Multicore Scheduling of Real-Time Irregular Parallel Algorithms in Linux

Face à estagnação da tecnologia uniprocessador registada na passada década, aos principais fabricantes de microprocessadores encontraram na tecnologia multi-core a resposta `as crescentes necessidades de processamento do mercado. Durante anos, os desenvolvedores de software viram as suas aplicações acompanhar os ganhos de performance conferidos por cada nova geração de processadores sequenciais, mas `a medida que a capacidade de processamento escala em função do número de processadores, a computação sequencial tem de ser decomposta em várias partes concorrentes que possam executar em paralelo, para que possam utilizar as unidades de processamento adicionais e completar mais rapidamente. A programação paralela implica um paradigma completamente distinto da programação sequencial. Ao contrário dos computadores sequenciais tipificados no modelo de Von Neumann, a heterogeneidade de arquiteturas paralelas requer modelos de programação paralela que abstraiam os programadores dos detalhes da arquitectura e simplifiquem o desenvolvimento de aplicações concorrentes. Os modelos de programação paralela mais populares incitam os programadores a identificar instruções concorrentes na sua lógica de programação, e a especificá-las sob a forma de tarefas que possam ser atribuídas a processadores distintos para executarem em simultâneo. Estas tarefas são tipicamente lançadas durante a execução, e atribuídas aos processadores pelo motor de execução subjacente. Como os requisitos de processamento costumam ser variáveis, e não são conhecidos a priori, o mapeamento de tarefas para processadores tem de ser determinado dinamicamente, em resposta a alterações imprevisíveis dos requisitos de execução. `A medida que o volume da computação cresce, torna-se cada vez menos viável garantir as suas restrições temporais em plataformas uniprocessador. Enquanto os sistemas de tempo real se começam a adaptar ao paradigma de computação paralela, há uma crescente aposta em integrar execuções de tempo real com aplicações interativas no mesmo hardware, num mundo em que a tecnologia se torna cada vez mais pequena, leve, ubíqua, e portável. Esta integração requer soluções de escalonamento que simultaneamente garantam os requisitos temporais das tarefas de tempo real e mantenham um nível aceitável de QoS para as restantes execuções. Para tal, torna-se imperativo que as aplicações de tempo real paralelizem, de forma a minimizar os seus tempos de resposta e maximizar a utilização dos recursos de processamento. Isto introduz uma nova dimensão ao problema do escalonamento, que tem de responder de forma correcta a novos requisitos de execução imprevisíveis e rapidamente conjeturar o mapeamento de tarefas que melhor beneficie os critérios de performance do sistema. A técnica de escalonamento baseado em servidores permite reservar uma fração da capacidade de processamento para a execução de tarefas de tempo real, e assegurar que os efeitos de latência na sua execução não afectam as reservas estipuladas para outras execuções. No caso de tarefas escalonadas pelo tempo de execução máximo, ou tarefas com tempos de execução variáveis, torna-se provável que a largura de banda estipulada não seja consumida por completo. Para melhorar a utilização do sistema, os algoritmos de partilha de largura de banda (capacity-sharing) doam a capacidade não utilizada para a execução de outras tarefas, mantendo as garantias de isolamento entre servidores. Com eficiência comprovada em termos de espaço, tempo, e comunicação, o mecanismo de work-stealing tem vindo a ganhar popularidade como metodologia para o escalonamento de tarefas com paralelismo dinâmico e irregular. O algoritmo p-CSWS combina escalonamento baseado em servidores com capacity-sharing e work-stealing para cobrir as necessidades de escalonamento dos sistemas abertos de tempo real. Enquanto o escalonamento em servidores permite partilhar os recursos de processamento sem interferências a nível dos atrasos, uma nova política de work-stealing que opera sobre o mecanismo de capacity-sharing aplica uma exploração de paralelismo que melhora os tempos de resposta das aplicações e melhora a utilização do sistema. Esta tese propõe uma implementação do algoritmo p-CSWS para o Linux. Em concordância com a estrutura modular do escalonador do Linux, ´e definida uma nova classe de escalonamento que visa avaliar a aplicabilidade da heurística p-CSWS em circunstâncias reais. Ultrapassados os obstáculos intrínsecos `a programação da kernel do Linux, os extensos testes experimentais provam que o p-CSWS ´e mais do que um conceito teórico atrativo, e que a exploração heurística de paralelismo proposta pelo algoritmo beneficia os tempos de resposta das aplicações de tempo real, bem como a performance e eficiência da plataforma multiprocessador.With sequential machines approaching their physical bounds, parallel computers are rapidly becoming pervasive in most areas of modern technology. To realize the full potential of parallel platforms, applications must split onto concurrent parts that can be assigned to different processors and execute in parallel. Parallel programming models abstract the myriad of parallel computer specifications to simplify the development of concurrent applications, allowing programmers to decompose their code onto concurrent tasks, and leaving it to the runtime system to schedule these tasks for parallel execution. The resulting parallelism is often input-dependent and irregular, requiring that the mapping of tasks to processors be performed at runtime in response to dynamic changes of the workload. Motivated by the promises of performance scalability and cost effectiveness, real-time researchers are now beginning to exploit the benefits of parallel processing, with ground-breaking scheduling heuristics to improve the efficiency of time-sensitive concurrent applications. Realtime developments are switching to open scenarios, where real-time tasks of variable and unpredictable size share the available processing resources with other applications, making it essential to utilize as much of the available processing capacity as possible. The p-CSWS algorithm employs bandwidth isolation, capacity-sharing and work-stealing to exploit the intra-task parallelism of hard and soft real-time executions on parallel platforms. This thesis proposes an implementation of the p-CSWS scheduler for the Linux kernel, to evaluate its applicability to real scenarios and bring Linux one step closer to becoming a viable open real-time platform. To the best of our knowledge we are the first to employ scheduling heuristics to exploit dynamic parallelism of real-time tasks on the Linux kernel. Through extensive tests, we show that...

