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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,693 records · Page 94

Managing a Cray supercomputer as a git branch

Summary Modern software engineering/DevOps techniques applied to Cray XC Series systems management enable higher fidelity translation from test to production environments, reduce administration costs by avoiding duplicate efforts, and increase reliability. This can be done by using a git repository to track and manage all system configurations on the SMW(s) (System Management Workstation) and then adapt a gitflow‐like development methodology. Using git improves change management with peer review of changes, identification of who made a change, knowing why a change was made, facilitating easier reversion of bad changes, and enables a workflow using the ideas from gitflow with individual branches for preparing, maintaining, and recording releases. Using branches enables multiple contributors to work on different types of changes without getting unexpected changes from another feature area. We will describe a process similar to that used at NERSC (National Energy Research Scientific Computing Center) to extract/abstract configuration data, manage it using git, and then re‐apply changes to the SMW(s).

Jacobsen, Douglas M.↗

Providing performance portable numerics for Intel GPUs

Summary With discrete Intel GPUs entering the high‐performance computing landscape, there is an urgent need for production‐ready software stacks for these platforms. In this article, we report how we enable the Ginkgo math library to execute on Intel GPUs by developing a kernel backed based on the DPC++ programming environment. We discuss conceptual differences between the CUDA and DPC++ programming models and describe workflows for simplified code conversion. We evaluate the performance of basic and advanced sparse linear algebra routines available in Ginkgo's DPC++ backend in the hardware‐specific performance bounds and compare against routines providing the same functionality that ship with Intel's oneMKL vendor library.

97 MATHEMATICS AND COMPUTING↗

Real‐time XFEL data analysis at SLAC and NERSC: A trial run of nascent exascale experimental data analysis

X‐ray scattering experiments using free electron lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID‐19 viral proteins). XFEL experiments are a challenge to computing in two ways: (i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; (ii) data‐collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min—sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS‐NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Completing data analysis within 10 min is a first for XFEL experiments and an important milestone if we are to keep up with data‐collection trends.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

SOMA: Observability, monitoring, and in situ analytics for exascale applications

With the rise of exascale systems and large, data-centric workflows, the need to observe and analyze high performance computing (HPC) applications during their execution is becoming increasingly important. HPC applications are typically not designed with online monitoring in mind, therefore, the observability challenge lies in being able to access and analyze interesting events with low overhead while seamlessly integrating such capabilities into existing and new applications. We explore how our service-based observation, monitoring, and analytics (SOMA) approach to collecting and aggregating both application-specific diagnostic data and performance data addresses these needs. Furthermore, we present our SOMA framework and demonstrate its viability with LULESH, a hydrodynamics proxy application. Then we focus on Astaroth, a multi-GPU library for stencil computations, highlighting the integration of the TAU and APEX performance tools and SOMA for application and performance data monitoring.

97 MATHEMATICS AND COMPUTING↗

17 O NMR Spectroscopy Reveals CO 2 Speciation and Dynamics in Hydroxide-Based Carbon Capture Materials

Carbon dioxide capture technologies are set to play a vital role in mitigating the current climate crisis. Solid-state 17 O NMR spectroscopy can provide key mechanistic insights that are crucial to effective sorbent development. In this work, we present the fundamental aspects and complexities for the study of hydroxide-based CO 2 capture systems by 17 O NMR. We perform static density functional theory (DFT) NMR calculations to assign peaks for general hydroxide CO 2 capture products, finding that 17 O NMR can readily distinguish bicarbonate, carbonate and water species. However, in application to CO 2 binding in two test case hydroxide-functionalised metal-organic frameworks (MOFs) – MFU-4l and KHCO 3 -cyclodextrin-MOF, we find that a dynamic treatment is necessary to obtain agreement between computational and experimental spectra. We therefore introduce a workflow that leverages machine-learning force fields to capture dynamics across multiple chemical exchange regimes, providing a significant improvement on static DFT predictions. In MFU-4l, we parameterise a two-component dynamic motion of the bicarbonate motif involving a rapid carbonyl seesaw motion and intermediate hydroxyl proton hopping. For KHCO 3 -CD-MOF, we combined experimental and modelling approaches to propose a new mixed carbonate-bicarbonate binding mechanism and thus, we open new avenues for the study and modelling of hydroxide-based CO 2 capture materials by 17 O NMR.

