista por parte de qualquer uma das réplicas. O mecanismo fundamental deste tipo de protocolos de replicação é a primitiva de difusão com garantia de ordem total, utilizada para definir a ordem de execução das transacções. Uma optimização normalmente utilizada pelos protocolos de ordenação total é a utilização da ordenação espontânea da rede como indicador da ordem das mensagens, e usar esta ordem espontânea para processar de forma optimista as mensagens em paralelo com a sua ordenação. Infelizmente, em redes de larga escala a espontaneidade de rede é praticamente residual, inviabilizando a utilização desta optimização precisamente no cenário em que a sua utilização seria mais vantajosa. Para contrariar esta adversidade propomos um novo protocolo de ordenação total com entrega optimista para redes de larga escala. Este protocolo utiliza informação estatística local a cada processo para "produzir" uma ordem espontânea muito mais coincidente com a ordem total obtida viabilizando a utilização deste tipo de optimizações em redes de larga escala. Permitir que protocolos de replicação de bases de dados baseados em certificação suportem replicação parcial coloca vários desafios que afectam directamente a forma com é executado o procedimento de certificação. Dependendo da abordagem à replicação parcial, a complexidade gerada pode até comprometer os propósitos da replicação parcial. Esta tese concebe, implementa e avalia duas variantes do protocolo da database state machine com suporte para replicação parcial, analisando os benefícios e adequação da replicação parcial ao teste padronizado de desempenho de bases de dados, o TPC-C.Fundação para a Ciência e a Tecnologia (FCT) - ESCADA (POSI/CHS/33792/2000)

Partial replication in the database state machine

This paper investigates the use of partial replication in the Database State Machine approach introduced ear- lier for fully replicated databases. It builds on the or- der and atomicity properties of group communication primitives to achieve strong consistency and proposes two new abstractions: Resilient Atomic Commit and Fast Atomic Broadcast. Even with atomic broadcast, partial replication re- quires a termination protocol such as atomic commit to ensure transaction atomicity. With Resilient Atomic Commit our termination protocol allows the commit of a transaction despite the failure of some of the par- ticipants. Preliminary performance studies suggest that the additional cost of supporting partial replica- tion can be mitigated through the use of Fast Atomic Broadcast

Evaluating certification protocols in the partial database state machine

Partial replication is an alluring technique to ensure the reliability of very large and geographically distributed databases while, at the same time, offering good performance. By correctly exploiting access locality most transactions become confined to a small subset of the database replicas thus reducing processing, storage access and communication overhead associated with replication. The advantages of partial replication have however to be weighted against the added complexity that is required to manage it. In fact, if the chosen replica configuration prevents the local execution of transactions or if the overhead of consistency protocols offsets the savings of locality, potential gains cannot be realized. These issues are heavily dependent on the application used for evaluation and render simplistic benchmarks useless. In this paper, we present a detailed analysis of Partial Database State Machine (PDBSM) replication by comparing alternative partial replication protocols with full replication. This is done using a realistic scenario based on a detailed network simulator and access patterns from an industry standard database benchmark. The results obtained allow us to identify the best configuration for typical on-line transaction processing applications.União Europeia - GORDA Project (FP6-IST/004758)

Group-based replication of on-line transaction processing servers

Several techniques for database replication using group communication have recently been proposed, namely, the Database State Machine, Postgres-R, and the NODO protocol. Although all rely on a totally ordered multicast for consistency, they differ substantially on how multicast is used. This results in different performance trade-offs which are hard to compare as each protocol is presented using a different load scenario and evaluation method. In this paper we evaluate the suitability of such protocols for replication of On-Line Transaction Processing (OLTP) applications in clusters of servers and over wide area networks. This is achieved by implementing them using a common infra-structure and by using a standard workload. The results allows us to select the best protocol regarding performance and scalability in a demanding but realistic usage scenario.Projecto STRONGRE (POSI/CHS/41285/2001) financiado pela Fundação para a Ciência e a Tecnologia (FCT)

Testing the dependability and performance of group communication based database replication protocols

