Master of Science

thesisThe Stochastic Time-Inverted Lagrangian Transport (STILT) model is comprised of a compiled Fortran executable that carries out advection and dispersion calculations as well as a higher level code layer for simulation control and user interaction, written in the open source data analysis language R. We introduce modifications to the STILT-R codebase with the aim to improve the model's applicability to fine-scale trace gas measurement approaches. The changes facilitate placement of spatially distributed receptors and provide high level methods for single and multinode parallelism. We present a kernel density estimator to calculate influence footprints and demonstrate improvements over previous methods. This framework provides a central source repository to reduce code fragmentation between STILT user groups as well as a systematic, well-documented workflow for users. We apply the modified STILT to lightrail measurements in Salt Lake City, UT and discuss how results from our analyses can inform future fine-scale measurement approaches and modeling efforts

General Purpose Flow Visualization at the Exascale

Exascale computing, i.e., supercomputers that can perform 1018 math operations per second, provide significant opportunity for improving the computational sciences. That said, these machines can be difficult to use efficiently, due to their massive parallelism, due to the use of accelerators, and due to the diversity of accelerators used. All areas of the computational science stack need to be reconsidered to address these problems. With this dissertation, we consider flow visualization, which is critical for analyzing vector field data from simulations. We specifically consider flow visualization techniques that use particle advection, i.e., tracing particle trajectories, which presents performance and implementation challenges. The dissertation makes four primary contributions. First, it synthesizes previous work on particle advection performance and introduces a high-level analytical cost model. Second, it proposes an approach for performance portability across accelerators. Third, it studies expected speedups based on using accelerators, including the importance of factors such as duration, particle count, data set, and others. Finally, it proposes an exascale-capable particle advection system that addresses diversity in many dimensions, including accelerator type, parallelism approach, analysis use case, underlying vector field, and more

Stepping beyond perfectly mixed conditions in soil hydrological modelling using a Lagrangian approach

A recent experiment of Bowers et al. (2020) revealed that diffusive mixing of water isotopes (δ$^2$H and δ$^{18}$O) over a fully saturated soil sample of a few centimetres in length required several days to equilibrate completely. In this study, we present an approach to simulate such time-delayed diffusive mixing processes, on the pore scale, beyond instantaneously and perfectly mixed conditions. The diffusive pore mixing (DIPMI) approach is based on a Lagrangian perspective on water particles moving by diffusion over the pore space of a soil volume and carrying concentrations of solutes or isotopes. The idea of DIPMI is to account for the self-diffusion of water particles across a characteristic length scale of the pore space using pore-size-dependent diffusion coefficients. The model parameters can be derived from the soil-specific water retention curve, and no further calibration is needed. We test our DIPMI approach by simulating diffusive mixing of water isotopes over the pore space of a saturated soil volume using the experimental data of Bowers et al. (2020). Simulation results show the feasibility of the DIPMI approach for reproducing the measured mixing times and concentrations of isotopes at different tensions over the pore space. This result corroborates the finding that diffusive mixing in soils depends on the pore size distribution and the specific soil water retention properties. Additionally, we perform a virtual experiment with the DIPMI approach by simulating mixing and leaching processes of a solute in a vertical, saturated soil column and compare the results against simulations with the common perfect mixing assumption. The results of this virtual experiment reveal that the frequently observed steep rise and long tailing of breakthrough curves, which are typically associated with non-uniform transport in heterogeneous soils, may also occur in homogeneous media as a result of imperfect subscale mixing in a macroscopically homogeneous soil matrix

The impact of nanoparticle aggregation on their size exclusion during transport in porous media: One- and three-dimensional modelling investigations

Greater particle mobility in subsurface environments due to larger size, known as size exclusion, has been responsible for colloid-facilitated transport of groundwater contaminants. Although size exclusion is not expected for primary engineered nanoparticles (NP), they can grow in size due to aggregation, thereby undergoing size exclusion. To investigate this hypothesis, an accurate population balance modelling approach and other colloid transport theories, have been incorporated into a three-dimensional transport model, MT3D-USGS. Results show that incorporating aggregation into the transport model improves the predictivity of current theoretical and empirical approaches to NP deposition in porous media. Considering an artificial size-variable acceleration factor in the model, NP breakthrough curves display an earlier arrival when aggregation is included than without. Disregarding the acceleration factor, aggregation enhances NP mobility at regions close to the injection point at a field scale and causes their retention at greater distances through alteration of their diffusivities, secondary interaction-energy minima, and settling behaviour. This results in a change of residual concentration profiles from exponential for non-aggregating dispersions to non-monotonic for aggregating dispersions. Overall, aggregation, hitherto believed to hinder the migration of NP in subsurface porous media, may under certain physicochemical conditions enhance their mobilities and deliver them to further distances

