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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Compressed basis GMRES on high-performance graphics processing units

Krylov methods provide a fast and highly parallel numerical tool for the iterative solution of many large-scale sparse linear systems. To a large extent, the performance of practical realizations of these methods is constrained by the communication bandwidth in current computer architectures, motivating the investigation of sophisticated techniques to avoid, reduce, and/or hide the message-passing costs (in distributed platforms) and the memory accesses (in all architectures). This article leverages Ginkgo’s memory accessor in order to integrate a communication-reduction strategy into the (Krylov) GMRES solver that decouples the storage format (i.e., the data representation in memory) of the orthogonal basis from the arithmetic precision that is employed during the operations with that basis. Given that the execution time of the GMRES solver is largely determined by the memory accesses, the cost of the datatype transforms can be mostly hidden, resulting in the acceleration of the iterative step via a decrease in the volume of bits being retrieved from memory. Together with the special properties of the orthonormal basis (whose elements are all bounded by 1), this paves the road toward the aggressive customization of the storage format, which includes some floating-point as well as fixed-point formats with mild impact on the convergence of the iterative process. We develop a high-performance implementation of the “compressed basis GMRES” solver in the Ginkgo sparse linear algebra library using a large set of test problems from the SuiteSparse Matrix Collection. We demonstrate robustness and performance advantages on a modern NVIDIA V100 graphics processing unit (GPU) of up to 50% over the standard GMRES solver that stores all data in IEEE double-precision.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Frequent Fulcrum Functions: The Basics of SCALE’s Graphical User Interface [Slides]

This tutorial introduces the Fulcrum graphical user interface and the basic functions that enhance the common activities of creating, editing, navigating, executing, and visualizing SCALE input files. This tutorial will help you become familiar with the Fulcrum input file text editor and the integrated input development environment features of autocompletion, automatic checking, cursor context, and input navigation. In addition, the Fulcrum and SCALE runtime environment will be reviewed to improve the understanding of job execution workflow. This tutorial does not cover data and geometry plotting. Please see the Advanced User Interface Capabilities tutorial for details regarding plotting data and geometry. No prior experience with SCALE is required. You can follow along using SCALE 6.2 or 6.3-beta.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters

The predominance of Kohn–Sham density functional theory (KS-DFT) for the theoretical treatment of large experimentally relevant systems in molecular chemistry and materials science relies primarily on the existence of efficient software implementations which are capable of leveraging the latest advances in modern high-performance computing (HPC). With recent trends in HPC leading toward increasing reliance on heterogeneous accelerator-based architectures such as graphics processing units (GPU), existing code bases must embrace these architectural advances to maintain the high levels of performance that have come to be expected for these methods. In this work, we purpose a three-level parallelism scheme for the distributed numerical integration of the exchange-correlation (XC) potential in the Gaussian basis set discretization of the Kohn–Sham equations on large computing clusters consisting of multiple GPUs per compute node. In addition, we purpose and demonstrate the efficacy of the use of batched kernels, including batched level-3 BLAS operations, in achieving high levels of performance on the GPU. We demonstrate the performance and scalability of the implementation of the purposed method in the NWChemEx software package by comparing to the existing scalable CPU XC integration in NWChem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Graphics Processing Unit (GPU) Approach to Large Eddy Simulation (LES) for Transport and Contaminant Dispersion

Recent advances in the development of large eddy simulation (LES) atmospheric models with corresponding atmospheric transport and dispersion (AT&D) modeling capabilities have made it possible to simulate short, time-averaged, single realizations of pollutant dispersion at the spatial and temporal resolution necessary for common atmospheric dispersion needs, such as designing air sampling networks, assessing pollutant sensor system performance, and characterizing the impact of airborne materials on human health. The high computational burden required to form an ensemble of single-realization dispersion solutions using an LES and coupled AT&D model has, until recently, limited its use to a few proof-of-concept studies. An example of an LES model that can meet the temporal and spatial resolution and computational requirements of these applications is the joint outdoor-indoor urban large eddy simulation (JOULES). A key enabling element within JOULES is the computationally efficient graphics processing unit (GPU)-based LES, which is on the order of 150 times faster than if the LES contaminant dispersion simulations were executed on a central processing unit (CPU) computing platform. JOULES is capable of resolving the turbulence components at a suitable scale for both open terrain and urban landscapes, e.g., owing to varying environmental conditions and a diverse building topology. In this paper, we describe the JOULES modeling system, prior efforts to validate the accuracy of its meteorological simulations, and current results from an evaluation that uses ensembles of dispersion solutions for unstable, neutral, and stable static stability conditions in an open terrain environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A geospatial risk analysis graphical user interface for identifying hazardous chemical emission sources

Background: Performing back trajectory and forward trajectory using the Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT) is a reliable approach for assessing particle transport after release among mid-field atmospheric models. HYSPLIT has an externally facing online interface that allows non-expert users to run the model trajectories without requiring extensive training or programming. However, the existing HYSPLIT interface is limited if simulations have a large amount of meteorological data and timesteps that are not coincident. The objective of this study is to design and develop a more robust tool to rapidly evaluate hazard transport conditions and to perform risk analysis, while still maintaining an intuitive and user-friendly interface. Methods: HYSPLIT calculates forward and backward trajectories of particles based on wind speed, wind direction, and the corresponding location, timestamp, and Pasquill stability classes of the regions of the atmosphere in terms of the wind speed, the amount of solar radiation, and the fractional cloud cover. The computed particle transport trajectories, combined with the online Proton Transfer Reaction-Mass Spectrometry (PTR-MS) data (https://figshare.com/articles/dataset/ARL_Data_from_PROS_station_at_Hanford_site/19993964), can be used to identify and quantify the sources and affected area of the hazardous chemicals’ emission using the potential source distribution function (PSDF). PSDF is an improved statistical function based on the well-known potential source contribution function (PSCF) in establishing the air pollutant source and receptor relationship. Performing this analysis requires a range of meteorological and pollutant concentration measurements to be statistically meaningful. The existing HYSPLIT graphical user interface (GUI) does not easily permit computations of trajectories of a dataset of meteorological data in high temporal frequency. To improve the performance of HYSPLIT computations from a large dataset and enhance risk analysis of the accidental release of material at risk, a geospatial risk analysis tool (GRAT-GUI) is created to allow large data sets to be processed instantaneously and to provide ease of visualization. Results: The GRAT-GUI is a native desktop-based application and can be run in any Windows 10 system without any internet access requirements, thus providing a secure way to process large meteorological datasets even on a standalone computer. GRAT-GUI has features to import, integrate, and convert meteorological data with various formats for hazardous chemical emission source identification and risk analysis as a self-explanatory user interface. The tool is available at https://figshare.com/articles/software/GRAT/19426742.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Sparse matrix‐vector and matrix‐multivector products for the truncated SVD on graphics processors

Summary Many practical algorithms for numerical rank computations implement an iterative procedure that involves repeated multiplications of a vector, or a collection of vectors, with both a sparse matrix and its transpose. Unfortunately, the realization of these sparse products on current high performance libraries often deliver much lower arithmetic throughput when the matrix involved in the product is transposed. In this work, we propose a hybrid sparse matrix layout, named CSRC, that combines the flexibility of some well‐known sparse formats to offer a number of appealing properties: (1) CSRC can be obtained at low cost from the popular CSR (compressed sparse row) format; (2) CSRC has similar storage requirements as CSR; and especially, (3) the implementation of the sparse product kernels delivers high performance for both the direct product and its transposed variant on modern graphics accelerators thanks to a significant reduction of atomic operations compared to a conventional implementation based on CSR. This solution thus renders considerably higher performance when integrated into an iterative algorithm for the truncated singular value decomposition (SVD), such as the randomized SVD or, as demonstrated in the experimental results, the block Golub–Kahan–Lanczos algorithm.

Aliaga, José I.↗
DOE OSTI2023

The sequence of prime gaps is graphic

Let us call a simple graph on $n$ ≥ 2 vertices a prime gap graph if its vertex degrees are 1 and the first $n$ - 1 prime gaps. We show that such a graph exists for every large n, and in fact for every $n$ ≥ 2 if we assume the Riemann hypothesis. Moreover, an infinite sequence of prime gap graphs can be generated by the so-called degree preserving growth process. This is the first time a naturally occurring infinite sequence of positive integers is identified as graphic. That is, we show the existence of an interesting, and so far unique, infinite combinatorial object.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Discrete element simulation of Pebble Bed Reactors on graphics processing units

Prediction of pebble positions in a Pebble Bed Reactor (PBR) is necessary for both reactor physics and thermal hydraulics simulations as the arrangement of pebbles has a significant impact on the resulting core power, coolant flow, and fuel temperature. Knowledge of pebble movement as the fuel is cycled through the core is also critical for predicting the fuel residence time and subsequently, the fuel burnup. Simulation with the Discrete Element Method (DEM) can provide knowledge of both the fuel packing and the fuel movement during cycling. Previous works that have performed 3D full-core DEM simulation of PBRs have used simplified models that neglect reflector wall features. This work employs a graphics processing unit (GPU)-enabled DEM code, Project Chrono, to analyze the differences in pebble packing and pebble velocities between a simplified smooth PBR reflector and a more realistic reflector that includes circular wall features. Additionally, a sensitivity study is performed on the depth of the wall features to ensure that crystallization is prevented. Project Chrono is also validated for PBR cycling applications using experimental data. It is found that wall features with a depth of at least 0.5 pebble diameters significantly reduce crystallization in the near-wall region, leading to discrepancies in both packing fraction and pebble velocity in this region compared to the simplified reflector models. These discrepancies are found to lead to roughly a 5–10% difference in the prediction of the near-wall porosity and a 10% difference in the prediction of the velocity of pebbles near the wall. As a result of these discrepancies, it is suggested that future DEM simulations of PBRs include wall features to reduce modeling errors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Physics-informed graphical neural network for power system state estimation

State estimation is highly critical for accurately observing the dynamic behavior of the power grids and minimizing risks from cyber threats. However, existing state estimation methods encounter challenges in accurately capturing power system dynamics, primarily because of limitations in encoding the grid topology and sparse measurements. Here, this paper proposes a physics-informed graphical learning state estimation method to address these limitations by leveraging both domain physical knowledge and a graph neural network (GNN). We employ a GNN architecture that can handle the graph-structured data of power systems more effectively than traditional data-driven methods. The physics-based knowledge is constructed from the branch current formulation, making the approach adaptable to both transmission and distribution systems. The validation results of three IEEE test systems show that the proposed method can achieve lower mean square error more than 20% than the conventional methods.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Integration of graphical approaches into optimization-based design of multistage liquid extraction

We propose two optimization models for designing two liquid extraction systems: simple multistage liquid extractors and extractors with extract reflux. Both models are motivated by the concepts of the modified McCabe-Thiele graphical method for multistage extractor design. The operating and equilibrium curves in the McCabe-Thiele method are represented by material balances and piece-wise linearized thermodynamics properties. The use of piece-wise approximations improves computational tractability of both optimization models. In addition, we consider some extensions such as dilute systems, insoluble solvents, and non-ideal stages. In conclusion, the applicability of the proposed models is demonstrated with four illustrative examples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

HydroEcoLSTM: A Python package with graphical user interface for hydro-ecological modeling with long short-term memory neural network

Machine learning (ML) is emerging as a promising tool for modeling hydro-ecological processes due to the increasing availability of large environmental data. However, the use of ML requires sufficient programming knowledge due to a lack of a graphical user interface (GUI). In this study, we introduced a GUI package, named HydroEcoLSTM, with the long short-term memory network (LSTM) as the core model, that allows non-ML experts to utilize their domain knowledge to construct complex ML models. We demonstrated the functionalities of HydroEcoLSTM with two practical examples, including (1) predictions of streamflow in both gauged and ungauged catchments and (2) predictions of multiple outputs (i.e., streamflow and isotope transport from two catchments). The simulation results obtained in both case experiments are satisfactory. In the first example, the average Nash–Sutcliffe Efficiency (NSE) for streamflow simulation during the testing period is 0.79 while the application of the trained model in two assumed ungauged catchments also achieves the average NSE of 0.68. In the second example, the average NSE for streamflow and instream isotope simulation during the testing period is 0.71. Ultimately, applications of HydroEcoLSTM with real-world examples demonstrate its potential use for practical applications and research without requiring extensive coding skills.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Acceleration of the particle-in-cell code Osiris with graphics processing units

