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

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

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

Mass movement processes in the Southwest Portuguese Continental Margin during the Late Pleistocene-Holocene : a multidisciplinary approach for volume quantification, estimation of recurrence times and hazard implications

The Alentejo Margin, in the Southwest Portuguese Continental Margin, is a very complex and dynamic geomorphological area, located near the Eurasia-Africa plate boundary and affected by the flow path of the Mediterranean Outflow Water (MOW). This margin comprises the Sines Contourite Drift (SCD), which is the most prominent depositional feature (~2311 km2, 303.9 km perimeter, 98 km length and 35 km width), emplaced in the continental slope of this margin, evolving in four main phases by the action of MOW, since the Late Pleistocene. The interaction between along-slope and downslope processes forms a mixed morphosedimentary setting, which is greatly affected by mass movement activity in the middle and lower continental slopes, during the Late Pleistocene-Holocene. This work analyses the occurrence of mass movement processes in the southwest Portuguese margin, in a total extent of ~85 km×82 km and identifies the main triggering and conditioning factors promoting slope instability during the Late Pleistocene-Holocene and assesses the morphosedimentary evolution of the Sines Contourite Drift. This study was performed through geophysical, sedimentological, physical, geochemical, and geotechnical analyses, using multibeam bathymetry, multichannel seismic and sub-bottom profiler, and gravity cores data. The Alentejo margin is an unstable area, where the presence of a contourite drift significantly contributes for slope instability in consequence of its sediment mechanical properties. The SCD hosts a cluster of dominantly small landslide scars, affecting both steep and smooth slopes. This scar concentration is mainly provided by local intrinsic conditions that favour slope instability in the area. Scars predominantly occur on slope angles steeper than 5º, however sediment properties, especially low consolidation, very low permeability, high pore-pressure, high compressibility and low shear strength greatly promote slope instability in the Alentejo Margin. The inherent instability conditions of the area are increased by frequent seismicity that promotes additional stress, leading to increased slope instability

Observations of storm morphodynamics using Coastal Lidar and Radar Imaging System (CLARIS): Importance of wave refraction and dissipation over complex surf-zone morphology at a shoreline erosional hotspot

Elevated water levels and large waves during storms cause beach erosion, overwash, and coastal flooding, particularly along barrier island coastlines. While predictions of storm tracks have greatly improved over the last decade, predictions of maximum water levels and variations in the extent of damage along a coastline need improvement. In particular, physics based models still cannot explain why some regions along a relatively straight coastline may experience significant erosion and overwash during a storm, while nearby locations remain seemingly unchanged. Correct predictions of both the timing of erosion and variations in the magnitude of erosion along the coast will be useful to both emergency managers and homeowners preparing for an approaching storm. Unfortunately, research on the impact of a storm to the beach has mainly been derived from pre and post storm surveys of beach topography and nearshore bathymetry during calm conditions. This has created a lack of data during storms from which to ground-truth model predictions and test hypotheses that explain variations in erosion along a coastline. We have developed Coastal Lidar and Radar Imaging System (CLARIS), a mobile system that combines a terrestrial scanning laser and an X-band marine radar system using precise motion and location information. CLARIS can operate during storms, measuring beach topography, nearshore bathymetry (from radar-derived wave speed measurements), surf-zone wave parameters, and maximum water levels remotely. In this dissertation, we present details on the development, design, and testing of CLARIS and then use CLARIS to observe a 10 km section of coastline in Kitty Hawk and Kill Devil Hills on the Outer Banks of North Carolina every 12 hours during a Nor\u27Easter (peak wave height in 8 m of water depth = 3.4 m). High decadal rates of shoreline change as well as heightened erosion during storms have previously been documented to occur within the field site. In addition, complex bathymetric features that traverse the surf-zone into the nearshore are present along the southern six kilometers of the field site. In addition to the CLARIS observations, we model wave propagation over the complex nearshore bathymetry for the same storm event. Data reveal that the complex nearshore bathymetry is mirrored by kilometer scale undulations in the shoreline, and that both morphologies persist during storms, contrary to common observations of shoreline and surf-zone linearization by large storm waves. We hypothesize that wave refraction over the complex nearshore bathymetry forces flow patterns which may enhance or stabilize the shoreline and surf-zone morphology during storms. In addition, our semi-daily surveys of the beach indicate that spatial and temporal patterns of erosion are strongly correlated to the steepness of the waves. Along more than half the study site, fifty percent or more of the erosion that occurred during the first 12 hours of the storm was recovered within 24 hours of the peak of the storm as waves remained large (\u3e2.5 m), but transitioned to long period swell. In addition, spatial variations in the amount of beach volume change during the building portion of the storm were strongly correlated with observed wave dissipation within the inner surf zone, as opposed to predicted inundation elevations or alongshore variations in wave height

