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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A unifying Bayesian framework for merging X-ray diffraction data

Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as reflections. To compute the electron density of a molecule, the intensity of each reflection must be estimated, and redundant observations reduced to consensus intensities. Systematic effects, however, lead to the measurement of equivalent reflections on different scales, corrupting observation of changes in electron density. Here, we present a modern Bayesian solution to this problem, which uses deep learning and variational inference to simultaneously rescale and merge reflection observations. We successfully apply this method to monochromatic and polychromatic single-crystal diffraction data, as well as serial femtosecond crystallography data. We find that this approach is applicable to the analysis of many types of diffraction experiments, while accurately and sensitively detecting subtle dynamics and anomalous scattering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Key issues of ultraviolet radiation of OH at high altitudes

Ultraviolet (UV) emissions radiated by hydroxyl (OH) is one of the fundamental elements in the prediction of radiation signature of high-altitude and high-speed vehicle. In this work, the OH A{sup 2}Σ{sup +}→X{sup 2}Π ultraviolet emission band behind the bow shock is computed under the experimental condition of the second bow-shock ultraviolet flight (BSUV-2). Four related key issues are discussed, namely, the source of hydrogen element in the high-altitude atmosphere, the formation mechanism of OH species, efficient computational algorithm of trace species in rarefied flows, and accurate calculation of OH emission spectra. Firstly, by analyzing the typical atmospheric model, the vertical distributions of the number densities of different species containing hydrogen element are given. According to the different dominating species containing hydrogen element, the atmosphere is divided into three zones, and the formation mechanism of OH species is analyzed in the different zones. The direct simulation Monte Carlo (DSMC) method and the Navier-Stokes equations are employed to compute the number densities of the different OH electronically and vibrationally excited states. Different to the previous work, the trace species separation (TSS) algorithm is applied twice in order to accurately calculate the densities of OH species and its excited states. Using a non-equilibrium radiation model, the OH ultraviolet emission spectra and intensity at different altitudes are computed, and good agreement is obtained with the flight measured data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

HAM: Hotspot-Aware Manager for Improving Communications with 3D-Stacked Memory

merging High-Performance Computing (HPC) workloads, such as graph analytics, machine learning, and big data science, are data-intensive. Data-intensive workloads usually present fine-grained memory accesses with limited or no data locality, and thus incur frequent cache misses and low utilization of memory bandwidth. 3D-stacked memory devices such as Hybrid Memory Cube (HMC) and High Bandwidth Memory (HBM) can provide significantly higher bandwidth than conventional memory modules. However, the traditional interfaces and optimization methods for JEDEC DDR devices do not allow to fully exploit the potential performance of 3D-stacked memory with the massive amount of irregular memory accesses of data-intensive applications. In this paper, we propose a novel Hotspot-Aware Manager (HAM) infrastructure for 3D-stacked memory devices capable of optimizing memory access streams via request aggregation, hotspot detection, and in-memory prefetching. %and an associated hotspot-aware page policy. We present the HAM design and implementation, and simulate it on a system using RISC-V embedded cores with attached HMC devices. We extensively evaluate HAM with over 12 benchmarks and applications representing diverse irregular memory access patterns. The results show that, on average, HAM reduces redundant requests by 37.51\% and increases the prefetch buffer hit rate by 4.2 times, compared to a baseline streaming prefetcher. On the selected benchmark set, HAM provides performance gains of 21.81\% in average (up to 34.28\%) and power savings of 35.07\% over a standard 3D-stacked memory.

Wang, Xi↗
DOE OSTI2014

IOPro: a parallel I/O profiling and visualization framework for high-performance storage systems

Efficient execution of large-scale scientific applications requires high-performance computing systems designed to meet the I/O requirements. To achieve high-performance, such data-intensive parallel applications use a multi-layer layer I/O software stack, which consists of high-level I/O libraries such as PnetCDF and HDF5, the MPI library, and parallel file systems. To design efficient parallel scientific applications, understanding the complicated flow of I/O operations and the involved interactions among the libraries is quintessential. Such comprehension helps identify I/O bottlenecks and thus exploits the potential performance in different layers of the storage hierarchy. To profile the performance of individual components in the I/O stack and to understand complex interactions among them, we have implemented a GUI-based integrated profiling and analysis framework, IOPro. IOPro automatically generates an instrumented I/O stack, runs applications on it, and visualizes detailed statistics based on the user-specified metrics of interest. We present experimental results from two different real-life applications and show how our framework can be used in practice. By generating an end-to-end trace of the whole I/O stack and pinpointing I/O interference, IOPro aids in understanding I/O behavior and improving the I/O performance significantly.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

