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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Parallel File System I/O Performance Testing On LANL Clusters

These are slides from a presentation on parallel file system I/O performance testing on LANL clusters. I/O is a known bottleneck for HPC applications. Performance optimization of I/O is often required. This summer project entailed integrating IOR under Pavilion and automating the results analysis. The slides cover the following topics: scope of the work, tools utilized, IOR-Pavilion test workflow, build script, IOR parameters, how parameters are passed to IOR, *run_ior: functionality, Python IOR-Output Parser, Splunk data format, Splunk dashboard and features, and future work.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

TH-AB-207A-05: A Fully-Automated Pipeline for Generating CT Images Across a Range of Doses and Reconstruction Methods

Purpose: To evaluate the robustness of CAD or Quantitative Imaging methods, they should be tested on a variety of cases and under a variety of image acquisition and reconstruction conditions that represent the heterogeneity encountered in clinical practice. The purpose of this work was to develop a fully-automated pipeline for generating CT images that represent a wide range of dose and reconstruction conditions. Methods: The pipeline consists of three main modules: reduced-dose simulation, image reconstruction, and quantitative analysis. The first two modules of the pipeline can be operated in a completely automated fashion, using configuration files and running the modules in a batch queue. The input to the pipeline is raw projection CT data; this data is used to simulate different levels of dose reduction using a previously-published algorithm. Filtered-backprojection reconstructions are then performed using FreeCT-wFBP, a freely-available reconstruction software for helical CT. We also added support for an in-house, model-based iterative reconstruction algorithm using iterative coordinate-descent optimization, which may be run in tandem with the more conventional recon methods. The reduced-dose simulations and image reconstructions are controlled automatically by a single script, and they can be run in parallel on our research cluster. The pipeline was tested on phantom and lung screening datasets from a clinical scanner (Definition AS, Siemens Healthcare). Results: The images generated from our test datasets appeared to represent a realistic range of acquisition and reconstruction conditions that we would expect to find clinically. The time to generate images was approximately 30 minutes per dose/reconstruction combination on a hybrid CPU/GPU architecture. Conclusion: The automated research pipeline promises to be a useful tool for either training or evaluating performance of quantitative imaging software such as classifiers and CAD algorithms across the range of acquisition and reconstruction parameters present in the clinical environment. Funding support: NIH U01 CA181156; Disclosures (McNitt-Gray): Institutional research agreement, Siemens Healthcare; Past recipient, research grant support, Siemens Healthcare; Consultant, Toshiba America Medical Systems; Consultant, Samsung Electronics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Automated and Distributed Monte Carlo Generation for GlueX

MCwrapper is a set of systems that manages the entire Monte Carlo production workflow for GlueX and provides standards for how that Monte Carlo is produced. MCwrapper was designed to be able to utilize a variety of batch systems in a way that is relatively transparent to the user, thus enabling users to quickly and easily produce valid simulated data at home institutions worldwide. Additionally, MCwrapper supports an autonomous system that takes user’s project submissions via a custom web application. The system then atomizes the project into individual jobs, matches these jobs to resources, and monitors the jobs status. The entire system is managed by a database which tracks almost all facets of the systems from user submissions to the individual jobs themselves. Users can interact with their submitted projects online via a dashboard or, in the case of testing failure, can modify their project requests from a link contained in an automated email. Beginning in 2018 the GlueX Collaboration began to utilize the Open Science Grid (OSG) to handle a bulk of simulation tasks; these tasks are currently being performed on the OSG automatically via MCwrapper. This talk will outline the entire system of MCwrapper, its use cases, and the unique challenges facing the system.