Structural lipid changes and Na+/K+-ATPase activity of gill cells'basolateral membranes during saltwater acclimation in sea lamprey (Petromyzon marinus, L.) juveniles

Seawater acclimation is a critical period for anadromous species and a process yet to be understood in lampreys. Considering that changes in lipid composition of the gill cells' basolateral membranes may disrupt the major transporter Na+K+-ATPase, the goal of this study was to detect changes at this level during juvenile sea lamprey seawater acclimation. The results showed that saltwater acclimation has a direct effect on the fatty acid composition of gill cells basolateral membrane's phospholipids. When held in full-strength seawater, the fatty acid profile of basolateral membrane's phospholipids suffered a restructure by increasing either saturation or the ratio between oleic acid and eicosapentaenoic acid. Simultaneously, the activity of Na+K+- 2 ATPase revealed a significant and positive correlation with basolateral membrane's cholesterol content in the presence of highest salinity. Our results pointed out for lipid adjustments involving the functional transporter present on the gill cell basolateral membranes to ensure the role played by branchial Na+K+-ATPase in ion transport during saltwater acclimation process. The responses observed contributed to the strategy adopted by gill cell's basolateral membranes to compensate for osmotic and ionic stressors, to ensure the success of the process of seawater acclimation associated with the downstream trophic migration of juvenile sea lamprey.This work was financially supported by the Foundation for Science and Technology (FCT) project PTDC/BIA-BEC/103258/2008 and project UID/MAR/04292/2013 (national funds FCT/MEC–PIDDAC through Acordo de Parceria PT2020)

SUB-LETHAL EFFECTS OF EXPOSURE TO ATRAZINE IN GILL CELLS OF SEA LAMPREY DOWNSTREAM MIGRANTS

In Portugal, atrazine (ATZ) was one of the most widely used herbicides in agriculture, and despite prohibited since 2007, it still continued to be detected in the surface and ground waters. Recent research demonstrated that the conditions experienced by anadromous fishes, while in freshwater, may be critical to their subsequent fitness and survival in the sea. Several studies established a decline in wild populations, most probably caused by a reduction in recruitment related with pollution. In the case of sea lamprey (Petromyzon marinus) trophic migration to the ocean, expose fish to several stress factors, including chemical stress. Thus, it is crucial to assess the effects of sub-lethal exposure to ATZ and predict potential consequences to juveniles of sea lamprey