Adaptive modelling of long-distance wave propagation and fine-scale flooding during the Tohoku tsunami

The 11 March 2011 Tohoku tsunami is simulated using the quadtree-adaptive Saint-Venant solver implemented within the Gerris Flow Solver. The spatial resolution is adapted dynamically from 250 m in flooded areas up to 250 km for the areas at rest. Wave fronts are tracked at a resolution of 1.8 km in deep water. The simulation domain extends over 73° of both latitude and longitude and covers a significant part of the north-west Pacific. The initial wave elevation is obtained from a source model derived using seismic data only. Accurate long-distance wave prediction is demonstrated through comparison with DART buoys timeseries and GLOSS tide gauges records. The model also accurately predicts fine-scale flooding compared to both satellite and survey data. Adaptive mesh refinement leads to orders-of-magnitude gains in computational efficiency compared to non-adaptive methods. The study confirms that consistent source models for tsunami initiation can be obtained from seismic data only. However, while the observed extreme wave elevations are reproduced by the model, they are located further south than in the surveyed data. Comparisons with inshore wave buoys data indicate that this may be due to an incomplete understanding of the local wave generation mechanisms

Towards basin-scale in-situ characterization of sea-ice using an Autonomous Underwater Glider

Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.This thesis presents an Autonomous Underwater Glider (AUG) architecture that is intended for basin-scale unattended survey of Arctic sea-ice. The distinguishing challenge for AUG operations in the Arctic environment is the presence of year-round sea-ice cover which prevents vehicle surfacing for localization updates and shore-side communication. Due to the high cost of operating support vessels in the Arctic, the proposed AUG architecture minimizes external infrastructure requirements to brief and infrequent satellite updates on the order of once per day. This is possible by employing onboard acoustic sensing for sea-ice observation and navigation, along with intelligent management of onboard resources. To enable unattended survey of Arctic sea-ice with an AUG, this thesis proposes a hierarchical acoustics-based sea-ice characterization scheme to perform science data collection and assess environment risk, a multi-factor terrain-aided navigation method that leverages bathymetric features and active ocean current sensing to limit localization error, and a set of energy-optimal propulsive and hotel policies that react to evolving environmental conditions to improve AUG endurance. These methods are evaluated with respect to laboratory experiments and preliminary field data, and future Arctic sea-ice survey mission concepts are discussed.Support for this research was provided through the National Science Foundation Navigating the New Arctic Grant #1839063 and the NASA PSTAR Grant #NNX16AL08G. Additionally, this research was supported by the Walter A. Rosenblith Presidential Fellowship

Quantifying submarine channel morphology and kinematics on structurally complex slopes: examples from the Niger Delta