Britton, Thomas↗
DOE OSTI2014

SU-E-T-497: Semi-Automated in Vivo Radiochromic Film Dosimetry Using a Novel Image Processing Algorithm

Purpose: To validate an automated image processing algorithm designed to detect the center of radiochromic film used for in vivo film dosimetry against the current gold standard of manual selection. Methods: An image processing algorithm was developed to automatically select the region of interest (ROI) in *.tiff images that contain multiple pieces of radiochromic film (0.5x1.3cm{sup 2}). After a user has linked a calibration file to the processing algorithm and selected a *.tiff file for processing, an ROI is automatically detected for all films by a combination of thresholding and erosion, which removes edges and any additional markings for orientation. Calibration is applied to the mean pixel values from the ROIs and a *.tiff image is output displaying the original image with an overlay of the ROIs and the measured doses. Validation of the algorithm was determined by comparing in vivo dose determined using the current gold standard (manually drawn ROIs) versus automated ROIs for n=420 scanned films. Bland-Altman analysis, paired t-test, and linear regression were performed to demonstrate agreement between the processes. Results: The measured doses ranged from 0.2-886.6cGy. Bland-Altman analysis of the two techniques (automatic minus manual) revealed a bias of -0.28cGy and a 95% confidence interval of (5.5cGy,-6.1cGy). These values demonstrate excellent agreement between the two techniques. Paired t-test results showed no statistical differences between the two techniques, p=0.98. Linear regression with a forced zero intercept demonstrated that Automatic=0.997*Manual, with a Pearson correlation coefficient of 0.999. The minimal differences between the two techniques may be explained by the fact that the hand drawn ROIs were not identical to the automatically selected ones. The average processing time was 6.7seconds in Matlab on an IntelCore2Duo processor. Conclusion: An automated image processing algorithm has been developed and validated, which will help minimize user interaction and processing time of radiochromic film used for in vivo dosimetry.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus

We report that the aqueous extract of yerba mate, a South American tea beverage made from Ilex paraguariensis leaves, has demonstrated bactericidal and inhibitory activity against bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). The gas chromatography-mass spectrometry (GC-MS) analysis of two unique fractions of yerba mate aqueous extract revealed 8 identifiable small molecules in those fractions with antimicrobial activity. For a more comprehensive analysis, a data analysis pipeline was assembled to prioritize compounds for antimicrobial testing against both MRSA and methicillin-sensitive S. aureus using forty-two unique fractions of the tea extract that were generated in duplicate, assayed for activity, and analyzed with GC-MS. As validation of our automated analysis, we checked our predicted active compounds for activity in literature references and used authentic standards to test for antimicrobial activity. 3,4-dihydroxybenzaldehyde showed the most antibacterial activity against MRSA at low concentrations in our bioassays. In addition, quinic acid and quercetin were identified using random forests analysis and 5-hydroxy pipecolic acid was identified using linear discriminant analysis. We also generated a ranked list of unidentified compounds that may contribute to the antimicrobial activity of yerba mate against MRSA. Here we utilized GC-MS data to implement an automated analysis that resulted in a ranked list of compounds that likely contribute to the antimicrobial activity of aqueous yerba mate extract against MRSA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Algorithms to automate gap-dependent integral tuning for the 2.8-meter long horizontal field undulator with a dynamic force compensation mechanism

A 2.8-meter long horizontal field prototype undulator with a dynamic force compensation mechanism has been developed and tested at the Advanced Photon Source (APS) at Argonne National Laboratory (Argonne). The magnetic tuning of the undulator integrals has been automated and accomplished by applying magnetic shims. A detailed description of the algorithms and performance is reported.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Testing Capabilities for Superconducting Magnets at Fermilab

This presentation will focus on the current testing capabilities for superconducting magnets at Fermilab, highlighting existing systems, recent upgrades, and future plans. The Vertical Magnet Test Facility (VMTF) remains a cornerstone for testing superconducting magnets in R&D applications, maintaining its established capabilities. Stand 4 continues to support the Hi-Lumi AUP production line of magnets in cryostats and has achieved significant improvements through a redesign of lead connections, resolving issues with liquid helium levels and resistance, culminating in a successful endurance test without interruption. Similarly, Stand 7 underwent commissioning and a lead redesign to reduce heat load, while its core testing capabilities remain unchanged. Looking forward, Stand 3 is undergoing a redesign, with plans to restart and begin commissioning by the end of 2025, introducing new features such as background magnetic field testing and upgraded power supplies. Fermilab is also advancing the High Field Vertical Magnet Test Facility (HFVMTF), designed to support the fusion and magnet R&D program, with commissioning scheduled for 2025 and critical components, including the cryostat and power supplies, being delivered. Enhancing all operations, the newly commissioned IB1 cryoplant now offers automated overnight helium production and efficient transfer to a 10,000-liter dewar, streamlining support across all test stands. This talk will provide a comprehensive overview of testing capabilities, and showcasing how Fermilab is advancing its capabilities to meet the evolving demands of superconducting magnet testing.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Investigation of Nanoparticle Degradation in Hydrogen Fuel Cell Systems through Automated Electron Microscopy

Proton exchange membrane fuel cells (PEMFC) are promising devices for the deployment of hydrogen-powered heavy-duty vehicles, providing a higher efficiency for similar driving range and fueling time than the existing ones. However, PEMFCs still encounter durability challenges mainly due to catalyst degradation in the cathode. Mitigating these performance losses requires a better understanding of the degradation mechanisms under heavy-duty accelerated stress tests (ASTs) [1]. Scanning transmission electron microscopy (STEM) combined with energy dispersive X-ray spectroscopy (EDS) are key tools for the analysis of Pt and PtCo nanoparticle size, spatial distribution and composition [2]. Electron tomography is also used to determine the rate and type of degradation of catalyst nanoparticles as a function of their position on the carbon support. In this work, automated data acquisition software, paired with a custom Python code, have been used to study the effect of different accelerated stress tests (ASTs) on nanoparticle coarsening [2]. Figure 1 shows high-angle annular dark-field (HAADF)-STEM images and EDS maps comparing the cathodes of membrane electrode assemblies (MEAs) following an electrocatalyst AST performed under H2/N2 with that of the heavy-duty AST performed under H2/air. We will discuss how AST conditions affect considerably the spatial distribution of the nanoparticles across the electrode between the membrane and microporous layer. Although the median particle size increased more in the MEA aged under the heavy-duty AST, as determined using a high-throughput image analysis, the quantitative EDS measurements demonstrate that the electrocatalyst AST resulted in more Pt and Co dissolution from the cathode, which is another important indicator of electrocatalyst degradation. We will further present the impact of the relative humidity (% RH) on the degradation mechanisms demonstrated using the same approach. Electron tomography has been used to distinguish the Pt nanoparticles residing on the carbon support surface (exterior) from those within the pore structure (interior) in order to determine the relative stability of interior and exterior nanoparticles. As shown in Figure 2, we will compare the Pt catalyst particle size at the beginning of test (BOT) and end of test (EOT), and discuss the importance of automating the electron tomography workflow, i.e. acquisition, reconstruction, and visualization, to increase sampling and determine the standard deviation of these measurement. The outlook for utilizing low-dose cryo-tomography for limiting damage to the catalyst, support, and especially proton-conducting ionomer will also be discussed [3].

Amichi, Lynda↗
DOE OSTI2024

A nuclear power plant digital twin for developing robot navigation and interaction

As robot technologies are rapidly improving, an increasing number of new ideas on utilizing robots for automated operation and maintenance tasks in nuclear power plants (NPPs) are being studied. However, due to safety concerns, researchers hardly found opportunities to test their new robot solutions on physical NPPs. In that sense, an efficient and realistic simulation environment plays a vital role in the development of automation systems for an NPP. In this paper, we propose the design of a 3D digital twin system capable of simulating NPP in real-time. This system obtains the data from a full-scope NPP simulator to reproduce the operating conditions of the plant. In addition, a scenario of a team of robots performing inspection tasks like temperature and pressure measurements will highlight its usability. This system enables development of intelligent robot swarms to deploy for inspection and maintenance purposes. It will positively impact autonomous control and operations for many types of reactors by reducing uncertainty in autonomous control and providing the tools necessary for remote intervention.

Energy & Fuels↗
DOE OSTI2017

A Review of Power Distribution Test Feeders in the United States and the Need for Synthetic Representative Networks

Under the increasing penetration of distributed energy resources and new smart network technologies, distribution utilities face new challenges and opportunities to ensure reliable operations, manage service quality, and reduce operational and investment costs. Simultaneously, the research community is developing algorithms for advanced controls and distribution automation that can help to address some of these challenges. However, there is a shortage of realistic test systems that are publically available for development, testing, and evaluation of such new algorithms. Concerns around revealing critical infrastructure details and customer privacy have severely limited the number of actual networks published and that are available for testing. In recent decades, several distribution test feeders and US-featured representative networks have been published, but the scale, complexity, and control data vary widely. This paper presents a first-of-a-kind structured literature review of published distribution test networks with a special emphasis on classifying their main characteristics and identifying the types of studies for which they have been used. As a result, this both aids researchers in choosing suitable test networks for their needs and highlights the opportunities and directions for further test system development. In particular, we highlight the need for building large-scale synthetic networks to overcome the identified drawbacks of current distribution test feeders.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2015

SU-E-P-31: Quantifying the Amount of Missing Tissue in a Digital Breast Tomosynthesis

Purpose: To automatically quantify the amount of missing tissue in a digital breast tomosynthesis system using four stair-stepped chest wall missing tissue gauges in the Tomophan™ from the Phantom Laboratory and image processing from Image Owl. Methods: The Tomophan™ phantom incorporates four stair-stepped missing tissue gauges by the chest wall, allowing measurement of missing chest wall in two different locations along the chest wall at two different heights. Each of the four gauges has 12 steps in 0.5 mm increments rising from the chest wall. An image processing algorithm was developed by Image Owl that first finds the two slices containing the steps then finds the signal through the highest step in all four gauges. Using the signal drop at the beginning of each gauge the distance to the end of the image gives the length of the missing tissue gauge in millimeters. Results: The Tomophan™ was imaged in digital breast tomosynthesis (DBT) systems from various vendors resulting in 46 cases used for testing. The results showed that on average 1.9 mm of 6 mm of the gauges are visible. A small focus group was asked to count the number of visible steps for each case which resulted in a good agreement between observer counts and computed data. Conclusion: First, the results indicate that the amount of missing chest wall can differ between vendors. Secondly it was shown that an automated method to estimate the amount of missing chest wall gauges agreed well with observer assessments. This finding indicates that consistency testing may be simplified using the Tomophan™ phantom and analysis by an automated image processing named Tomo QA. In general the reason for missing chest wall may be due to a function of the beam profile at the chest wall as DBT projects through the angular sampling. Research supported by Image Owl, Inc., The Phantom Laboratory, Inc. and Raforninn ehf; Mallozzi and Healy employed by The Phantom Laboratory, Inc.; Goodenough is a consultant to The Phantom Laboratory, Inc.; Fredriksson, Kristbjornsson, Olafsson, Oskarsdottir and Olafsdottir are employed by Raforninn, Ehf.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Using GIS for Processing, Analysis and Visualization of Hydrological Model Data - 16202

The Applied Research Center at Florida International University (ARC-FIU) is supporting the soil and groundwater remediation efforts of the U.S. Department of Energy's (DOE's) Savannah River Site (SRS) by developing a surface water model to simulate the hydrology and the fate and transport of contaminants and sediment in the Tims Branch watershed. Advances in ArcGIS software through the development of spatial GIS database (geo-database) technology, coupled with the development of data models such as ArcHydro which possesses a spatial relational database management system (RDMS) schema and relationship structure specific to hydrologic systems, provides modelers with tools and applications to assist in the processing, analysis and visualization of flow and contaminant transport data. In addition, the coupling of this type of geo-database structure with a numerical modeling package such as MIKE SHE/MIKE 11 can serve as an efficient tool that significantly reduces the time needed for data preparation. The MIKE modeling system has a geographic information systems (GIS) user interface built into its system that can directly use GIS data for model inputs. GIS-based hydrologic models can provide a spatial element that other hydrologic models lack. GIS is important for processing and analysis of large spatio-temporal datasets derived from multiple sources that are being used for setting up of models, model calibration and simulation of flow and contaminant fate and transport. GIS-based approaches in hydrological modeling can also provide the benefit of combining different layers of geographic data to create new integrated information which can be quite useful for creating dependent or independent hydrological variables. ARC-FIU has developed an ArcGIS geo-database to support the hydrological modeling work being conducted at SRS. The SRS geo-database was developed based on the ArcHydro and ArcGIS Base Map data models with modifications made for project specific input parameters. The significance of this approach was to ensure its replicability for potential application at other DOE sites. The SRS geo-database assists in the storage and management of GIS and time series data being used for hydrological model development at Savannah River Site. Other GIS tools such as ArcGIS Model Builder coupled with Python scripting have enabled the automation of many of the repetitive geo-processing tasks required for pre- and post-processing of the hydrological modeling data. Automation of many of the data processing tasks has facilitated faster and hence more complex analyses of field test data. The toolbox created is also a scalable and reusable application that can be implemented in other watersheds. This paper describes the use of ArcGIS tools for the pre-processing, spatial delineation and analysis of hydrological model data; for automation of repetitive geo-processing tasks; and for visualization of different hydrological components of the Tims Branch watershed. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Nonlocal Means Denoising of Self-Gated and k-Space Sorted 4-Dimensional Magnetic Resonance Imaging Using Block-Matching and 3-Dimensional Filtering: Implications for Pancreatic Tumor Registration and Segmentation

Purpose: To denoise self-gated k-space sorted 4-dimensional magnetic resonance imaging (SG-KS-4D-MRI) by applying a nonlocal means denoising filter, block-matching and 3-dimensional filtering (BM3D), to test its impact on the accuracy of 4D image deformable registration and automated tumor segmentation for pancreatic cancer patients. Methods and Materials: Nine patients with pancreatic cancer and abdominal SG-KS-4D-MRI were included in the study. Block-matching and 3D filtering was adapted to search in the axial slices/frames adjacent to the reference image patch in the spatial and temporal domains. The patches with high similarity to the reference patch were used to collectively denoise the 4D-MRI image. The pancreas tumor was manually contoured on the first end-of-exhalation phase for both the raw and the denoised 4D-MRI. B-spline deformable registration was applied to the subsequent phases for contour propagation. The consistency of tumor volume defined by the standard deviation of gross tumor volumes from 10 breathing phases (σ-GTV), tumor motion trajectories in 3 cardinal motion planes, 4D-MRI imaging noise, and image contrast-to-noise ratio were compared between the raw and denoised groups. Results: Block-matching and 3D filtering visually and quantitatively reduced image noise by 52% and improved image contrast-to-noise ratio by 56%, without compromising soft tissue edge definitions. Automatic tumor segmentation is statistically more consistent on the denoised 4D-MRI (σ-GTV = 0.6 cm{sup 3}) than on the raw 4D-MRI (σ-GTV = 0.8 cm{sup 3}). Tumor end-of-exhalation location is also more reproducible on the denoised 4D-MRI than on the raw 4D-MRI in all 3 cardinal motion planes. Conclusions: Block-matching and 3D filtering can significantly reduce random image noise while maintaining structural features in the SG-KS-4D-MRI datasets. In this study of pancreatic tumor segmentation, automatic segmentation of GTV in the registered image sets is shown to be more consistent on the denoised 4D-MRI than on the raw 4D-MRI.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Modelica buildings library

This paper describes the Buildings library, a free open-source library that is implemented in Modelica, an equation-based object-oriented modeling language. The library supports rapid prototyping, as well as design and operation of building energy and control systems. First, we describe the scope of the library, which covers HVAC systems, multi-zone heat transfer and multi-zone airflow and contaminant transport. Next, we describe differentiability requirements and address how we implemented them. We describe the class hierarchy that allows implementing component models by extending partial implementations of base models of heat and mass exchangers, and by instantiating basic models for conservation equations and flow resistances. We also describe associated tools for pre- and post-processing, regression tests, co-simulation and real-time data exchange with building automation systems. Furthermore, the paper closes with an example of a chilled water plant, with and without water-side economizer, in which we analyzed the system-level efficiency for different control setpoints.

42 ENGINEERING↗
DOE OSTI2025

Exploring Large Language Model Agents in Cybersecurity: A Literature Review with Experiments

The accelerated development and integration of large language model (LLM) agents have led researchers and developers to explore their effectiveness in cybersecurity, specifically with penetration testing (pentesting). Recent research efforts have attempted to use LLM agents to automate the process of pentesting because of the cost and time requirements that are required to perform a manual review. However, not all of the tools perform as expected. This paper reviews some of the newest and most popular autonomous pentesting frameworks, highlighting the capabilities and limitations of each one with the goal of providing the components needed to successfully and effectively build an autonomous pentesting agent in the future.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

An Automated Disruption-Tolerant Key Management Framework for Critical Systems

Key management is critical to secure operation. Distributed control systems, such as Supervisory Control and Data Acquisition (SCADA) systems, have unique operational requirements that make conventional key management solutions less effective and burdensome. This paper presents a novel Kerberos-based framework for automated, disruption-tolerant key management for control system environments. Here, experimental tests and their results are presented to quantify the expected performance overhead of this approach. Additionally, Zeek sensor analytics are presented to aid in monitoring the health and security of the key management framework operation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Cyberbiosecurity and Public Health in the Age of COVID-19

Cyberbiosecurity, the aspect of biosecurity involving the digital representation of biological data, had already been emerging as a matter of public concern even prior to the onset of the COVID-19 pandemic. Key issues of concern include, among others, the privacy of patient data, the security of public health databases, the integrity of diagnostic test data, the integrity of public biological databases, the security implications of automated laboratory systems and the security of proprietary biological engineering advances. With the onset of the COVID-19 pandemic, and the importance of digital resources in combatting it, concern about the potential for cyber attacks by state-based or non-state actors has been elevated. To illuminate the challenges, we focus on the cyber vulnerabilities that need to be addressed in public health activities such as disease surveillance and outbreak management. In particular, we examine cyber issues raised by the accelerated pace of development for COVID mitigations, treatments, and vaccines.

cybersecurity, biosecurity↗
DOE OSTI2016

Pursuing Cost Effective Tank Waste Characterization at the Savannah River Site - 16172

The U. S. Department of Energy Office of Environmental Management has tasked the Savannah River National Laboratory (SRNL) with developing strategies and technologies to understand, optimize, scale, and speed up tank waste characterization. This scope is part of a multi-year project with the end goal of implementing programmatic changes that accelerate tank waste processing and tank closure schedules, and at the same time reduce characterization costs, while maintaining data integrity. The project is currently in its second year. During the first year of the project, SRNL completed a series of activities focused on understanding the range of current characterization practices, needs, gaps, risks, and potential alternative approaches. Based on the results, conclusions were drawn regarding aspects of the programs that are most costly and time consuming; particular waste constituents that drive costs, schedule, and program risks; alternative characterization approaches (other than sampling and analysis) that are less expensive and more rapid; new laboratory methods holding the greatest promise for reducing characterization costs and schedule; and in whole, the primary areas where current characterization practices can be improved. SRNL's current scope is focusing on three primary activities: 1) development of a technical basis/strategy for improving the cost effectiveness and schedule of SRNL's tank closure characterization program; 2) design/assembly of hardware, plumbing, and software for automating select radiochemical separation and waste removal processes; and 3) development and testing of alternative radiochemical separation protocols most likely to improve high resource demand/time consuming analysis methods (such as Ra-226, Pa-231, Tc-99/I-129, and/or Y/trivalent actinide separations). (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