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DOE OSTI2024

UMap: An application-oriented user level memory mapping library

Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Down-selection of Innovative Fusion Materials

The goal of this proposal is to develop and fundamentally understand the microstructure of refractory multi-component alloys (MCA) as fusion-relevant plasma facing and structural materials, a step to down-select innovative fusion materials prior to the process of advancing their technology readiness level (TRL). Developing materials is paramount to enable fusion as energy source since no existing material is capable of coping with such extreme conditions. We will aim at understanding the role of chemistry and microstructure in these complex multi-component alloys systematically comparing their performance with pure tungsten materials in terms of mechanical properties and manufacturability. Such understanding will open opportunities to optimize MCAs for fusion applications and has a potential of attracting industry partnership.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Slow control and data acquisition systems in the Mu2e experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinolessconversion of a muon into an electron in the field of an aluminum nucleus with a sensitivityimprovement by a factor of 10,000 over existing limits. The Mu2e Trigger and Data AcquisitionSystem (TDAQ) usesotsdaqas the online Data Acquisition System (DAQ) solution. Developed atFermilab,otsdaqintegrates both theartdaqDAQ and theartanalysis frameworks for event transfer,filtering, and processing.otsdaqis an online DAQ software suite with a focus on flexibility andscalability and provides a multi-user, web-based, interface accessible through a web browser. Thedata stream from the detector subsystems is read by a software filter algorithm that selects eventswhich are combined with the data flux coming from a Cosmic Ray Veto System. The DetectorControl System (DCS) has been developed using the Experimental Physics and Industrial ControlSystem (EPICS) open source platform for monitoring, controlling, alarming, and archiving. TheDCS System has been integrated intootsdaq. A prototype of the TDAQ and the DCS systems hasbeen built at Fermilab’s Feynman Computing Center. In this paper, we report on the progress ofthe integration of this prototype in the onlineotsdaqsoftware.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Abstract Motivation Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Supplementary information Supplementary data are available at Bioinformatics online.

Ma, Jian↗

DOE OSTI2016

Lighting system with thermal management system

Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

MENUS—Materials engineering by neutron scattering

Materials engineering by neutron scattering (MENUS) at the second target station will be a transformational high-flux, versatile, multiscale materials engineering diffraction beamline with unprecedented new capabilities for the study of complex materials and structures. It will support both fundamental and applied materials research in a broad range of fields. MENUS will combine unprecedented long-wavelength neutron flux and unique detector coverage to enable real-time studies of complex structural and functional materials under external stimuli. The incorporated small angle neutron scattering and transmission/imaging capabilities will extend its sensitivity to larger length scales and higher spatial resolution. Multimodal MENUS will provide crystallographic and microstructure data to the materials science and engineering community to understand lattice strain/phase transition/microstructure/texture evolution in three orthogonal directions in complex material systems under combined extreme applied conditions. Finally, the capabilities of MENUS will open new scientific opportunities and meet the research needs for science challenges to enable studies of a range of phenomena and answer the key questions in material design/exploration, advanced material processing, transformative manufacturing, and material operations of national impacts in our daily life.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Database development and exploration of process–microstructure relationships using variational autoencoders

The paper demonstrates graphical representation of a large database containing process–microstructure relationships using an unsupervised machine learning algorithm. Correlating microstructural features to processing is an essential first step to answer the difficult problem of process sequence design. Here, a large database of 346,200 orientation distribution functions resulting from a variety of process sequences is constructed, where each sequence comprises up to four stages of tension, compression and rolling along different directions in various permutations. This open-source database is constructed for collaborative development of process design algorithms. The paper demonstrates a novel application of the large database: graphical representation of texture–process relationships. A variational autoencoder is used to reduce the entire database to a two dimensional latent space where variations in processes and properties can be visualized. Using proximity analysis in this latent space, we can quickly unearth multiple process solutions to the problem of texture or property design.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Quantitative Analysis of Color Differences within High Contrast, Low Power Reversible Electrophoretic Displays

Here, quantitative color analysis is performed on videos of high contrast, low power reversible electrophoretic deposition (EPD)-based displays operated under different applied voltages. This analysis is coded in an open-source software, relies on a color differentiation metric, ΔE * 00 , derived from digital video, and provides an intuitive relationship between the operating conditions of the devices and their performance. Time-dependent ΔE * 00 color analysis reveals color relaxation behavior, recoverability for different voltage sequences, and operating conditions that can lead to optimal performance.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Online DAQ and slow control interface for the Mu2e experiment

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Machine Learning for Geothermal Resource Exploration in the Tularosa Basin, New Mexico

