Search NASA⌕ Search

Engineering topics

Thornton, Peter

Publications and source records attributed to Thornton, Peter.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Enabling kilometer-scale E3SM land model simulation over North America: A new integrated framework solution

This study introduces a novel framework designed to enhance the performance, scalability, and portability of the kilometer-scale E3SM Land Model (km-ELM) within the E3SM modeling infrastructure. By seamlessly integrating cutting-edge data tools, we address existing challenges such as slow performance, limited scalability, and difficulties in software integration in current data-driven ELM simulation over large geographic areas. Our innovative approach leverages the KiloCraft data toolkit to generate unified inputs for simulations ranging from a single-cite case, to a 72,083-cell regional case to a continental configuration encompassing 21.6 million land grid cells at a 1 km × 1 km resolution. We conduct extensive strong- and weak-scaling experiments on three state-of-the-art supercomputers, utilizing up to 100,800 CPU cores across 2400 compute nodes to evaluate end-to-end metrics including wall-clock time, simulation-years-per-day (SYPD), initialization costs, and I/O throughput. Our results reveal the land (LND) component’s efficient scaling, demonstrating near-ideal weak scaling and strong-scaling parallel efficiencies reaching up to 87% at 50,400 cores. We confirm portability and reproducibility through bitwise-equivalent outputs across different machines using identical inputs over supported machines. Notably, at extreme scales, we identify I/O as a critical bottleneck and that leads to effective solution with the SCORPIO/ADIOS stack. Collectively, these findings validate the deployment of km-ELM at a continental scale with high parallel efficiency and provide essential guidance on configuration, decomposition, and I/O settings for optimized kilometer-scale land simulations in E3SM. This work emphasizes the innovative design and practical solutions that enhance the operational capabilities of km-ELM, focusing on software performance and scalability while leaving detailed scientific evaluations of simulated land processes for future investigations.

E3SM land model (ELM), km-ELM, scalability, perfor↗
DOE OSTI2024

Understanding and modeling current and future coastal wetland methane dynamics (Final Report)

The coastal terrestrial-aquatic interface (TAI) is a highly dynamic component of the Earth system that plays a critical role in biogeochemical cycling. Due to its dynamic nature, the processes that regulate decomposition and methane (CH 4 ) emissions are of greater significance at the TAI than in upland systems. Despite this, we have limited mechanistic understanding of how climate stressors interact to regulate the electron acceptors and donors that determine decomposition pathways within TAIs, including the generation of hot spots and hot moments. Accurately modeling these processes is critical for incorporating the coastal TAI into Earth systems models, such as DOE’s E3SM. With previous DOE support, we adapted an aerobic terrestrial representation of decomposition using PFLOTRAN, a reactive flow and transport model, and added anerobic decomposition pathways, salinity, and oxygen (O 2 ) that fluctuates independently of water table level. However, because this model (PFLOTRAN TAI ) is based on decomposition rates and organic matter carbon to nitrogen ratios from terrestrial systems, its performance in TAI systems is currently limited by the lack of empirical data to properly parameterize variables. In addition, while PFLOTRAN TAI can simulate movement of O 2 into sediments, it is not currently capable of tracking the movement of CH 4 gas through plant tissues due to both current model structure and lack of available data. Our overall objective of the project was the increase our mechanistic understanding of CH 4 dynamics in response to environmental change, such that we can improve the representation of these dynamics in PFLOTRAN. We installed automated flux chambers in a new field-scale active soil warming experiment and set up marsh organs (mesocosms) to test effects of warming, flooding, and salinity. This resulted in a new dataset consisting of chamber-level CH 4 flux measurements across multiple sites, ecological conditions, and timeframes, as well as corresponding measurements on porewater chemistry, soil carbon quality, plant biomass, and redox reaction rates. Using these data, we improved PFLOTRAN TAI to more accurately model CH 4 dynamics and successfully tested our hypotheses. This grant contributed to the professional development of 3 postdocs, 4 undergraduate interns, 4 teacher interns, 17 technicians, and 15 participatory scientists. The automated chamber technology designed for this grant has also been shared with multiple new projects.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Data for: A Synoptic System for Capturing Ecosystem Control Points Across Terrestrial-Aquatic Interfaces