NMR spectroscopy↗

Using KBase to Assemble and Annotate Prokaryotic Genomes

The DOE Systems Biology Knowledgebase is an open–access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execute, collaborate on, and share reproducible analyses of their biological data in the context of public data and private collaborator data. For microbiologists researching prokaryotes, KBase offers analysis tools for performing quality control and assessment of Next–Generation Sequencing reads, de novo assembly, genome annotation, and tools for analyzing structural and functional features of genomes. As a result, this unit demonstrates an example workflow for taking a comparative and iterative approach to assembly and annotation of prokaryotic genomes using KBase that can be used by microbiologists seeking to perform isolate analysis in a rapid and reproducible fashion.

59 BASIC BIOLOGICAL SCIENCES↗

Simulation-based characterization of the variability of earthquake risk to buildings in the near-field

Recent advancements in high performance computing platforms and computational workflow for regional-scale simulations are enabling unprecedented modeling of fault-to-structure earthquake processes. Regional simulations resolving ground motions at frequencies relevant to engineered systems are becoming computationally viable and provide a new capability to improve understanding of the geographical distribution and intensity of risk to buildings and critical infrastructure. As computational capabilities advance, it is essential to move beyond illustrative single rupture realizations for scenario earthquake events towards the development of a full suite of rupture realizations that appropriately characterize the range of risk to building systems. The work described in this article investigates the application of a suite of fault rupture realizations with the objective of assessing near-fault, site-specific seismic demand variability for building structures. A representative high-performance regional-scale computational model is utilized to execute ground motion and building response simulations based on 18 kinematic rupture realizations of an M7 strike-slip scenario earthquake. The fault rupture models for the scenario earthquake are created by systematically perturbing the hypocenter location and stochastically generating rupture parameters (slip, rise time, rake angle) to represent a breadth of ground motion intensities resulting from the spatial and temporal variabilities of an earthquake rupture process. The resulting seismic demand variability for three-story (short period) and forty-story (long period) steel moment-resisting frame buildings is characterized in terms of the median and distribution of peak inter-story drift ratio for a range of near-fault sites. The full suite of 18 fault rupture realizations and approximately 280,000 nonlinear dynamic building simulations indicate that the three-story building undergoes higher median seismic demand and significantly greater variability of demand at a given site than the forty-story building, which has important implications for the level of certainty in predicting building performance during an earthquake. The simulations performed provide deeper insight into the relationship between fault rupture parameterization and building response, which is essential information for developing a representative suite of rupture realizations for specific earthquake scenarios.

58 GEOSCIENCES↗

Estimating active layer thickness and volumetric water content from ground penetrating radar measurements in Barrow, Alaska

Ground penetrating radar (GPR) has emerged as an effective tool for estimating active layer thickness (ALT) and volumetric water content (VWC) within the active layer. In August 2013, we conducted a series of GPR and probing surveys using a 500 MHz antenna and metallic probe around Barrow, Alaska. Here, we collected about 15 km of GPR data and 1.5 km of probing data. We describe the GPR data processing workflow from raw GPR data to the estimated ALT and VWC. We then include the corresponding uncertainties for each measured and estimated parameter. The estimated average GPR-derived ALT was 41 cm, with a standard deviation of 9 cm. The average probed ALT was 40 cm, with a standard deviation of 12 cm. The average GPR-derived VWC was 0.65, with a standard deviation of 0.14.