The high level trigger and express data production at STAR

To meet the demands of the Beam Energy Scan phase-II (BES-II) program, the STAR experiment at the Relativistic Heavy Ion Collider (RHIC) developed a dual real-time framework consisting of a High Level Trigger (HLT) and an Express Data Production system (xProduction). The HLT operates online within the Data Acquisition (DAQ) chain on a dedicated multi-core CPU cluster with the option to offload compute-intensive kernels to Xeon Phi coprocessors. It uses parallelized algorithms, such as the Cellular Automaton (CA) Track Finder, to perform rapid tracking, vertexing, and event filtering. This allows it to select events of interest in real time and provide immediate feedback on detector and beam conditions. In contrast, the xProduction workflow runs concurrently and independently of the DAQ loop. It applies near offline-quality calibration and reconstruction within hours of data collection. The xProduction input is the express data stream, whose content can be enriched by HLT trigger/priority selections under DAQ/HLT resource constraints, and it uses the STAR calibration/conditions framework, incorporating online calibration/QA information when available. This enables early preliminary physics analysis, including the reconstruction of rare signals, such as hyperons and hypernuclei. It also provides collaboration-wide access to analysis-ready datasets. Together, the HLT and xProduction systems form a complementary architecture: the HLT performs online event selection while the xProduction chain delivers high-quality results within a short amount of time. This integrated framework has enabled the prompt reconstruction of the $^5_Λ$ He hypernucleus with high statistical significance and the efficient processing of hundreds of millions of heavy-ion collision events. In conclusion, its demonstrated scalability and robustness establish a model for future high-luminosity experiments requiring both online event filtering and rapid access to analysis-quality data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Using NVMe Gen3 PCIe SSD Cards in High-density Servers for High-performance Big Data Transfer Over Multiple Network Channels

This Technical Note describes how the Zettar team came up with a data transfer cluster design that convincingly proved the feasibility of using high-density servers for high-performance Big Data transfers. It then outlines the tests, operations, and observations that address a potential over-heating concern regarding the use of Non-Volatile Memory Host Controller Interface Specification (NVMHCI aka NVM Express or NVMe) Gen 3 PCIe SSD cards in high-density servers. Finally, it points out the possibility of developing a new generation of high-performance Science DMZ data transfer system for the data-intensive research community and commercial enterprises.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments

Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g. disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred from one or more measured peptides. In recent years, many computational approaches to relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

High Energy Physics Network Requirements Review: Two-Year Update

The Energy Sciences Network (ESnet) is the high-performance network user facility for the US Department of Energy (DOE) Office of Science (SC) and delivers highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the DOE science mission by connecting all its laboratories and facilities in the US and abroad. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. ESnet interconnects DOE national laboratories, user facilities, and major experiments so that scientists can use remote instruments and computing resources as well as share data with collaborators, transfer large datasets, and access distributed data repositories. ESnet is specifically built to provide a range of network services tailored to meet the unique requirements of the DOE’s data-intensive science. In July 2023, the Energy Sciences Network (ESnet) and the High Energy Physics program (HEP) of the DOE SC organized an interim ESnet requirements review of HEP-supported activities, to follow up on the work started during the 2020 HEP Network Requirements Review. Preparation for these events included checking back with the key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare updates to their previously submitted case study documents, so that ESnet could update the understanding of any changes to the current, near-term, and long-term status, expectations, and processes that will support the science activities of the program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

HOSS!

The Hall-D Online Skim System (HOSS) was developed to simultaneously solve two issues for the high intensity GlueX experiment. One was to parallelize the writing of raw data files to disk in order to improve bandwidth. The other was to distribute the raw data across multiple compute nodes in order to produce calibration skims of the data online. The highly configurable system employs RDMA, RAM disks, and zeroMQ driven by Python to simultaneously store and process the full high intensity GlueX data stream.

Lawrence, David↗
DOE OSTI2023

High-throughput terahertz imaging: progress and challenges

Abstract Many exciting terahertz imaging applications, such as non-destructive evaluation, biomedical diagnosis, and security screening, have been historically limited in practical usage due to the raster-scanning requirement of imaging systems, which impose very low imaging speeds. However, recent advancements in terahertz imaging systems have greatly increased the imaging throughput and brought the promising potential of terahertz radiation from research laboratories closer to real-world applications. Here, we review the development of terahertz imaging technologies from both hardware and computational imaging perspectives. We introduce and compare different types of hardware enabling frequency-domain and time-domain imaging using various thermal, photon, and field image sensor arrays. We discuss how different imaging hardware and computational imaging algorithms provide opportunities for capturing time-of-flight, spectroscopic, phase, and intensity image data at high throughputs. Furthermore, the new prospects and challenges for the development of future high-throughput terahertz imaging systems are briefly introduced.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Optical neural engine for solving scientific partial differential equations