The investigation of how climate change and water level fluctuations impact variable and interconnected ecosystems, like the interfaces between terrestrial and aquatic environments, requires the collection and integration of many data types. We describe an integrative and autonomous environmental monitoring approach that uses environmental sensors and data loggers to monitor surface water, groundwater, soil, and vegetation changes and generate essential data for predictive models. We established the network at seven sites along the Chesapeake Bay and Lake Erie coastlines, including a large-scale flood manipulation experiment, collectively generating over three million observations per month. Such sensor networks hold great promise for tracking and comprehending environmental changes where land and water intersect. The sensor system and overall approach to sensor management that we have designed is intended to be widely accessible for research teams spanning in size from an individual investigator to large multi-institution projects. This dataset shows example data generated by the sensor network described above. Data output for data loggers connected to groundwater water quality sondes measuring dissolved oxygen, pH, oxidative redox potential (ORP), groundwater elevation, groundwater salinity and temperature, and groundwater elevation; replicate soil moisture and conductivity probes installed at 10 and 30 cm below the ground surface; rainfall and solar radiation; and mean sap flow from 8 replicate probes. Sensors are installed at upland forest (UP), wetlands (W), and transitional locations between these ecosystems (TR). Example datasets are from Goodwin Islands in the Chesapeake Bay and Portage River along the Lake Erie coastline.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

An ultrahigh-resolution E3SM land model simulation framework and its first application to the Seward Peninsula in Alaska

The availability of supercomputers and state-of-science datasets has made it possible to conduct large-scale land simulations at an ultrahigh-resolution. This study reported a computational framework for land surface simulation using the E3SM land model (ELM) at an unprecedented resolution (1 km x 1 km gridcell). The ultrahigh-resolution ELM (uELM) simulation framework includes three parts: (1) high-resolution atmospheric forcing and surface properties dataset generation, (2) massive gridcell-based simulation, and (3) large-scale simulation results analysis. Additionally, we implemented the uELM simulation framework and completed the first 1 km x 1 km terrestrial ecosystem simulation (from 1850 to 2014) over the Seward Peninsula in Alaska (78,000 km 2 ). The experiment contained two phases: a spin-up simulation and a transient simulation, and required five weeks of calculations using 320 cores in a 44-node Linux HPC computer. It created approximately 1.3 TB of data from the transient simulation alone (1850 - present). We selected sample results (monthly and daily simulation outputs) to illustrate the temporal and spatial variations of several variables in high-latitude Arctic ecosystems’ water, energy, and carbon cycles. At last, we summarized the lessons learned and proposed new developments for full-scale uELM simulations over the entire North American continent (approximately 22,000,000 km 2 ).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Improving the Estimation of the Atmospheric Water Vapor Pressure Using Interpretable Long Short-Term Memory Networks: Dataset, Python code, and trained models

Atmospheric water vapor pressure is an essential meteorological control on land surface and hydrologic processes. It is not as frequently observed as other meteorologic conditions, but often inferred through the August–Roche–Magnus formula by simply assuming dew point and daily minimum temperatures are equivalent or by empirically correlating the two temperatures using an aridity correction. The performance of both methods varies considerably across different regions and during different time periods; obtaining consistently accurate estimates across space and time remains a great challenge. We applied an interpretable Long Short-Term Memory (iLSTM) network conditioned on static, location specific attributes to estimate daily vapor pressure for 83 FLUXNET sites in the United States and Canada. This data package includes all raw data of the 83 FLUXNET sites, input data for model training/validation/test, trained models and results, and python codes for the manuscript "Improving the Estimation of the Atmospheric Water Vapor Pressure Using an Interpretable Long Short-term Memory Network". Specifically, it consists of five parts. - First, "1_Daymet_data_83sites.zip" includes raw data downloaded from Daymet for the 83 sites used in the paper according to their longitude and latitude, in which vapor pressure is used. It also includes a pre-processed CSV data file combining all data from the 83 sites which is specifically used for the paper. - Second, "2_Fluxnet2015_data_83sites.zip" includes raw half hourly data of the 83 sites downloaded from FLUXNET2015 data portal, pre-processed daily data of the 83 sites, a CSV file including combined pre-processed daily data of the 83 sites, and a CSV file including the information (site ID, site name, latitude, longitude, data available period) of the 83 sites. - Third, "3_MODIS_LAI_data_83sites_raw.zip" includes raw leaf area index (LAI) data downloaded from the AppEEARs data portal. - Fourth, "4_Scripts.zip" includes all scripts related to model training and post-processing of a trained model, and a jupyter notebook showing an example for model post-processing. Two typo errors in files titled "run2get_args.py" and "postprocess.py" were corrected on March 27, 2024 to avoid confusions. - Finally, "Trained_models_and_results.zip" includes three folders and three files with suffix ".npy", and each folder corresponds to one file with suffix ".npy" with the same title. Each of the three folders include all trained models associated with one iLSTM model configuration (35 models for each configuration, details are described in the paper). Each file with suffix ".npy" includes the post-processed results of the corresponding 35 models under one iLSTM model configuration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Towards Ultra-high-resolution E3SM Land Modeling on Exascale Computers