Fully relativistic particle-in-cell (PIC) simulations are crucial for advancing our knowledge of plasma physics. Modern supercomputers based on graphics processing units (GPUs) offer the potential to perform PIC simulations of unprecedented scale, but require robust and feature-rich codes that can fully leverage their computational resources. In this work, this demand is addressed by adding GPU acceleration to the PIC code Osiris. An overview of the algorithm, which features a CUDA extension to the underlying Fortran architecture, is given. Detailed performance benchmarks for thermal plasmas are presented, which demonstrate excellent weak scaling on NERSC's Perlmutter supercomputer and high levels of absolute performance. The robustness of the code to model a variety of physical systems is demonstrated via simulations of Weibel filamentation and laser-wakefield acceleration run with dynamic load balancing. Finally, measurements and analysis of energy consumption are provided that indicate that the GPU algorithm is up to ~14 times faster and ~7 times more energy efficient than the optimized CPU algorithm on a node-to-node basis. The described development addresses the PIC simulation community's computational demands both by contributing a robust and performant GPU-accelerated PIC code and by providing insight into efficient use of GPU hardware.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions

Here, a framework to offload four-index two-electron repulsion integrals to graphical processing units (GPUs) using OpenMP is discussed. The method has been applied to the Fock build for low angular momentum s and p functions in both the restricted Hartree–Fock (RHF) and in the effective fragment molecular orbital (EFMO) framework. Benchmark calculations for the GPU code for the pure RHF method show an increasing speedup relative to the existing OpenMP CPU code in GAMESS from 1.04 to 52× for clusters of 70–569 water molecules. The parallel efficiency on 24 NVIDIA V100 GPU boards also increases when increasing the system size: from 75 to 94% for water clusters that contain 303–1120 molecules. In the EFMO framework, the GPU Fock build shows a high linear scalability up to 4608 V100s with a parallel efficiency of 96% for calculations on a solvated mesoporous silica nanoparticle system with ~67,000 basis functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Enabling Multireference Calculations on Multimetallic Systems with Graphic Processing Units

Modeling multimetallic systems efficiently enables faster prediction of desirable chemical properties and the design of new materials. This work describes an initial implementation for performing multireference wave function method localized active-space self-consistent field (LASSCF) calculations through the use of multiple graphics processing units (GPUs) to accelerate time-to-solution. Density fitting is leveraged to reduce memory requirements, and we demonstrate the ability to fully utilize multi-GPU compute nodes. Performance improvements of 5–10x in total application runtime were observed in LASSCF calculations for multimetallic catalyst systems up to 1200 AOs and an active space of (22e,40o) using up to four NVIDIA A100 GPUs. Furthermore, written with performance portability in mind, a comparable performance is also observed in early runs on the Aurora exascale system using Intel Max Series GPUs.

Algorithms↗
DOE OSTI2022

Active learning of chemical reaction networks via probabilistic graphical models and Boolean reaction circuits

Discerning networks of many reactions among multiple interconverting species is challenging. Here, we present a reaction network identification methodology. Our methodology enumerates all stoichiometrically and chemically feasible reactions and requires statistical evidence from effluent concentrations for the inclusion or exclusion of each from the reaction network, contrasting with the commonly seen incremental approach and other work of relying heavily upon chemical intuition and assuming the reactions occurring. Using graph theory alongside an active learning design of experiments that propose maximally informative feeds, we identify the underlying reaction network with minimal laboratory runs. Here, we introduce chemistry-probabilistic graphical modeling and Boolean reaction circuits to statistically quantify which reactions occur from effluent concentrations. Our methodology accurately discerns active reactions, as showcased upon a laboratory network of cross-ketonization of furoic and lauric acid and validated upon simulated networks of thermal and CO 2 -assisted ethane dehydrogenation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem’s speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. Finally, this greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

High-speed feedback control of an oscillating magnetic helicity injector using a graphics processing unit

A real-time control system has been developed to control the amplitude, phase, and offset of bulk plasma parameters inside an oscillating magnetic helicity injector. Control software running entirely on an Nvidia Tesla P40 graphical processing unit is able to receive digitizer inputs and send response patterns to a Pulse Width Modulation (PWM) controller with a minimum control loop period of 12.8μs. With an input digitization rate of 10 MS/s, a three-parameter proportional integral differential controller is shown to be sufficient to inform the PWM controller to drive the desired oscillating plasma waveform with a frequency of 16.6 kHz that is located near the resonance of a coupled RLC circuit. In particular, the temporal phase of the injector waveform is held within 10 degrees of the target value. Control is demonstrated over the toroidal modal structure of the imposed magnetic perturbations of the helicity injection system, allowing a new class of discharges to be studied.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption

A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.

97 MATHEMATICS AND COMPUTING↗