The Brazilian Developments on the Regional Atmospheric Modeling System (BRAMS 5.2): An Integrated Environmental Model Tuned for Tropical Areas

We present a new version of the Brazilian developments on the Regional Atmospheric Modeling System where different previous versions for weather, chemistry and carbon cycle were unified in a single integrated software system. The new version also has a new set of state-of-the-art physical parameterizations and greater computational parallel and memory usage efficiency. Together with the description of the main features are examples of the quality of the transport scheme for scalars, radiative fluxes on surface and model simulation of rainfall systems over South America in different spatial resolutions using a scale-aware convective parameterization. Besides, the simulation of the diurnal cycle of the convection and carbon dioxide concentration over the Amazon Basin, as well as carbon dioxide fluxes from biogenic processes over a large portion of South America are shown. Atmospheric chemistry examples present model performance in simulating near-surface carbon monoxide and ozone in Amazon Basin and Rio de Janeiro megacity. For tracer transport and dispersion, it is demonstrated the model capabilities to simulate the volcanic ash 3-d redistribution associated with the eruption of a Chilean volcano. Then, the gain of computational efficiency is described with some details. BRAMS has been applied for research and operational forecasting mainly in South America. Model results from the operational weather forecast of BRAMS on 5 km grid spacing in the Center for Weather Forecasting and Climate Studies, INPE/Brazil, since 2013 are used to quantify the model skill of near surface variables and rainfall. The scores show the reliability of BRAMS for the tropical and subtropical areas of South America. Requirements for keeping this modeling system competitive regarding on its functionalities and skills are discussed. At last, we highlight the relevant contribution of this work on the building up of a South American community of model developers

pyParaOcean: A System for Visual Analysis of Ocean Data

Visual analysis is well adopted within the field of oceanography for the analysis of model simulations, detection of different phenomena and events, and tracking of dynamic processes. With increasing data sizes and the availability of multivariate dynamic data, there is a growing need for scalable and extensible tools for visualization and interactive exploration. We describe pyParaOcean, a visualization system that supports several tasks routinely used in the visual analysis of ocean data. The system is available as a plugin to Paraview and is hence able to leverage its distributed computing capabilities and its rich set of generic analysis and visualization functionalities. pyParaOcean provides modules to support different visual analysis tasks specific to ocean data, such as eddy identification and salinity movement tracking. These modules are available as Paraview filters and this seamless integration results in a system that is easy to install and use. A case study on the Bay of Bengal illustrates the utility of the system for the study of ocean phenomena and processes.Comment: 8 pages, EnvirVis202

The Brazilian developments on the Regional Atmospheric Modeling System (BRAMS 5.2): an integrated environmental model tuned for tropical areas

