DisPar Methods and Their Implementation on a Heterogeneous PC Cluster

Esta dissertação avalia duas áreas cruciais da simulação de advecção- difusão. A primeira parte é dedicada a estudos numéricos. Foi comprovado que existe uma relação directa entre os momentos de deslocamento de uma partícula de poluente e os erros de truncatura. Esta relação criou os fundamentos teóricos para criar uma nova família de métodos numéricos, DisPar. Foram introduzidos e avaliados três métodos. O primeiro é um método semi-Lagrangeano 2D baseado nos momentos de deslocamento de uma partícula para malhas regulares, DisPar-k. Com este método é possível controlar explicitamente o erro de truncatura desejado. O segundo método também se baseia nos momentos de deslocamento de uma partícula, sendo, contudo, desenvolvido para malhas uniformes não regulares, DisParV. Este método também apresentou uma forte robustez numérica. Ao contrário dos métodos DisPar-K e DisParV, o terceiro segue uma aproximação Eulereana com três regiões de destino da partícula. O método foi desenvolvido de forma a manter um perfil de concentração inicial homogéneo independentemente dos parâmetros usados. A comparação com o método DisPar-k em situações não lineares realçou as fortes limitações associadas aos métodos de advecção-difusão em cenários reais. A segunda parte da tese é dedicada à implementação destes métodos num Cluster de PCs heterogéneo. Para o fazer, foi desenvolvido um novo esquema de partição, AORDA. A aplicação, Scalable DisPar, foi implementada com a plataforma da Microsoft .Net, tendo sido totalmente escrita em C#. A aplicação foi testada no estuário do Tejo que se localiza perto de Lisboa, Portugal. Para superar os problemas de balanceamento de cargas provocados pelas marés, foram implementados diversos esquemas de partição: “Scatter Partitioning”, balanceamento dinâmico de cargas e uma mistura de ambos. Pelos testes elaborados, foi possível verificar que o número de máquinas vizinhas se apresentou como o mais limitativo em termos de escalabilidade, mesmo utilizando comunicações assíncronas. As ferramentas utilizadas para as comunicações foram a principal causa deste fenómeno. Aparentemente, o Microsoft .Net remoting 1.0 não funciona de forma apropriada nos ambientes de concorrência criados pelas comunicações assíncronas. Este facto não permitiu a obtenção de conclusões acerca dos níveis relativos de escalabilidade das diferentes estratégias de partição utilizadas. No entanto, é fortemente sugerido que a melhor estratégia irá ser “Scatter Partitioning” associada a balanceamento dinâmico de cargas e a comunicações assíncronas. A técnica de “Scatter Partitioning” mitiga os problemas de desbalanceamentos de cargas provocados pelas marés. Por outro lado, o balanceamento dinâmico será essencialmente activado no inicio da simulação para corrigir possíveis problemas nas previsões dos poderes de cada processador.This thesis assesses two main areas of the advection-diffusion simulation. The first part is dedicated to the numerical studies. It has been proved that there is a direct relation between pollutant particle displacement moments and truncation errors. This relation raised the theoretical foundations to create a new family of numerical methods, DisPar. Three methods have been introduced and appraised. The first is a 2D semi- Lagrangian method based on particle displacement moments for regular grids, DisPar-k. With this method one can explicitly control the desired truncation error. The second method is also based on particle displacement moments but it is targeted to regular/non-uniform grids, DisParV. The method has also shown a strong numerical capacity. Unlike DisPar-k and DisParV, the third method is a Eulerian approximation for three particle destination units. The method was developed so that an initial concentration profile will be kept homogeneous independently of the used parameters. The comparison with DisPar-k in non-linear situations has emphasized the strong shortcomings associated with numerical methods for advection-diffusion in real scenarios. The second part of the dissertation is dedicated to the implementation of these methods in a heterogeneous PC Cluster. To do so, a new partitioning method has been developed, AORDA. The application, Scalable DisPar, was implemented with the Microsoft .Net framework and was totally written in C#. The application was tested on the Tagus Estuary, near Lisbon (Portugal). To overcome the load imbalances caused by tides scatter partitioning was implemented, dynamic load balancing and a mix of both. By the tests made, it was possible to verify that the number of neighboring machines was the main factor affecting the application scalability, even with asynchronous communications. The tools used for communications mainly caused this. Microsoft .Net remoting 1.0 does not seem to properly work in environments with concurrency associated with the asynchronous communications. This did not allow taking conclusions about the relative efficiency between the partitioning strategies used. However, it is strongly suggested that the best approach will be to scatter partitioning with dynamic load balancing and with asynchronous communications. Scatter partitioning mitigates load imbalances caused by tides and dynamic load balancing is basically trigged at the begging of the simulation to correct possible problems in processor power predictions