58 GEOSCIENCES↗

Leveraging operational information from wastewater injection wells to evaluate CO 2 injection performance for carbon storage applications in the Appalachian Basin

Abstract Geologic parameters, geophysical logging, injection testing, and operational metrics from wastewater injection wells were integrated to develop a preliminary design of a carbon storage facility in the Appalachian Basin. A scattered group of 10–20 commercial wastewater injection wells dispose off produced water from oil and gas wells in the region, utilizing a sequence of stacked deep saline formations for injection zones. These wastewater injection wells provide practical benchmarks for understanding the feasibility of carbon dioxide (CO 2 ) storage. Geologic models were developed based on characterization data from the wastewater injection wells. Reservoir simulations were calibrated according to injection testing and operational data from the wastewater injection wells. Long‐term operational data on injection flow rates and pressures measured in the wastewater injection wells were especially useful to evaluate the performance of carbon storage applications. The simulations were used to estimate injection pressures, radius of CO 2 saturation, and pressure response for industrial scale CO 2 storage applications. Results were also used to provide a design basis in terms of number of injection wells, well spacing, area of review, injection system components, monitoring plan, and CO 2 pipeline distribution system. The analysis demonstrates that there is sufficient injectivity in the deep saline formations in the west‐central Appalachian Basin to store commercial volumes of anthropogenic CO 2 . The geologic system appears suitable for supporting CO 2 injection rates of 0.5–1.0 million metric tons per year at injection pressures below formation fracture pressure in a single well. The long‐term operational data of wastewater injection wells within the study area suggested a lower permeability‐thickness values than indicated by initial reservoir tests. A workflow for developing realistic permeability values for input into reservoir simulations is presented. © 2020 Society of Chemical Industry and John Wiley & Sons, Ltd.

Valluri, Manoj↗

Quantitative interpretation of time-lapse seismic data at Farnsworth field unit: Rock physics modeling, and calibration of simulated time-lapse velocity responses

Here, this study investigates the contribution of fluid saturation variation to the time-lapse velocity response by performing fluid substitution modeling. The methodology is exemplified by the time-lapse seismic monitoring of carbon dioxide at Farnsworth field unit (FWU). In order to evaluate the fluid distribution in a matured oil reservoir, the Southwest Regional Partnership (SWP) acquired multiple vertical seismic profile (VSP) surveys at different times during the CO 2 –water alternatinggas (WAG) injection period. In this work, we present a thorough methodology for computing the elastic response of the saturated rock for different fluid saturations using a site-specific petro-elastic model (PEM). The output from the PEM was combined with results from a fluid compositional model to compute the seismic velocities at times corresponding to each VSP survey. To produce a calibrated simulated response, the measured time-lapse seismic velocities were integrated into the numerical simulation model. The mismatches between the predicted and measured time-lapse velocities were minimized through an iterative calibration process using a trained artificial neural network proxy (ANN) coupled with a particle swarm optimizer (PSO). Our study indicates that the hybrid optimization workflow can effectively perform the history matching. With an accurate prediction of the hydrodynamic properties, the migration of CO 2 within the subsurface was modeled by predicting the spatial velocity distribution for a radius of 305 m around the injection well. The technology demonstrated and the expertise gained from this study can guide similar CO 2 -WAG projects.

58 GEOSCIENCES↗

Modelling the Effects of Wetland Restoration on Coastal Hydrology: A Case Study of Elkhorn Slough Watershed, California

ABSTRACT Coastal wetlands, some of the most productive ecosystems on Earth, provide critical ecosystem services, including support of biodiversity, carbon sequestration and flood protection. In recent decades, these ecosystems have experienced extensive coastal wetland loss. Coastal wetland restoration provides a beacon of hope, offering a chance to reclaim these important habitats. However, even with billions of dollars invested worldwide in restoring coastal wetlands, we still lack comprehensive knowledge about the effectiveness of these restoration efforts in recovering wetland ecosystem functions and how future climate change may affect these efforts. The ability to evaluate how these ecosystems will function in the future is vital for examining current investments and developing future protection and management plans. We selected Elkhorn Slough, a tidal estuary, in California, to investigate the impact of wetland restoration and sea level rise (SLR) on coastal hydrology using the process‐based coastal hydrologic model, Advanced Terrestrial Simulator (ATS), informed by site‐specific data. We designed a novel modelling workflow for incorporating wetland restoration features into land cover and soil properties for the model parameterization. The validation results demonstrate a strong agreement between modelled and observed data. We studied the characteristics of coastal watershed hydrology, then focused on the surface water dynamics at two wetland sites within Elkhorn Slough, a reference site and a restored site. Our simulation results indicate that the restored site successfully maintains surface elevation, resulting in reduced surface inundation. We also examined the impact of wetland restoration under expected SLR over the next few decades. The low‐lying Yampah Marsh, the reference site, is likely to be inundated due to future SLR when highest tides arrive, while a higher percentage of Hester Marsh, the restored site, would retain marsh vegetation in coming decades, regardless of tidal conditions. Our study provides important information for examining the outcome of restoration practices that include surface elevation in tidal wetlands under climate changes.

advanced terrestrial simulator↗

What's Left for a Computational Chemist To Do in the Age of Machine Learning?

Machine learning (ML) has become a central focus of the computational chemistry community. In this paper, I will first discuss my personal history in the field. Then I will provide a broader view of how this resurgence in ML interest echoes and advances upon earlier efforts. Although numerous changes have brought about this latest wave, one of the most significant is the increased accuracy and efficiency of low-cost methods (e.g., density functional theory or DFT) that have made it possible to generate large data sets for ML models. ML has also been used to bypass, guide, or improve DFT. The field of computational chemistry thus finds itself at a crossroads as ML both augments and supersedes traditional efforts. I will present what I believe the role of the computational chemist will be in this evolving landscape, with specific focus on my experience in the development of autonomous workflows in computational materials discovery for open-shell transition-metal chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The microbiologist's guide to metaproteomics

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

bioinformatics↗

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron Microscopy Transfer System to Protect Atmosphere‐Sensitive Materials for Scanning Electron Microscopy Characterization

Atmosphere- and/or moisture-sensitive materials can be challenging to characterize using electron microscopy techniques due to sample preparation workflows that generally require exposure to ambient conditions. Here, we describe a novel preparation method that uses aluminum foil in combination with a commercial cryo-EM transfer system to circumvent undesired exposure to the atmosphere. First, hygroscopic MgCl 2 was used as a model material, and prepared samples (both protected and unprotected) were placed in a controlled-humidity environment (> 80% relative humidity) for various exposure lengths (circa seconds to hours). Following this, the effectiveness of the sample preparation method was determined by comparing qualitative photos and quantitative X-ray diffraction patterns between the two sample subsets. The combined results of these experiments suggest that the outlined preparation method effectively protects MgCl 2 from atmospheric contamination compared to MgCl 2 samples that had no protective measures taken. Finally, the preparation method was utilized to protect a highly hygroscopic crystalline BaO thin film for characterization via scanning electron microscopy, thereby demonstrating a functional application of the outlined preparation technique and an additional use for the commercial cryo-EM transfer system beyond its intended application.

atmosphere-sensitive materials↗

A Step-by-Step Protocol from METASPACE to Biological Interpretation

Mass spectrometry imaging (MSI) represents an exceptional tool for exploring complex biological systems spatially at the molecular level. However, due to its multidimensional nature and large-scale data output, it presents considerable challenges when it comes to extracting meaningful biological insights. Recent advancements, such as the METASPACE platform, have enabled researchers to efficiently process, annotate, and interpret MSI datasets by leveraging machine learning and cloud-based infrastructure. In this tutorial, we present a detailed and user-friendly R-pipeline designed to help METASPACE users navigate untargeted metabolomic annotations and transform them into practical insights about their biological systems. By combining METASPACE annotations with rapid R-based screening, this workflow not only streamlined the analytical process but also enhanced the understanding of spatial molecular distribution, especially for complex systems. Here, this easy-to-follow approach has the potential for applications in diagnostics, drug discovery, environmental and ecological processes, and more. We envision this pipeline to be particularly useful for newcomers to the field of MSI and

Moreno Pedraza, Abigail↗

Uncertainty analysis of correlated parameters in automated reaction mechanism generation