Abstract Solving partial differential equations (PDEs) is the cornerstone of scientific research and development. Data-driven machine learning (ML) approaches are emerging to accelerate time-consuming and computation-intensive numerical simulations of PDEs. Although optical systems offer high-throughput and energy-efficient ML hardware, their demonstration for solving PDEs is limited. Here, we present an optical neural engine (ONE) architecture combining diffractive optical neural networks for Fourier space processing and optical crossbar structures for real space processing to solve time-dependent and time-independent PDEs in diverse disciplines, including Darcy flow equation, the magnetostatic Poisson’s equation in demagnetization, the Navier-Stokes equation in incompressible fluid, Maxwell’s equations in nanophotonic metasurfaces, and coupled PDEs in a multiphysics system. We numerically and experimentally demonstrate the capability of the ONE architecture, which not only leverages the advantages of high-performance dual-space processing for outperforming traditional PDE solvers and being comparable with state-of-the-art ML models but also can be implemented using optical computing hardware with unique features of low-energy and highly parallel constant-time processing irrespective of model scales and real-time reconfigurability for tackling multiple tasks with the same architecture. The demonstrated architecture offers a versatile and powerful platform for large-scale scientific and engineering computations.

Tang, Yingheng (ORCID:0009000153622546)↗
DOE OSTI2023

High-throughput calculations of charged point defect properties with semi-local density functional theory—performance benchmarks for materials screening applications

Abstract Calculations of point defect energetics with Density Functional Theory (DFT) can provide valuable insight into several optoelectronic, thermodynamic, and kinetic properties. These calculations commonly use methods ranging from semi-local functionals with a-posteriori corrections to more computationally intensive hybrid functional approaches. For applications of DFT-based high-throughput computation for data-driven materials discovery, point defect properties are of interest, yet are currently excluded from available materials databases. This work presents a benchmark analysis of automated, semi-local point defect calculations with a-posteriori corrections, compared to 245 “gold standard” hybrid calculations previously published. We consider three different a-posteriori correction sets implemented in an automated workflow, and evaluate the qualitative and quantitative differences among four different categories of defect information: thermodynamic transition levels, formation energies, Fermi levels, and dopability limits. We highlight qualitative information that can be extracted from high-throughput calculations based on semi-local DFT methods, while also demonstrating the limits of quantitative accuracy.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Computational approaches to model X-ray photon correlation spectroscopy from molecular dynamics

X-ray photon correlation spectroscopy (XPCS) allows for the resolution of dynamic processes within a material across a wide range of length and time scales. X-ray speckle visibility spectroscopy (XSVS) is a related method that uses a single diffraction pattern to probe ultrafast dynamics. Interpretation of the XPCS and XSVS data in terms of underlying physical processes is necessary to establish the connection between the macroscopic responses and the microstructural dynamics. To aid the interpretation of the XPCS and XSVS data, we present a computational framework to model these experiments by computing the X-ray scattering intensity directly from the atomic positions obtained from molecular dynamics simulations. We compare the efficiency and accuracy of two alternative computational methods: the direct method computing the intensity at each diffraction vector separately, and a method based on fast Fourier transform that computes the intensities at all diffraction vectors at once. Furthermore, the computed X-ray speckle patterns capture the density fluctuations over a range of length and time scales and are shown to reproduce the known properties and relations of experimental XPCS and XSVS for liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2016

INTEGRATION OF PANDA WORKLOAD MANAGEMENT SYSTEM WITH SUPERCOMPUTERS

Abstract The Large Hadron Collider (LHC), operating at the international CERN Laboratory in Geneva, Switzerland, is leading Big Data driven scientific explorations. Experiments at the LHC explore the funda- mental nature of matter and the basic forces that shape our universe, and were recently credited for the dis- covery of a Higgs boson. ATLAS, one of the largest collaborations ever assembled in the sciences, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System for managing the workflow for all data processing on over 140 data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data cen- ters are physically scattered all over the world. While PanDA currently uses more than 250000 cores with a peak performance of 0.3+ petaFLOPS, next LHC data taking runs will require more resources than Grid computing can possibly provide. To alleviate these challenges, LHC experiments are engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with supercomputers in United States, Europe and Russia (in particular with Titan supercomputer at Oak Ridge Leadership Com- puting Facility (OLCF), Supercomputer at the National Research Center Kurchatov Institute , IT4 in Ostrava, and others). The current approach utilizes a modified PanDA pilot framework for job submission to the supercomputers batch queues and local data management, with light-weight MPI wrappers to run single- threaded workloads in parallel on Titan s multi-core worker nodes. This implementation was tested with a variety of Monte-Carlo workloads on several supercomputing platforms. We will present our current accom- plishments in running PanDA WMS at supercomputers and demonstrate our ability to use PanDA as a portal independent of the computing facility s infrastructure for High Energy and Nuclear Physics, as well as other data-intensive science applications, such as bioinformatics and astro-particle physics.