Here we present an ultra-high-resolution E3SM land model (uELM) for high-fidelity land simulations targeting new Exascale computers. After considering modeling infrastructure compatibility and ELM software features, we designed a parallel model for the uELM development targeting hybrid architectures of new US Exascale computers. We also described a function unit test framework to expedite the piece-wise code porting (with compiler directives), verification, and global variable management. Furthermore, in this study, we report an early uELM model development using OpenACC within a function unit test framework on a pre-Exascale computer, demonstrate the performance of a uLEM submodel with a 3.0-time speedup, and summarize the code porting experience regarding global variable handling, deepcopy, memory reduction, and parallel loop reconstruction.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Soil-related developments of the Biome-BGCMuSo v6.2 terrestrial ecosystem model

Terrestrial biogeochemical models are essential tools to quantify climate–carbon cycle feedback and plant–soil relations from local to global scale. In this study, a theoretical basis is provided for the latest version of the Biome-BGCMuSo biogeochemical model (version 6.2). Biome-BGCMuSo is a branch of the original Biome-BGC model with a large number of developments and structural changes. Earlier model versions performed poorly in terms of soil water content (SWC) dynamics in different environments. Moreover, lack of detailed nitrogen cycle representation was a major limitation of the model. Since problems associated with these internal drivers might influence the final results and parameter estimation, additional structural improvements were necessary. In this paper the improved soil hydrology as well as the soil carbon and nitrogen cycle calculation methods are described in detail. Capabilities of the Biome-BGCMuSo v6.2 model are demonstrated via case studies focusing on soil hydrology, soil nitrogen cycle, and soil organic carbon content estimation. Soil-hydrology-related results are compared to observation data from an experimental lysimeter station. The results indicate improved performance for Biome-BGCMuSo v6.2 compared to v4.0 (explained variance increased from 0.121 to 0.8 for SWC and from 0.084 to 0.46 for soil evaporation; bias changed from -0.047 to -0.007 m 3 m -3 for SWC and from -0.68 to -0.2 mm d -1 for soil evaporation). Simulations related to nitrogen balance and soil CO 2 efflux were evaluated based on observations made in a long-term field experiment under crop rotation. The results indicated that the model is able to provide realistic nitrate content estimation for the topsoil. Soil nitrous oxide (N 2 O) efflux and soil respiration simulations were also realistic, with overall correspondence with the observations (for the N 2 O efflux simulation bias was between -0.13 and -0.1 mgNm -2 d -1 , and normalized root mean squared error (NRMSE) was 32.4 %–37.6 %; for CO 2 efflux simulations bias was 0.04–0.17 gCm -2 d -1 , while NRMSE was 34.1 %–40.1 %). Sensitivity analysis and optimization of the decomposition scheme are presented to support practical application of the model. The improved version of Biome-BGCMuSo has the ability to provide more realistic soil hydrology representation as well as nitrification and denitrification process estimation, which represents a major milestone.

58 GEOSCIENCES↗
DOE OSTI2021

Mapping classes of carbon

With rising fossil fuel consumption and ongoing land cover change, humanity is burning through its remaining carbon budget. Here, recent work puts a ‘Do not disturb’ sign on biospheric carbon we can’t afford to lose.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Supporting data for climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics

This data supports the conclusions found in climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics. Included here are (i) the binarized geolocation vectors used for exhaustive vector comparisons, (ii) the resulting climatic networks, (iii) the results of applying Markov clustering to the climatic networks, and (iv) the results of applying Correlation-of-Correlations (cor-cor) to the climatic networks. The set of binarized geolocation vectors that are used as inputs for the Combinatorial Metrics library (CoMet) are of the form comet-UUUUUxVVVVV-XXXX-YYYY.shuffled.tped where UUUUU is the number of vectors, VVVVV is the length of each vector, XXXX is the starting year, and YYYY is the ending year. Each line corresponds to a geolocation vector of binary elements A (i.e., 0) and T (i.e., 1). The set of climatic networks that are used for downstream network analysis are of the form network-U-way-XXXX-YYYY.parsed.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, and YYYY is the ending year. Each line corresponds to an edge linking two geolocations (defined by latitude and longitude) with its corresponding edge weight (i.e., DUO score). The set of cluster results are of the form clusters-U-way-XXXX-YYYY-thresh-VVVV-inflation-WWW.clustered.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, YYYY is the ending year, VVVV is the similarity threshold, and WWW is the Markov clustering inflation rate. Each line corresponds to a single cluster and is composed of a number of corresponding geolocations (defined by latitude and longitude). The set of cor-cor results are of the form corcor-U-way-XXXX-YYYY.cumulative.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, and YYYY is the ending year. Each line corresponds to a single geolocation with it's corresponding cor-cor value.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Dynamics of Fungal and Bacterial Biomass Carbon in Natural Ecosystems: Site-level Applications of the CLM-Microbe Model