Session D2: Coimbra Fishway: Restoring Connectivity in River Mondego

Abstract: River Mondego is the largest Portuguese river with its basin entirely within national territory. The Açude-Ponte dam was built in Mondego in the 80’s, along with three other large dams to mitigate floods and to allow the integrated use of river basin water resources for hydroelectric power generation, public supply, industry and irrigation. Considering the river importance for several fish species, namely sea-lamprey and shad, a fishway was constructed. Several structural and hydraulic problems soon revealed that this fishway was inefficient therefore this dam became the first impassable obstacle in the River Mondego. In 2011, after several years of biological and hydraulic monitoring, and once the reasons for the fishway inefficiency were perfectly identified, a vertical-slot fishway was built to restore river connectivity. The efficiency and effectiveness of the Coimbra Fishway has been studied since 2012 using several monitoring techniques (visual counts, biotelemetry techniques and CPUE abundance with electrofishing). Monitoring results show that several autochthonous species use the fishway, including the diadromous sea-lamprey, allis and twaite shad and European-eel. More than 1,500.000 fish have used the fishway during the upstream or downstream migration. PIT telemetry has shown an efficiency of 30% for Petromyzon marinus and 14% for Luciobarbus bocagei. Pre and post fishway construction electrofishing monitoring shows improvements in sealamprey larvae abundance both upstream and downstream from the Açude-Ponte dam. Coimbra Fishway project is improving fish migration in River Mondego, but it’s also an integrated project involving other important aspects such as fisheries and river basin management and environmental education. Changes in exploitation regimes of upstream hydropower dams and in the Açude-Ponte are also planned to increase the fishway efficiency. Finally, several activities have been carried out in association with this project to raise public awareness regarding environmental issues, particularly those related with river longitudinal continuity

Salinity and Atrazine Sublethal Levels Induce Gill Cells Basolateral Membrane Phospholipids Modulation in Sea Lamprey Downstream Migrants

Conditions experienced by anadromous fishes while in freshwater may be critical to their subsequent survival in the sea. During the trophic migration to the ocean, juveniles of sea lamprey (Petromyzon marinus L.) are exposed to several stress factors, including different types of pollutants. We analyzed gill histopathological biomarkers, characterized the lipid profile of the basolateral membrane (BLM) of gill cells, and determined NKA activity, in order to evaluate if BLM lipid profile system plays a part in modulation of NKA activity and may be involved in the successful acclimation of sea lamprey juveniles during downstream migration

Structural lipid changes and NKA activity of gill cells´ basolateral membranes as response to increasing salinity and atrazine stressors in sea lamprey (Petromyzon marinus, L.) juveniles

In the last decades, several authors have pointed out a reduction in the sea lamprey population abundance in Portuguese rivers. In spite of this, studies concerning downstream migration and the conditions experienced by sea lamprey juveniles during this process are yet to be understood. Considering that changes in lipid composition of the gill cells´ basolateral membrane (BLM) may disrupt the major transporter Na+K+-ATPase (NKA), this study goals were to detect changes at this level either during seawater acclimation (0 to 35) or after the exposure to atrazine (50 and 100 μg/L atrazine during 30 days). This would give us information about the gill cells´ BLM strategy to response to increasing salinity and atrazine (ATZ) stressors and consequently information on the recruitment success of sea lamprey populations.This work was financially supported by Foundation for Science and Technology (FCT): project PTDC/BIA-BEC/103258/2008 and project UID/MAR/04292/2013 (national funds FCT/MEC - PIDDAC through Acordo de Parceria PT2020)

Manual para a avaliação biológica da qualidade da água em sistemas fluviais segundo a Directiva Quadro da Água - Protocolo de amostragem e análise para a fauna piscícola

A Directiva nº 2000/60/CE do Parlamento Europeu e do Conselho, de 23 de Outubro de 2000 (Directiva Quadro da Água - DQA), transposta para a legislação nacional pela Lei da Água, Lei nº58/2005, de 29 de Dezembro e pelo Decreto-Lei nº77/2006, de 30 de Março, veio tornar mais premente a necessidade de, a nível nacional, se desenvolver um esforço de normalização quanto a métodos de amostragem de elementos de qualidade biológicos designadamente na perspectiva dos programas de monitorização. Na elaboração do presente protocolo para a fauna piscícola teve-se em conta a Norma EN 14011 (2003) Water quality - Sampling of fish with electricity com as necessárias alterações dadas as características dos cursos de água portugueses e a necessidade de produzir um protocolo na medida do possível simples, claro e objectivo

Session D1: Modelling the Efficiency of a Vertical Slot Fishway for Anadromous Fishes

