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Η εργασία που παρουσιάζεται αφορά την ανάπτυξη ενός ενσωματωμένου συστήματος σε πολλαπλές επαναπρογραμματιζόμενες συσκευές (FPGAs), η επικοινωνία των οποίων γίνεται με τη χρήση του πρωτόκολλου επικοινωνίας TCP/IP. Αρχικά ορίστηκε σε κάθε επαναπρογραμματιζόμενη συσκευή, ένας ενσωματωμένος επεξεργαστής ΜicroBlaze, που ακολουθεί αρχιτεκτονικά την τεχνολογία RISC. Για την κατασκευή της TCP/IP συνδεσιμότητας, αναπτύθηκε σε κάθε core το απαιτούμενο λογισμικό σε γλώσσα προγραμματισμού C, με τη χρήση του open source πρωτοκόλλου επικοινωνίας Light Weight IP. Το συγκεκριμένο πρωτόκολλο είναι ειδικά κατασκευασμένο για σχεδίαση ενσωματωμένων συστημάτων και οι δυνατότητες του οδήγησαν στην ανάπτυξη λογισμικού, προσαρμοσμένο στις απαιτήσεις της ΤCP επικονωνίας και των διαθέσιμων πόρων του επιλεγμένου ενσωματωμένου επεξεργαστή. Η μεταφορά δεδομένων μεταξύ των FPGAs, πραγματοποιήθηκε με την σύνδεση των boards σε έναν μεταγωγέα επιπέδου ζεύξης(Ethernet switch) και Ethernet καλωδίων επικοινωνίας. Ακολούθως, σε κάθε core υλοποίηθηκε σχεδίαση υλικού, η οποία ενσωματώθηκε στο υπόλοιπο υλικό μέσω του διαύλου επικοινωνίας του MicroBlaze επεξεργαστή, με τη μορφή ενός περιφεριακού IP core. Για την επικοινωνία του επιπρόσθετου υλικού με το ενσωματωμένο λογισμικό, χρησιμοποιήθηκαν μηχανισμοί υλικού όπως ουρές δεδομένων εισόδου και εξόδου. Mε αυτόν τον τρόπο, κατέστη δυνατή η ανάπτυξη ενός μηχανισμού που περιλαμβάνει την αποστολή δεδομένων από το κομμάτι του λογισμικού στο υλικό, τη λήψη των δεδομένων από την custom περιφερειακή λογική, την επεξεργασία τους στο κομμάτι του υλικού, την ανάγνωση τους από το λογισμικό και την μετάδοση τους μέσω TCP/IP σύνδεσης σε ένα άλλο αναπτυξιακό, το οποίο μπορεί με τον ίδιο μηχανισμό να επεξεργαστεί τα ληφθέντα δεδομένα. Συμπερασματικά , με έναν αρκετά συμβατό τρόπο , γίνεται εφικτή η κατανομή οποιασδήποτε λογικής σχεδίασης, σε κομμάτια υλικού, τα οποία έχοντας ενσωματωθεί σε ξεχωριστά αναπτυξιακά boards, έχουν τη δυνατότητα να μεταφέρουν και να επεξεργάζονται δεδομένα μεταξύ τους, με χρήση ενός μηχανισμού λογισμικού, υπεύθυνο για τη διαμόρφωση της TCP επικοινωνίας. / This paper presents the development of an embedded system in multiple fpgas, which communicate with each other using ΤCP/IP communication protocol. Initially, a RISC-based embedded MicroBlaze Processor was set, at each device. In order to construct the TCP/IP connectivity, the required software part was developed at each core in programming language C, using the open source communication protocol Light Weight IP. This specific protocol is developed especially for embedded system design and its capabilities allow the construction of a software application, tailored to the requirements of a ΤCP communication and the available resources of the chosen embedded core. The data transfer between the FPGAs, was made with the use of an Ethernet Switch. Each FPGA was connected to an Ethernet switch port via a two directional Ethernet cable. Subsequently, a hardware design was developed at each core, and the custom logic was connected to the MicroBlaze processor local bus as a custom ΙP core peripheral. The communication between the additional hardware part and the embedded software was established with the use of first-in-first-out hardware components for the inputs and outpus of the ΙP core. This led to a successful developed mechanism which includes the transfer of data from software to hardware, the data processing in hardware design, the software reading of the processed data, and finally the data transmission to another FPGA Βoard via TCP/IP communication. In conclusion, a hardware design distribution in multiple FPGAs can be made in a convetional way. The hardware parts, which are embedded in different boards, are able to process, send and receive data across the network, using the appropriate software which is responsible for the configuration of the TCP/IP communication.