Database replication based on group communication systems has recently been proposed as an efficient and resilient solution for large-scale data management. However, its evaluation has been conducted either on simplistic simulation models, which fail to assess concrete implementations, or on complete system implementations which are costly to test with realistic large-scale scenarios. This paper presents a tool that combines implementations of replication and communication protocols under study with simulated network, database engine, and traffic generator models. Replication components can therefore be subjected to realistic large scale loads in a variety of scenarios, including fault-injection, while at the same time providing global observation and control. The paper shows first how the model is configured and validated to closely reproduce the behavior of a real system, and then how it is applied, allowing us to derive interesting conclusions both on replication and communication protocols and on their implementationsFundação para a Ciência e a Tecnologia (FCT) - Project STRONGREP (POSI/CHS/41285/2001)

Corpo docente da Universidade do Minho: caraterização demográgica e estratégias de rejuvenescimento

Este relatório apresenta os principais resultados da pesquisa iniciada no final de 2019, relativa ao projeto “DocentesUM -- Corpo Docente: caracterização demográfica e estratégias de rejuvenescimento”. Tem um duplo objetivo: por um lado, caracterizar em termos demográficos a situação atual do corpo docente da UMinho e, por outro lado, apresentar propostas de intervenção geracional concordantes com o desígnio de reforçar a sustentabilidade da UMinho, a médio e longo prazo. A partir da análise de dados do corpo docente da Universidade do Minho que permitiram mapear as principais tendências relativas ao volume de aposentações nos próximos anos, o relatório apresenta as principais perceções dos docentes e investigadores auscultados e procura discernir algumas opções de política para a mitigação dos efeitos do envelhecimento, no quadro de estratégias institucionais mais gerais e, de algum modo, interdisciplinares. Na prática, o estudo envolveu o cruzamento de diversas técnicas de diagnóstico de índole qualitativa (entrevistas semiestruturadas e grupos de discussão) e quantitativa (dados administrativos e inquérito por questionário), procurando favorecer a participação alargada da população académica na compreensão do problema. A informação recolhida e tratada permite concluir que o envelhecimento docente é uma preocupação estrutural para a grande maioria das Escolas/Institutos e que reflete algumas tensões já constituintes dos quotidianos da gestão académica, em particular no que se refere à atribuição de serviço docente e, em consequência, a necessidade crescente de recorrer semestralmente a contratações de pessoas em regimes mais flexíveis e pouco estáveis. Ainda que o envelhecimento seja percebido de forma muito particular em algumas escolas com dinâmicas muito específicas no que respeita ao modo de estruturar o ensino, genericamente é entendido como um fenómeno que implica atenção especial à oferta formativa e à capacidade de manutenção de certas áreas e/ou cursos. Todavia, o estudo permite identificar outros vértices colaterais do problema, nomeadamente no que se refere ao desenvolvimento dos recursos docentes e ao interesse em se repensar alguns dos enquadramentos legais existentes, em especial no que se refere à ativação de modalidades que facilitam as decisões estratégicas a respeito das carreiras dos docentes e mudança/reconfiguração dos universos culturais que caraterizam os modos de estar na academia.Conselho Geral da Universidade do Minho. UIDB/00736/202

Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal

Pathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the highest impact on case numbers and fitted them into a global context, finding evidence that several international sublineages probably emerged or spread early in Portugal. We estimated a 62% infection reporting rate and that 1.3% of the population of men who have sex with men in Portugal were infected. We infer the critical role played by sexual networks and superspreader gatherings, such as sauna attendance, in the dissemination of mpox virus. Overall, our findings highlight genomic epidemiology as a tool for the real-time monitoring and control of mpox epidemics, and can guide future vaccine policy in a highly susceptible population.info:eu-repo/semantics/publishedVersio

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

P1402 Isolation of pulmonary veins with duty-cycled circular multi-polar catheter : randomized controlled clinical trial

Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2019. For permissions please email: [email protected]. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)Introduction: Pulmonary vein isolation (PVI) is the central element in the ablation of atrial fibrillation (AF), and can be obtained with different ablation modalities. The duty­cycled circular multi­pole catheter PVAC® (Medtronic) allows linear application of radiofrequency energy, with the production of circumferential lesions. Conceptually, it can make ablation simpler and faster in patients with favorable anatomy.info:eu-repo/semantics/publishedVersio