Abstract Uncertainty analysis is a useful tool for inspecting and improving detailed kinetic mechanisms because it can identify the greatest sources of model output error. Owing to the very nonlinear relationship between kinetic and thermodynamic parameters and computed concentrations, model predictions can be extremely sensitive to uncertainties in some parameters while uncertainties in other parameters can be irrelevant. Error propagation becomes even more convoluted in automatically generated kinetic models, where input uncertainties are correlated through kinetic rate rules and thermodynamic group values. Local and global uncertainty analyses were implemented and used to analyze error propagation in Reaction Mechanism Generator (RMG), an open‐source software for generating kinetic models. A framework for automatically assigning parameter uncertainties to estimated thermodynamics and kinetics was created, enabling tracking of correlated uncertainties. Local first‐order uncertainty propagation was implemented using sensitivities computed natively within RMG. Global uncertainty analysis was implemented using adaptive Smolyak pseudospectral approximations as implemented in the MIT Uncertainty Quantification Library to efficiently compute and construct polynomial chaos expansions to approximate the dependence of outputs on a subset of uncertain inputs. Cantera was used as a backend for simulating the reactor system in the global analysis. Analyses were performed for a phenyldodecane pyrolysis model. Local and global methods demonstrated similar trends; however, many uncertainties were significantly overestimated by the local analysis. Both local and global analyses show that correlated uncertainties based on kinetic rate rules and thermochemical groups drastically reduce a model's degrees of freedom and have a large impact on the determination of the most influential input parameters. These results highlight the necessity of incorporating uncertainty analysis in the mechanism generation workflow.

Gao, Connie W.↗

Parallel beamlet dose calculation via beamlet contexts in a distributed multi‐GPU framework

Purpose Dose calculation is one of the most computationally intensive, yet essential tasks in the treatment planning process. With the recent interest in automatic beam orientation and arc trajectory optimization techniques, there is a great need for more efficient model‐based dose calculation algorithms that can accommodate hundreds to thousands of beam candidates at once. Foundational work has shown the translation of dose calculation algorithms to graphical processing units ( GPU s), lending to remarkable gains in processing efficiency. But these methods provide parallelization of dose for only a single beamlet, serializing the calculation of multiple beamlets and under‐utilizing the potential of modern GPU s. In this paper, the authors propose a framework enabling parallel computation of many beamlet doses using a novel beamlet context transformation and further embed this approach in a scalable network of multi‐ GPU computational nodes. Methods The proposed context‐based transformation separates beamlet‐local density and TERMA into distinct beamlet contexts that independently provide sufficient data for beamlet dose calculation. Beamlet contexts are arranged in a composite context array with dosimetric isolation, and the context array is subjected to a GPU collapsed‐cone convolution superposition procedure, producing the set of beamlet‐specific dose distributions in a single pass. Dose from each context is converted to a sparse representation for efficient storage and retrieval during treatment plan optimization. The context radius is a new parameter permitting flexibility between the speed and fidelity of the dose calculation process. A distributed manager‐worker architecture is constructed around the context‐based GPU dose calculation approach supporting an arbitrary number of worker nodes and resident GPU s. Phantom experiments were executed to verify the accuracy of the context‐based approach compared to Monte Carlo and a reference CPU ‐ CCCS implementation for single beamlets and broad beams composed by addition of beamlets. Dose for representative 4 π beam sets was calculated in lung and prostate cases to compare its efficiency with that of an existing beamlet‐sequential GPU ‐ CCCS implementation. Code profiling was also performed to evaluate the scalability of the framework across many networked GPU s. Results The dosimetric accuracy of the context‐based method displays <1.35% and 2.35% average error from the existing serialized CPU ‐ CCCS algorithm and Monte Carlo simulation for beamlet‐specific PDD s in water and slab phantoms, respectively. The context‐based method demonstrates substantial speedup of up to two orders of magnitude over the beamlet‐sequential GPU ‐ CCCS method in the tested configurations. The context‐based framework demonstrates near linear scaling in the number of distributed compute nodes and GPU s employed, indicating that it is flexible enough to meet the performance requirements of most users by simply increasing the hardware utilization. Conclusions The context‐based approach demonstrates a new expectation of performance for beamlet‐based dose calculation methods. This approach has been successful in accelerating the dose calculation process for very large‐scale treatment planning problems ‐ such as automatic 4 π IMRT beam orientation and VMAT arc trajectory selection, with hundreds of thousands of beamlets ‐ in clinically feasible timeframes. The flexibility of this framework makes it as a strong candidate for use in a variety of other very large‐scale treatment planning tasks and clinical workflows.

Neph, Ryan↗