We present a new version of the Brazilian developments on the Regional Atmospheric Modeling System (BRAMS), in which different previous versions for weather, chemistry, and carbon cycle were unified in a single integrated modeling system software. This new version also has a new set of state-of-the-art physical parameterizations and greater computational parallel and memory usage efficiency. The description of the main model features includes several examples illustrating the quality of the transport scheme for scalars, radiative fluxes on surface, and model simulation of rainfall systems over South America at different spatial resolutions using a scale aware convective parameterization. Additionally, the simulation of the diurnal cycle of the convection and carbon dioxide concentration over the Amazon Basin, as well as carbon dioxide fluxes from biogenic processes over a large portion of South America, are shown. Atmospheric chemistry examples show the model performance in simulating near-surface carbon monoxide and ozone in the Amazon Basin and the megacity of Rio de Janeiro. For tracer transport and dispersion, the model capabilities to simulate the volcanic ash 3-D redistribution associated with the eruption of a Chilean volcano are demonstrated. The gain of computational efficiency is described in some detail. BRAMS has been applied for research and operational forecasting mainly in South America. Model results from the operational weather forecast of BRAMS on 5 km grid spacing in the Center for Weather Forecasting and Climate Studies, INPE/Brazil, since 2013 are used to quantify the model skill of near-surface variables and rainfall. The scores show the reliability of BRAMS for the tropical and subtropical areas of South America. Requirements for keeping this modeling system competitive regarding both its functionalities and skills are discussed. Finally, we highlight the relevant contribution of this work to building a South American community of model developers.CNPqFAPESPEarth System Research Laboratory at the National Oceanic and Atmospheric Administration (ESRL/NOAA), Boulder, USAInst Nacl Pesquisas Espaciais, Ctr Previsao Tempo & Estudos Climat, Cachoeira Paulista, SP, BrazilDiv Ciência da Computação, Instituto Tecnológico de Aeronáutica, São José dos Campos, SP, BrazilUniv Estadual Paulista Unesp, Fac Ciencias, Bauru, SP, BrazilCtr Meteorol Bauru IPMet, Bauru, SP, BrazilUniv Fed Sao Paulo, Dept Ciencias Ambientais, Diadema, SP, BrazilUniv Sao Paulo, Inst Astron Geofis & Ciencias Atmosfer, Sao Paulo, SP, BrazilUniv Fed Campina Grande, Dept Ciencias Atmosfer, Campina Grande, PB, BrazilEmbrapa Informat Agr, Campinas, SP, BrazilUniv Fed Sao Paulo, Inst Ciencia & Tecnol, Sao Jose Dos Campos, SP, BrazilUniv Fed Rio Grande do Norte, Dept Ciencias Atmosfer & Climat, Programa Pos Grad Ciencias Climat, Natal, RN, BrazilInst Nacl Pesquisas Espaciais, Ctr Ciencias Sistema, Sao Jose Dos Campos, SP, BrazilUniv Fed Sao Joao Del Rei, Dept Geociencias, Sao Joao Del Rei, MG, BrazilInst Nacl Pesquisas Espaciais, Lab Associado Computacao & Matemat Aplica, Sao Jose Dos Campos, BrazilUniv Evora, Inst Ciencias Agr & Ambientais Mediterr, Evora, PortugalUniv Lusofona Humanidades & Tecnol, Ctr Interdisciplinar Desenvolvimento Ambient Gest, Lisbon, PortugalUniv Fed Pelotas, Fac Meteorol, Pelotas, RS, BrazilUnive Tecnol Fed Parana, Londrina, PR, BrazilNASA, Goddard Space Flight Ctr, Univ Space Res Assoc, Goddard Earth Sci Technol & Res Global Modeling &, Greenbelt, MD USAUniv Fed Sao Paulo, Inst Ciencia & Tecnol, Sao Jose Dos Campos, SP, BrazilUniv Fed Sao Paulo, Inst Ciencia & Tecnol, Sao Jose Dos Campos, SP, BrazilCNPq: 306340/2011-9FAPESP: 2014/01563-1FAPESP: 2015/10206-0FAPESP: 2014/01564-8Web of Scienc

The Brazilian Developments On The Regional Atmospheric Modeling System (brams 5.2): An Integrated Environmental Model Tuned For Tropical Areas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)We present a new version of the Brazilian developments on the Regional Atmospheric Modeling System (BRAMS), in which different previous versions for weather, chemistry, and carbon cycle were unified in a single integrated modeling system software. This new version also has a new set of state-of-the-art physical parameterizations and greater computational parallel and memory usage efficiency. The description of the main model features includes several examples illustrating the quality of the transport scheme for scalars, radiative fluxes on surface, and model simulation of rainfall systems over South America at different spatial resolutions using a scale aware convective parameterization. Additionally, the simulation of the diurnal cycle of the convection and carbon dioxide concentration over the Amazon Basin, as well as carbon dioxide fluxes from biogenic processes over a large portion of South America, are shown. Atmospheric chemistry examples show the model performance in simulating near-surface carbon monoxide and ozone in the Amazon Basin and the megacity of Rio de Janeiro. For tracer transport and dispersion, the model capabilities to simulate the volcanic ash 3-D redistribution associated with the eruption of a Chilean volcano are demonstrated. The gain of computational efficiency is described in some detail. BRAMS has been applied for research and operational forecasting mainly in South America. Model results from the operational weather forecast of BRAMS on 5km grid spacing in the Center for Weather Forecasting and Climate Studies, INPE/Brazil, since 2013 are used to quantify the model skill of near-surface variables and rainfall. The scores show the reliability of BRAMS for the tropical and subtropical areas of South America. Requirements for keeping this modeling system competitive regarding both its functionalities and skills are discussed. Finally, we highlight the relevant contribution of this work to building a South American community of model developers. © Author(s) 2017.1011892222014/01563-1, FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo2014/01564-8, FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo2015/10206-0, FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo306340/2011-9, Conselho Nacional de Desenvolvimento Científico e TecnológicoFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq