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

A Survey of Ocean Simulation and Rendering Techniques in Computer Graphics

This paper presents a survey of ocean simulation and rendering methods in computer graphics. To model and animate the ocean's surface, these methods mainly rely on two main approaches: on the one hand, those which approximate ocean dynamics with parametric, spectral or hybrid models and use empirical laws from oceanographic research. We will see that this type of methods essentially allows the simulation of ocean scenes in the deep water domain, without breaking waves. On the other hand, physically-based methods use Navier-Stokes Equations (NSE) to represent breaking waves and more generally ocean surface near the shore. We also describe ocean rendering methods in computer graphics, with a special interest in the simulation of phenomena such as foam and spray, and light's interaction with the ocean surface

A fully coupled 3D wave-current interaction model on unstructured grids

We present a new modeling system for wave-current interaction based on unstructured grids and thus suitable for very large-scale high-resolution multiscale studies. The coupling between the 3D current model (SELFE) and the 3rd generation spectral wave model (WWM-II) is done at the source code level and the two models share same sub-domains in the parallel MPI implementation in order to ensure parallel efficiency and avoid interpolation. We demonstrate the accuracy, efficiency, stability and robustness of the coupled SELFE-WWM-II model with a suite of progressively challenging benchmarks with analytical solution, laboratory data, and field data. The coupled model is shown to be able to capture important physics of the wave-current interaction under very different scales and environmental conditions with excellent convergence properties even in complicated test cases. The challenges in simulating the 3D wave-induced effects are highlighted as well, where more research is warranted

A 3D unstructured grid nearshore hydrodynamic model based on the vortex force formalism

Acknowledgments This work was partly supported by joint Engineering and Physical Science Research Council (EPSRC) UK and Technology Foundation STW Netherlands funded SINBAD (EP/J005541/1) project. P. Zheng was supported by the China Scholarship Council during his four-year PhD study at the University of Liverpool. We would like to thank Prof. C.S. Chen of the University of Massachusetts-Dartmouth for providing the source code of FVCOM and also the SWAN developers for developing and providing this open source code. We would also like to thank the staff and personnel involved in collecting and maintaining the DUCK’94 experiment dataset and the anonymous reviewers for their constructive comments and suggestions. Computational support was provided by the Chadwick High Performance Computer at University of Liverpool and also the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (EP/K000225/1).Peer reviewedPublisher PD

High-performance tsunami modelling with modern GPU technology

PhD ThesisEarthquake-induced tsunamis commonly propagate in the deep ocean as long waves and develop into sharp-fronted surges moving rapidly coastward, which may be effectively simulated by hydrodynamic models solving the nonlinear shallow water equations (SWEs). Tsunamis can cause substantial economic and human losses, which could be mitigated through early warning systems given efficient and accurate modelling. Most existing tsunami models require long simulation times for real-world applications. This thesis presents a graphics processing unit (GPU) accelerated finite volume hydrodynamic model using the compute unified device architecture (CUDA) for computationally efficient tsunami simulations. Compared with a standard PC, the model is able to reduce run-time by a factor of > 40. The validated model is used to reproduce the 2011 Japan tsunami. Two source models were tested, one based on tsunami waveform inversion and another using deep-ocean tsunameters. Vertical sea surface displacement is computed by the Okada model, assuming instantaneous sea-floor deformation. Both source models can reproduce the wave propagation at offshore and nearshore gauges, but the tsunameter-based model better simulates the first wave amplitude. Effects of grid resolutions between 450-3600 m, slope limiters, and numerical accuracy are also investigated for the simulation of the 2011 Japan tsunami. Grid resolutions of 1-2 km perform well with a proper limiter; the Sweby limiter is optimal for coarser resolutions, recovers wave peaks better than minmod, and is more numerically stable than Superbee. One hour of tsunami propagation can be predicted in 50 times on a regular low-cost PC-hosted GPU, compared to a single CPU. For 450 m resolution on a larger-memory server-hosted GPU, performance increased by ~70 times. Finally, two adaptive mesh refinement (AMR) techniques including simplified dynamic adaptive grids on CPU and a static adaptive grid on GPU are introduced to provide multi-scale simulations. Both can reduce run-time by ~3 times while maintaining acceptable accuracy. The proposed computationally-efficient tsunami model is expected to provide a new practical tool for tsunami modelling for different purposes, including real-time warning, evacuation planning, risk management and city planning

Parallel implementation of the SHYFEM (System of HydrodYnamic Finite Element Modules) model

This paper presents the message passing interface (MPI)-based parallelization of the three-dimensional hydrodynamic model SHYFEM (System of HydrodYnamic Finite Element Modules). The original sequential version of the code was parallelized in order to reduce the execution time of high-resolution configurations using state-of-the-art high-performance computing (HPC) systems. A distributed memory approach was used, based on the MPI. Optimized numerical libraries were used to partition the unstructured grid (with a focus on load balancing) and to solve the sparse linear system of equations in parallel in the case of semi-to-fully implicit time stepping. The parallel implementation of the model was validated by comparing the outputs with those obtained from the sequential version. The performance assessment demonstrates a good level of scalability with a realistic configuration used as benchmark

Coastal ocean forecasting with an unstructured grid model in the southern Adriatic and northern Ionian seas

Abstract. SANIFS (Southern Adriatic Northern Ionian coastal Forecasting System) is a coastal-ocean operational system based on the unstructured grid finite-element three-dimensional hydrodynamic SHYFEM model, providing short-term forecasts. The operational chain is based on a downscaling approach starting from the large-scale system for the entire Mediterranean Basin (MFS, Mediterranean Forecasting System), which provides initial and boundary condition fields to the nested system. The model is configured to provide hydrodynamics and active tracer forecasts both in open ocean and coastal waters of southeastern Italy using a variable horizontal resolution from the open sea (3–4 km) to coastal areas (50–500 m). Given that the coastal fields are driven by a combination of both local (also known as coastal) and deep-ocean forcings propagating along the shelf, the performance of SANIFS was verified both in forecast and simulation mode, first (i) on the large and shelf-coastal scales by comparing with a large-scale survey CTD (conductivity–temperature–depth) in the Gulf of Taranto and then (ii) on the coastal-harbour scale (Mar Grande of Taranto) by comparison with CTD, ADCP (acoustic doppler current profiler) and tide gauge data. Sensitivity tests were performed on initialization conditions (mainly focused on spin-up procedures) and on surface boundary conditions by assessing the reliability of two alternative datasets at different horizontal resolution (12.5 and 6.5 km). The SANIFS forecasts at a lead time of 1 day were compared with the MFS forecasts, highlighting that SANIFS is able to retain the large-scale dynamics of MFS. The large-scale dynamics of MFS are correctly propagated to the shelf-coastal scale, improving the forecast accuracy (+17 % for temperature and +6 % for salinity compared to MFS). Moreover, the added value of SANIFS was assessed on the coastal-harbour scale, which is not covered by the coarse resolution of MFS, where the fields forecasted by SANIFS reproduced the observations well (temperature RMSE equal to 0.11 °C). Furthermore, SANIFS simulations were compared with hourly time series of temperature, sea level and velocity measured on the coastal-harbour scale, showing a good agreement. Simulations in the Gulf of Taranto described a circulation mainly characterized by an anticyclonic gyre with the presence of cyclonic vortexes in shelf-coastal areas. A surface water inflow from the open sea to Mar Grande characterizes the coastal-harbour scale

Online proceedings of the papers submitted to the 2020 TELEMAC-MASCARET User Conference October 2020

Hydrodynamic

Modelling scour around submerged objects with TELEMAC3D - GAIA

Hydrodynamic

The future of coastal and estuarine modeling: Findings from a workshop

This paper summarizes the findings of a workshop convened in the United States in 2018 to discuss methods in coastal and estuarine modeling and to propose key areas of research and development needed to improve their accuracy and reliability. The focus of this paper is on physical processes, and we provide an overview of the current state-of-the-art based on presentations and discussions at the meeting, which revolved around the four primary themes of parameterizations, numerical methods, in-situ and remote-sensing measurements,and high-performance computing. A primary outcome of the workshop was agreement on the need to reduce subjectivity and improve reproducibility in modeling of physical processes in the coastal ocean. Reduction of subjectivity can be accomplished through development of standards for benchmarks, grid generation, and validation, and reproducibility can be improved through development of standards for input/output, coupling and model nesting, and reporting. Subjectivity can also be reduced through more engagement with the applied mathematics and computer science communities to develop methods for robust parameter estimation anduncertainty quantification. Such engagement could be encouraged through more collaboration between thef orward and inverse modeling communities and integration of more applied math and computer science into oceanography curricula. Another outcome of the workshop was agreement on the need to develop high-resolution models that scale on advanced HPC systems to resolve, rather than parameterize, processes with horizontal scales that range between the depth and the internal Rossby deformation scale. Unsurprisingly,more research is needed on parameterizations of processes at scales smaller than the depth, includingparameterizations for drag (including bottom roughness, bedforms, vegetation and corals), wave breaking, and air–sea interactions under strong wind conditions. Other topics that require significantly more work to better parameterize include nearshore wave modeling, sediment transport modeling, and morphodynamics. Finally, it was agreed that coastal models should be considered as key infrastructure needed to support research, just like laboratory facilities, field instrumentation, and research vessels. This will require a shift in the way proposals related to coastal ocean modeling are reviewed and funded