Explicitly representing microbial processes has been recognized as a key improvement to Earth system models for the realistic projections of soil carbon (C) and climate dynamics. The CLM-Microbe model builds upon the CLM4.5 and explicitly represents two major soil microbial groups, fungi and bacteria. Based on the compiled time-series data of fungal (FBC) and bacterial (BBC) biomass C from nine biomes, we parameterized and validated the CLM-Microbe model, and further conducted sensitivity analysis and uncertainty analysis for simulating C cycling. The model performance was evaluated with mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R2) for relative change in FBC and BBC. The CLM-Microbe model is able to reasonably capture the seasonal dynamics of FBC and BBC across biomes, particularly for tropical/subtropical forest, temperate broadleaf forest, and grassland, with MAE < 0.49 for FBC and <0.36 for BBC and RMSE <0.52 FBC and <0.39 for BBC, while R2 values are relatively smaller in some biomes (e.g., shrub) due to small sample sizes. We found good consistencies between simulated and observed FBC (R 2 =0.70, P<0.001) and BBC (R 2 =0.26, P<0.05) on average across biomes, but the model is not able to fully capture the large variation in observed FBC and BBC. Sensitivity analysis shows the most critical parameters are turnover rate, carbon-to-nitrogen ratio of fungi and bacteria, and microbial assimilation efficiency. This study confirms that the explicit representation of soil microbial mechanisms enhances model performance in simulating C variables such as heterotrophic respiration and soil organic C density. The further application of the CLM-Microbe model would deepen our understanding of microbial contributions to the global C cycle.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Coastal Wetland Carbon Sequestration in a Warmer Climate (Final Report)

Coastal wetlands are global hotspots of carbon storage and locations where carbon and nitrogen cycles have a disproportionately large impact on land, water, and air in comparison to the area they occupy. The extremely high rates of carbon sequestration in these systems are the result of complex feedbacks between vegetation and the physical environment. The plant and microbial interactions that drive these feedbacks are absent in ecosystem- and global-scale Earth System models. The goal of this proposal was to address the uncertain response of the coastal carbon sink to climate change, a critical knowledge gap in coastal carbon research and a significant barrier to incorporating coastal wetlands into Earth System Models. The Salt Marsh Accretion Response to Temperature eXperiment (SMARTX) was designed to understand the ecosystem-scale consequences of warming and elevated CO₂ (eCO₂) in tidal wetlands at the coastal terrestrial-aquatic interface. We successfully designed and built a novel whole-ecosystem warming and eCO₂ experiment in a coastal wetland. The gradient design of the warming treatments (+0, +1.7, +3.4, +5.1 ⁰C) allowed us to discover unexpected non-linear and non-additive responses arising from plant-microbe interactions. We concluded that these non-linear responses to warming were the result of plants and microbes responding to temperature at different thresholds, with important consequences for forecasting terrestrial ecosystem responses to climate change and understanding global trends.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Characteristics of human-climate feedbacks differ at different radiative forcing levels

The human and Earth systems are intricately linked: climate influences agricultural production, renewable energy potential, and water availability, for example, while anthropogenic emissions from industry and land use change alter temperature and precipitation. Such feedbacks have the potential to significantly alter future climate change. These feedbacks may also exert significant changes on 21st-century energy, agriculture, land use and carbon cycle projections, but little is known about their possible magnitudes, or about regional and sector dynamics under different forcing scenarios. Here we use an integrated Earth System Model (ESM) featuring bidirectional information exchange between an economically-oriented integrated assessment model and the ESM to examine how human-natural feedbacks operate under high and medium radiative forcing (RF) scenarios. Specifically, we examine the effect of changing land productivity on human systems, and the effect of changing land use/land cover and CO2 emissions on the Earth system. We find that the effect of coupling differs across radiative forcing levels and across regions, due to differences in the climate signal, human responses to those signals, and regional characteristics. In particular, we find reductions in cropland area due to feedbacks in both the medium and high RF scenarios. In the medium RF scenario, these reductions result in increased area for bioenergy and afforestation and reduced energy system CO2 emissions, as the carbon price in this scenario incentivizes low carbon energy sources and terrestrial carbon storage; these incentives are absent in the high RF scenario. These differences are key to understanding the possible future evolution pathways of the integrated Earth system in response to 21st century climate change. Additional models and hypothesis testing are needed to determine exactly when and how bidirectional feedbacks between human and Earth systems should be considered in future assessments.

Calvin, Katherine V.↗