This thesis investigates TCP connection management mechanisms in order to understand the behaviour and improve the performance of Internet servers during overload conditions such as flash crowds. We study several alternatives for implementing TCP connection establishment, reviewing approaches taken by existing TCP stacks as well as proposing new mechanisms to improve server throughput and reduce client response times under overload. We implement some of these connection establishment mechanisms in the Linux TCP stack and evaluate their performance in a variety of environments. We also evaluate the cost of supporting half-closed connections at the server and assess the impact of an abortive release of connections by clients on the throughput of an overloaded server. Our evaluation demonstrates that connection establishment mechanisms that eliminate the TCP-level retransmission of connection attempts by clients increase server throughput by up to 40% and reduce client response times by two orders of magnitude. Connection termination mechanisms that preclude support for half-closed connections additionally improve server throughput by up to 18%.

This thesis presents research on transport layer behavior in wireless networks. As the Internet is expanding its reach to include mobile devices, it has become apparent that some of the original design assumptions for the dominant transport protocol, TCP, are approaching their limits. A key feature of TCP is the congestion control algorithm, constructed with the assumption that packet loss is normally very low, and that packet loss therefore is a sign of network congestion. This holds true for wired networks, but for mobile wireless networks non-congestion related packet loss may appear. The varying signal power inherent with mobility and handover between base-stations are two example causes of such packet loss. This thesis provides an overview of the challenges for TCP in wireless networks together with a compilation of a number of suggested TCP optimizations for these environments. A TCP modification called TCP-L is proposed. It allows an application to increase its performance, in environments where residual bit errors normally give a degraded throughput, by making a reliability tradeoff. The performance of TCP-L is experimentally evaluated with an implementation in the Linux kernel. The transport layer performance in a 4G scenario is also experimentally investigated, focusing on the impact of the link layer design and its parameterization. Further, for emulation-based protocol evaluations, controlled packet loss and bit error generation is shown to be an important aspect.

Várias características da Internet mudaram drasticamente desde que o TCP foi criado, como o maior compartilhamento de recursos devido à maior quantidade de usuários, maior largura de banda disponível, a existência de muitas conexões que podem percorrer longas distâncias e a ubiquidade das redes sem fio. Confrontado com essas novas características, o TCP apresenta diversas limitações. Dentre elas estão a subutilização da rede quando a largura de banda é da ordem de centenas de Gbps, o favorecimento de conexões que possuem pouco atraso (poucas dezenas de milisegundos), a incapacidade de distinção de causas de perdas de pacote e a demora para estabelecimento de conexões seguras (até 3 RTTs). Nesse contexto, com o objetivo de tornar o transporte de dados na Internet mais rápido e eficiente, a Google desenvolveu o protocolo QUIC. O QUIC propõe diversos avanços em relação aos protocolos existentes, como um novo mecanismo para estabelecimento de conexão e controle de congestionamento otimizado. Resultados apresentados pela Google mostraram claro ganho de desempenho em relação ao TCP, justificando o trabalho de tornar o QUIC um padrão IETF da Internet. Porém, esses resultados são impossíveis de serem verificados porque nos relatórios divulgados não há informação suficiente para que os cenários de teste sejam reproduzidos e porque é implausível possuir a mesma infraestrutura para os testes que a Google tem. Neste trabalho, avaliamos o desempenho do protocolo QUIC em diversos cenários de rede, comparando-o com o desempenho de várias implementações do TCP, principalmente o CUBIC. Diferente do realizado na literatura, todos os cenários utilizados são bem descritos, permitindo a reprodutibilidade dos experimentos. Além disso, para a realização dos experimentos foi criado um novo módulo que implementa o QUIC no simulador de redes NS-3. Este módulo está disponível como software livre, permitindo que outros pesquisadores usem o módulo para replicar e verificar nossos experimentos e para criarem novos experimentos de forma reprodutível. Ademais, eles também podem usar o módulo como uma ferramenta para avaliar, de maneira rápida, o comportamento de novas técnicas dentro do protocolo. / Many characteristics of the Internet have drastically changed since TCP was created such as the increase on resource sharing due to a larger number of Internet users, the growth of available bandwidth, the existence of many connections that may travel long distances and the ubiquity of wireless networks. When faced with those new characteristics, TCP showed severe limitations. Among them are network underutilization in high bandwidth environments of hundreds of Gbps, favoring of connections with small delays (few tens of milliseconds), incapacity of distinguishing packet loss causes and high delays for establishing secure connections (up to 3 RTTs). In this context, with the goal of making Internet data transport faster and more efficient, Google has developed the QUIC protocol. QUIC proposes many advances compared to existing protocols, such as a new mechanism for establishing connections and an optimized congestion control algorithm. Google has reported results indicating that QUIC performs better than TCP, justifying the work on making QUIC an IETF Internet standard. However, those results cannot be verified because on the published reports there is not enough information to reproduce the test scenarios and it is implausible to have the same test infrastructure Google has. In this work, we evaluate QUICs performance in a number of network scenarios, comparing it with the performance of different TCP flavours, specially TCP CUBIC. Unlike other works in the literature, all scenarios are well described, enabling experiment replicability. Furthermore, to run experiments we created a new module that implements QUIC on the network simulator NS-3. The module is available as free software, allowing other researchers to use it to reproduce and verify our experiments and to create new ones in a replicable way. Additionally, they can use the module as a tool to quickly assess the behaviour of new techniques in the protocol.

O florescimento é um processo chave no desenvolvimento vegetal. A mudança de identidade do meristema apical de vegetativo para reprodutivo desencadeia reprogramação genética com efeitos em todo o corpo vegetal. Arabidopsis thaliana é conhecida como o principal modelo de estudo para esse processo apresentando até o momento cinco principais vias genéticas regulatórias. Tais vias apresentam redundância, sendo complexa a eliminação total da transição de fase nessa espécie. A via AGE, regulada pela idade da planta, tem como principais reguladores o mir156 e seus alvos diretos, os fatores de transcrição da família SPL/SBP (SQUAMOSA PROMOTER BINDING PROTEIN-like). Uma segunda via é controlada pelo fitohormônio giberelina (GA), o qual atua de maneira oposta em Arabidopsis thaliana (arabidopsis) e Solanum lycopersicum L. (tomateiro). Em tomateiro, diferentemente de arabidopsis, o cruzamento entre mutantes com conteúdo alterado de GA e plantas transgênicas superexpressando o miR156 (156OE; SILVA et al., 2014) demonstraram efeito sinérgico no atraso do tempo de florescimento. A aplicação de GA3 em plantas 156OE apresenta efeito similar aos cruzamentos citados sobre a transição do meristema apical. Em um dos cruzamentos entre mutantes da via GA e plantas 156OE, foi possível obter plantas apresentando completo bloqueio da transição de fase vegetativo-reprodutivo. A oferta extra do florígeno SINGLE FLOWER TRUSS (SFT) via enxertia não foi suficiente para restaurar a transição de fase nessas plantas, sugerindo que vias associadas à GA e AGE regulam alvos em comum, os quais podem ser independentes da regulação por SFT. Além disso, a regulação transcricional, e possivelmente pós-transcricional de alguns genes SBPs por diferentes vias associadas à GA, sugere uma complexa inter-relação entre as vias GA e AGE em tomateiro durante o florescimento. A ação combinada das vias GA e AGE foi capaz de inibir completamente o florescimento em tomateiro, regulação oposta ao verificado na planta modelo Arabidopsis thaliana. O efeito inibitório de GA sobre o florescimento é também visualizado em plantas lenhosas, sugerindo que as descobertas científicas realizadas em tomateiro podem ser expandidas para essas espécies, nas quais a experimentação é lenta e laboriosa / The flowering process is a major developmental event during the plant life cicle. The meristem identity switches from vegetative to reproductive, triggering substantial genetic modifications that affect the whole plant body. Arabidopsis thaliana is a major model for flowering with five different pathways controlling this process. These pathways are redundant, making complex the complete elimination of phase change in this species. One of the pathways is termed AGE since it is regulated by the time of development. The miR156 and its direct target SBP (SQUAMOSA PROMOTER BINDING PROTEIN-like) are the main regulators of the AGE pathway. A second pathway is controlled by the phytohormone gibberellin (GA), which acts in opposite ways when comparing Arabidopsis thaliana and tomato. In tomato, unlike Arabidopsis, the cross between mutants with altered contents of GA and transgenic plants overexpressing the miR156 (156OE; SILVA et al, 2014) showed synergistic effect in delayed flowering time. Treatments of GA3 in plants 156OE lead to similar effects visualized on the crosses above related to meristem transition. Among the crosses between GA mutants and 156OE plants, one double mutant could completely abolish the phase change in tomato. An extra offer of the florigen (SINGLE FLOWER TRUSS or SFT) by grafting experiments was unable to restore the flowering process in this double mutant. It suggests, pathways associated to GA and AGE regulate common downstream targets, which could be independent of SFT regulation. Moreover, the transcriptional regulation, and possible the post-transcriptionally regulation of some SBP targets by different pathways associated to GA, suggest a complex network between GA and AGE during the flowering in tomato. The combined action of GA and AGE pathways can complete impaired the flowering in tomato, this interaction is opposed to the model Arabidopsis thaliana. The negative effect of GA over the time of flowering is presented in wood plants, suggesting the scientific discoveries in tomato could be expanded to these species, which experiments are slow and laborious