De, K↗
DOE OSTI2011

On the Origin of Ultra High Energy Cosmic Rays II

We show that accretion disks around Active Galactic Nuclei (AGNs) could account for the enormous power in observed ultra high energy cosmic rays {approx}10{sup 20} eV (UHEs). In our model, cosmic rays are produced by quasi-steady acceleration of ions in magnetic structures previously proposed to explain jets around Active Galactic Nuclei with supermassive black holes. Steady acceleration requires that an AGN accretion disk act as a dynamo, which we show to follow from a modified Standard Model in which the magnetic torque of the dynamo replaces viscosity as the dominant mechanism accounting for angular momentum conservation during accretion. A black hole of mass M{sub BH} produces a steady dynamo voltage V {proportional_to} {radical}M{sub BH} giving V {approx} 10{sup 20} volts for M{sub BH} {approx} 10{sup 8} solar masses. The voltage V reappears as an inductive electric field at the advancing nose of a dynamo-driven jet, where plasma instability inherent in collisionless runaway acceleration allows ions to be steadily accelerated to energies {approx} V, finally ejected as cosmic rays. Transient events can produce much higher energies. The predicted disk radiation is similar to the Standard Model. Unique predictions concern the remarkable collimation of jets and emissions from the jet/radiolobe structure. Given MBH and the accretion rate, the model makes 7 predictions roughly consistent with data: (1) the jet length; (2) the jet radius; (3) the steady-state cosmic ray energy spectrum; (4) the maximum energy in this spectrum; (5) the UHE cosmic ray intensity on Earth; (6) electron synchrotron wavelengths; and (7) the power in synchrotron radiation. These qualitative successes motivate new computer simulations, experiments and data analysis to provide a quantitative verification of the model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Models, data, and scripts associated with “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning”

This data package is associated with the publication “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning’’ submitted to the Journal of Geophysical Research: Machine Learning and Computation (Scheibe et al. 2024). River sediment respiration observations are expensive and labor intensive to obtain and there is no physical model for predicting this quantity. The Worldwide Hydrobiogeochemisty Observation Network for Dynamic River Systems (WHONDRS) observational data set (Goldman et al.; 2020) is used to train machine learning (ML) models to predict respiration rates at unsampled sites. This repository archives training data, ML models, predictions, and model evaluation results for the purposes of reproducibility of the results in the associated manuscript and community reuse of the ML models trained in this project. One of the key challenges in this work was to find an optimum configuration for machine learning models to work with this feature-rich (i.e. 100+ possible input variables) data set. Here, we used a two-tiered approach to managing the analysis of this complex data set: 1) a stacked ensemble of ML models that can automatically optimize hyperparameters to accelerate the process of model selection and tuning and 2) feature permutation importance to iteratively select the most important features (i.e. inputs) to the ML models. The major elements of this ML workflow are modular, portable, open, and cloud-based, thus making this implementation a potential template for other applications. This data package is associated with the GitHub repository found at Please see the file level metadata (flmd; “sl-archive-whondrs_flmd.csv”) for a list of all files contained in this data package and descriptions for each. Please see the data dictionary (dd; “sl-archive-whondrs_dd.csv”) for a list of all column headers contained within comma separated value (csv) files in this data package and descriptions for each. The GitHub repository is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning models trained on the data in “input_data”; (3) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; (4) “examples” contains the visualization of the results in this repository including plotting scripts for the manuscript (e.g., model evaluation, FPI results) and scripts for running predictions with the ML models (i.e., reusing the trained ML models); (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. Furthermore, depending on the number of features used to train the ML models, the preprocessing and postprocessing scripts, and their intermediate results, can also be different branch-to-branch. The “main-*” branches are meant to be starting points (i.e. trunks) for each model branch (i.e. sprouts). Please see the Branch Navigation section in the top-level README.md in the GitHub repository for more details. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please the top-level README.md in the GitHub repository for more details on the automation.

13C↗