Parallel Simulation of 3-D Flow and Transport Models within the NOWESP Project

this paper, a short overview of project 3 "Advanced Flux Modelling" in the NOWESP project of the MAST II programme is given. The computational requirements of large scale 3-D flow and transport models of the North-West European Shelf are considered. The possibilities and implications of massively parallel processors for the simulation of these models are discussed. We also present some of the results and experience obtained in parallelising the shallow water flow and transport models within the NOWESP project

Tracing Nutrients and Contaminants in Nearshore Food Web

Sewage derived organic matter from domestic and municipal wastewater, promotes enhanced secondary productivity, eutrophication and trace metal contamination, reduction in oxygen levels, and biodiversity. It poses a potential impact on human health, contamination of seafood and water and ecological disturbances in the natural aquatic ecosystem. Thus, this research examined the impact of improvement in treatment and disposal schemes employed by a municipal sewage treatment facility on a previously sewage contaminated coastal marine system. It took a critical look into the influence of the discharged of inadequately treated sewage effluent and the modern improved mitigating efforts put in place to ensure proper treatment and disposal by the municipal wastewater treatment plant on the coastal marine waters. It also investigated the influence of other potential terrestrial organic nutrients and contaminants on the coastal marine waters, the flow of energy and their fate through the natural coastal marine food web. Stable isotope analyses incorporated with mixing models, other independent chemical tracers such as (i.e. faecal sterol, fatty acid and elemental analyses) were utilised to infer change in the sewage derived organic matter dynamics of the coastal marine waters. The detected change was attributed to the modification in wastewater treatment and disposal techniques adopted by the municipal wastewater treatment plant. The differences in the carbon and nitrogen isotope ratios of Mytilus galloprovincialis (sentinel organism) were assessed in a preliminary survey to determine the tissues of choice as indicative tools for long-term ecological-based study aimed at tracing the sources and fate of sewage organic materials in the coastal marine waters. The preliminary survey aided the experimental design of the study. Isotope mass balance mixing models were fitted to quantify the contributions of land-based organic materials as part of the diet constituents to examine the influence of terrigenous materials on observed diet switching changes from sewage-derived nutrient source to marine nutrient source in Mytilus galloprovincialis, a prevalent resident marine bivalve collected at the nearshore marine waters. Biochemical compositions and elemental concentrations (independent tracers) in Mytilus galloprovincialis were analysed and used as independent indicative tools for testing the assumptions obtained from the stable isotope analysis mixing models. The tracers indicated the source of nourishment to the resident organism and provided additional insight into the organic nutrient supply and contaminant dynamics of the coastal marine waters. The independent tracers revealed that the marine particulate organic matter was main source of nourishment to the marine bivalve. The sea lion colony provided a minor contribution of faecal matter to the nearshore marine waters. The chemical tracers affirmed that the improvement in the treatment and disposal methods had a positive impact on the nearshore marine waters. Trace metal levels and human health risk assessment on the nearshore marine bivalve affirmed the safe human consumption of the nearshore marine fisheries