Abstract: Several types of fish passage are increasingly being installed in river barriers to restore the longitudinal connectivity of fragmented riverine habitats. A vertical slot fishway installed in the Açude-Ponte weir at Coimbra (River Mondego, Portugal) was monitored to model the efficiency of this infrastructure for anadromous fishes (i.e., sea lamprey Petromyzon marinus L.; allis shad Alosa alosa L. and twaite shad Alosa fallax Lacépède, 1800) throughout 2013 and 2014 spawning seasons. Fish passage was assessed using a video recording system. Simultaneously, eight abiotic parameters, considered as potential predictors of fishway’s use by anadromous fishes, were continuously recorded during the entire study period. Boosted Regression Trees (BRTs) analysis was applied to relate the use of the fishway by sea lamprey and Alosa spp. with the abiotic predictors. To complement this data, a passive integrated transponder (PIT) antenna system was used to quantify passage efficiency for sea lampreys. Size frequency distribution and total biomass of fishes that successfully transposed the fishway was also estimated. Video data show that in the migratory seasons of 2013 and 2014, 8333 and 21979 sea lampreys passed through fishway, respectively, and a total of 7503 and 3404 Alosa spp. individuals transposed this infrastructure during the same period. About 30% of PIT tagged lampreys transposed the fishway. BRT models identified the river flow as the most important variable to explain use of the fishway by anadromous fishes. The relationships of this variable with the fish passages suggest that sea lampreys and Alosa spp. use the fishway preferentially at relatively low flow conditions that maximize the attraction efficiency of the fishway entrance. Finally, results obtained with this study were used to implement a sub-sampling methodology (video processing) to estimate the total amount of fish (lamprey and shads) that annually use the fishway during their spawning migrations

Tipologia de rios em Portugal Continental no âmbito da implementação da Directiva Quadro da Água. I - Caracterização abiótica.

Os tipos são grupos de massas de água com características geográficas e hidrológicas relativamente homogéneas, consideradas relevantes para a determinação das condições ecológicas. O objectivo da definição de tipos é permitir que sejam correctamente estabelecidas condições de referência e que sejam comparáveis as classificações de estado ecológico dentro de cada grupo de rios com características semelhantes. Na definição da Tipologia para Rios, procedeu-se inicialmente à aplicação do sistema A (Anexo II, DQA) tendo-se obtido 18 tipos. Estando a generalidade dos tipos representada em todo o território continental, considerou-se que este sistema não traduziria a heterogeneidade ecológica existente, não reflectindo o gradiente climático Norte – Sul, particularmente evidente para a temperatura e precipitação. Nesse sentido entendeu-se necessário aplicar o Sistema B (Anexo II, DQA)

High Piezoelectric Output Voltage from Blue Fluorescent N,N-Dimethyl-4-nitroaniline Nano Crystals in Poly-L-Lactic Acid Electrospun Fibers

N,N-dimethyl-4-nitroaniline is a piezoelectric organic superplastic and superelastic charge transfer molecular crystal that crystallizes in an acentric structure. Organic mechanical flexible crystals are of great importance as they stand between soft matter and inorganic crystals. Highly aligned poly-l-lactic acid polymer microfibers with embedded N,N-dimethyl-4-nitroaniline nanocrystals are fabricated using the electrospinning technique, and their piezoelectric and optical properties are explored as hybrid systems. The composite fibers display an extraordinarily high piezoelectric output response, where for a small stress of 5.0 × 103 Nm−2, an effective piezoelectric voltage coefficient of geff = 4.1 VmN−1 is obtained, which is one of the highest among piezoelectric polymers and organic lead perovskites. Mechanically, they exhibit an average increase of 67% in the Young modulus compared to polymer microfibers alone, reaching 55 MPa, while the tensile strength reaches 2.8 MPa. Furthermore, the fibers show solid-state blue fluorescence, important for emission applications, with a long lifetime decay (147 ns) lifetime decay. The present results show that nanocrystals from small organic molecules with luminescent, elastic and piezoelectric properties form a mechanically strong hybrid functional 2-dimensional array, promising for applications in energy harvesting through the piezoelectric effect and as solid-state blue emitters.This research was funded by Fundação para a Ciência e Tecnologia through FEDER (European Fund for Regional Development)-COMPETE-QREN-EU (ref. UID/FIS/04650/2013 and UID/FIS/04650/2019) and E-Field - "Electric-Field Engineered Lattice Distortions (E-FiELD) for optoelectronic devices", ref. PTDC/NAN-MAT/0098/2020