Submarine channels form pronounced morphological features on the seafloor and play an important role in shaping the stratigraphic record. Over the last two decades, their morphology and architectural evolution have been studied in detail using a range of modern and ancient examples. While structural deformation is recognised as a major control, the temporal and spatial complexity associated with these systems means aspects of submarine channel dynamics and how their geomorphic expression translates into time-integrated sedimentary architecture, remain poorly understood. For example, structurally driven changes in slope morphology may locally enhance or diminish a channel’s ability to incise, aggrade and migrate laterally. In this thesis, I explore the sensitivity of submarine channel morphology to structural deformation and evaluate how channel-structure interactions are recorded in seismic stratigraphic architecture. I use novel seismic attribute analysis alongside concepts from landscape dynamics to provide quantitative insights into how the growth of structure on the southern Niger Delta slope has influenced submarine channel morphology and time-integrated stratigraphic architecture. From a 3D, time-migrated seismic reflection volume, I quantify a range of morphometric parameters including, channel gradient, width, depth, sinuosity, curvature, and stratigraphic mobility, on a number of modern and ancient submarine channel systems as they interact with structure. My results show that submarine channel morphology and longitudinal profile are unambiguously linked to the underlying structural template. The modern seafloor expression of submarine channels can be up to an order of magnitude higher aspect ratio and markedly more variable than their ancient, stratigraphic counterpart. Their depositional architectures are composite stratigraphic features that record the morphological response to spatial and temporal variations in structural growth rate. Based on this, three end-member styles of submarine channel architecture are recognised on structured slopes: pre-channel structural bathymetry, coeval positive relief, and coeval negative relief. This thesis quantifies how submarine channel systems integrate kinematic processes at the scale of the fundamental architectural unit, a channel element, and documents the systematic change in channel element kinematics on structured segments of the slope. My observations demonstrate the sensitivity of submarine channels to structural deformation and help us to constrain some of the most important sediment transport systems on planet Earth.Open Acces

Bedform Geometry and Bedload Sediment Flux in Coastal Wave, Current, and Combined Wave-Current Flows

Ripples and megaripples aggregate our coastlines, inlets, and rivers. This dissertation provides evidence for the contribution of small scale bedform migration to the evolution of larger coastal morphology. Using the connection between scales as a justification for continued research into the dynamics of growth and sediment flux associated with the mobility of ripples and megaripples in our coastal areas, this dissertation examines the dynamics between current dominant, wave dominant, and combined wave-current dominant bedforms on the multi-ripple and intra-ripple scales. Finally, this dissertation proposes that the bedload sediment flux is correlated with the total kinetic energy in the flow field as well as the bed shear stress. However, the results provide evidence to suggest that the kinetic energy formulation may provide higher skill than shear stress based models when detailed boundary layer measurements are unavailable. On the multi-ripple scale, bedforms are shown to have an adjustment time scale for growth or decay that is a function of the total kinetic energy in the flow. The relationship between the bedform volumetric growth or decay and the bedload sediment flux is modeled using a time varying sediment continuity analysis. Additionally, findings show that the bedload sediment transport associated with bedform migration is a function of the total kinetic energy in the flow field. The bedload sediment transport is shown to be robustly modeled using a modification of the energetics set of bedload transport equations regardless of whether the flow is current dominant, wave dominant, or combined wave-current flow, such that the structure for a combined roughness and bedload transport model is outlined supporting that the bedload sediment transport can be represented as a function of the total kinetic energy in the combined wave-current flow. The unified model may be applicable to predicting large scale coastal change without dependence on a robust estimate of the bed shear stress. On the intra-ripple scale, dynamics of bedload transport were investigated in both mean flows and oscillatory flows at the mobile sediment layer of the ripple crest. The mobile bed layer was shown to have a decay in applied stress with up to an 80% reduction in shear stress between the top of the mobile layer and the immobile layer, and a sign change of the applied shear stress at the immobile surface in oscillatory flow. At some of the smallest scales of sediment transport, findings have implications for understanding the mechanisms of bedload transport under waves and currents as well as the shear structure within the mobile layer. A momentum integral method formulated to estimate the bed/wall shear stress was validated and extended to investigate the gradients of momentum through the mobile layer as well as through separated flows and flows around complex geometries. The technique will be useful to investigations with detailed measurements or simulations of the boundary layer momentum structure