Esta dissertação descreve os métodos, medidas e análises feitas para otimizar a rede de comunicação de dados do Instituto de Física de São Carlos. As tecnologias e protocolos utilizados na rede são apresentados. Especial atenção é dada a análise do desempenho de VLANs utilizando inicialmente o protocolo LANE no núcleo ATM da rede. Neste caso a rede é composta de switches ATM e ATM-Ethernet. Medidas comparativas foram realizadas com a utilização da tecnologia Fast Ethernet no backbone, que possui uma capacidade de transmissão relativamente próxima da ATM de 155Mbps. Melhores resultados obtidos com a implementação de sub-redes maiores, reduzindo em um numero menor de sub-redes, são discutidos e apresentados. Análises estatísticas baseadas apenas no tempo de resposta da rede são apresentados para avaliar o desempenho das alterações efetuadas nas configurações da rede. Mesmo que o tráfego tenha aumentado muito durante esses anos e que vários serviços tenha sido agregados a esta rede, foi possível adequar o desempenho as novas necessidades beneficiando-se da evolução tecnológica que os equipamentos de rede de dados trouxeram ao IFSC. / This work describes the methods, measures and analyses performed aiming to optimize the data communication network from the Physics Institute of Sao Carlos as well as the technologies and protocols used in the network recently. Special care is given to the analysis of the VLANs performance using, initially, the LANE protocol over ATM which has its core based on pure ATM and ATM-Ethernet switches. Comparative measures had been carried out using a backbone working on a Fast Ethernet technology, which seems to have a very close transmission rate from the ATM 155Mbps. This work also discusses best results acquired with the implementation of larger networks reducing the number of subnetworks, statistical analyses based on time delay of the network in order to evaluate the performance of the changes made on its configuration. Even though the traffic from the Institute has been increased over these years and several services have been added to the network, it was completely possible to adapt the performance to the needs, using the benefits of the technological evolution which the network equipments had brought to the Institute.

Voice over IP and video applications continue to increase the amount of traffic over the Internet. These applications utilize the UDP protocol because TCP is not suitable for streaming applications. The flow and congestion control mechanisms of TCP can change the connection transmission rate too drastically, affecting the user-perceived quality of the transmission. Also, the TCP protocol provides a level of reliability that may waste network resources, retransmitting packets that have no value. On the other hand, the use of end-to-end flow and congestion control mechanisms for streaming applications has been acknowledged as an important measure to ease or eliminate the unfairness problem that exist when TCP and UDP share the same congested bottleneck link. Actually, router-based and end-to-end solutions have been proposed to solve this problem. This thesis introduces a new end-to-end protocol based on TCP SACK called SF-SACK that promises to be smooth enough for streaming applications while implementing the known flow and congestion control mechanisms available in TCP. Through simulations, it is shown that in terms of smoothness the SF-SACK protocol is considerably better than TCP SACK and only slightly worse than TFRC. Regarding friendliness, SF-SACK is not completely fair to TCP but considerably fairer than UDP. Furthermore, if SF-SACK is used by both streaming and data-oriented applications, complete fairness is achieved. In addition, SF-SACK only needs sender side modifcations and it is simpler than TFRC.

<p>This thesis presents research on transport layer behavior in wireless networks. As the Internet is expanding its reach to include mobile devices, it has become apparent that some of the original design assumptions for the dominant transport protocol, TCP, are approaching their limits. A key feature of TCP is the congestion control algorithm, constructed with the assumption that packet loss is normally very low, and that packet loss therefore is a sign of network congestion. This holds true for wired networks, but for mobile wireless networks non-congestion related packet loss may appear. The varying signal power inherent with mobility and handover between base-stations are two example causes of such packet loss. This thesis provides an overview of the challenges for TCP in wireless networks together with a compilation of a number of suggested TCP optimizations for these environments. A TCP modification called TCP-L is proposed. It allows an application to increase its performance, in environments where residual bit errors normally give a degraded throughput, by making a reliability tradeoff. The performance of TCP-L is experimentally evaluated with an implementation in the Linux kernel. The transport layer performance in a 4G scenario is also experimentally investigated, focusing on the impact of the link layer design and its parameterization. Further, for emulation-based protocol evaluations, controlled packet loss and bit error generation is shown to be an important aspect.</p>