Geothermal energy is considered an essential renewable resource to generate flexible electricity. Geothermal resource assessments conducted by the U.S. Geological Survey showed that the southwestern basins in the U.S. have a significant geothermal potential for meeting domestic electricity demand. Within these southwestern basins, play fairway analysis (PFA), funded by the U.S. Department of Energy’s (DOE) Geothermal Technologies Office, identified that the Tularosa Basin in New Mexico has significant geothermal potential. This short communication paper presents a machine learning (ML) methodology for curating and analyzing the PFA data from the DOE’s geothermal data repository. The proposed approach to identify potential geothermal sites in the Tularosa Basin is based on an unsupervised ML method called non-negative matrix factorization with custom k-means clustering. This methodology is available in our open-source ML framework, GeoThermalCloud (GTC). Using this GTC framework, we discover prospective geothermal locations and find key parameters defining these prospects. Our ML analysis found that these prospects are consistent with the existing Tularosa Basin’s PFA studies. This instills confidence in our GTC framework to accelerate geothermal exploration and resource development, which is generally time-consuming.

15 GEOTHERMAL ENERGY↗

DOE OSTI2016

SU-F-T-260: Using Portal Image Device for Pre-Treatment QA in Volumetric Modulated Arc Plans with Flattening Filter Free (FFF) Beams

Purpose: To implement and validate a method of using electronic portal image device (EPID) for pre-treatment quality assurance (QA) of volumetric modulated arc therapy (VMAT) plans using flattering filter free (FFF) beams for stereotactic body radiotherapy (SBRT). Methods: On Varian Edge with 6MV FFF beam, open field (from 2×2 cm to 20×20 cm) EPID images were acquired with 200 monitor unit (MU) at the image device to radiation source distance of 150cm. With 10×10 open field and calibration unit (CU) provided by vendor to EPID image pixel, a dose conversion factor was determined by dividing the center dose calculated from the treatment planning system (TPS) to the corresponding CU readout on the image. Water phantom measured beam profile and the output factors for various field sizes were further correlated to those of EPID images. The dose conversion factor and correction factors were then used for converting the portal images to the planner dose distributions of clinical fields. A total of 28 VMAT fields of 14 SBRT plans (8 lung, 2 prostate, 2 liver and 2 spine) were measured. With 10% low threshold cutoff, the delivered dose distributions were compared to the reference doses calculated in water phantom from the TPS. A gamma index analysis was performed for the comparison in percentage dose difference/distance-to-agreement specifications. Results: The EPID device has a linear response to the open fields with increasing MU. For the clinical fields, the gamma indices between the converted EPID dose distributions and the TPS calculated 2D dose distributions were 98.7%±1.1%, 94.0%±3.4% and 70.3%±7.7% for the criteria of 3%/3mm, 2%/2mm and 1%/1mm, respectively. Conclusion: Using a portal image device, a high resolution and high accuracy portal dosimerty was achieved for pre-treatment QA verification for SBRT VMAT plans with FFF beams.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Open Source Visualization and Analysis Platform for 3D Reconstructions of Materials by Transmission Electron Microscopy

Three-dimensional characterization of materials at the nano- and meso-scale has become possible with transmission and scanning transmission electron microscopes (S/TEM). Its importance has extended to a wide class of nanomaterials such as hydrogen fuel cells, solar cells, industrial catalysts, new battery materials and semiconductor devices, as well as spanning high-tech industry, universities, and national labs. While capable instrumentation is abundant, this rapidly expanding demand for high-resolution tomography is bottlenecked by software that is instead tailored for lower-dose, biological applications and not optimized for higher-resolution materials applications. Existing tomography fails to utilize the chemical information provided by S/TEM spectrometers. To address this problem, this project delivered a scalable, fully functional, freely-distributable, open Source materials tomography package with a modern user interface that enables automated acquisition, alignment, and real-time reconstruction of raw tomography data, and provides advanced segmentation, three-dimensional chemical visualization and analysis optimized for materials applications. It has established an extendable framework capable of automation for high-throughput for the tomography of materials from data acquisition to visualization. Phase I and II delivered a full-featured, cross-platform, clean and integrated application for S/TEM materials tomography. It can read projection data from the microscope, with graphical tools for alignment of data, tomographic reconstruction, segmentation, and visualization of the reconstructed 3D volume. The entire pipeline can be saved to an XML state file, enabling fully reproducible data processing and analysis with a full Python environment for the development of custom algorithms, processing, and analysis requirements. Phase IIB extended the application to provide real-time tomographic reconstruction, "live updates" as data is processed, analysis of big data, and multi-channel tomography. Here, quantitative assessment of nanomaterials can occur as data is being recorded on a 3D visualization platform that accommodates additional information from multiple channels. We provide unmatched high-throughput tomography, where the complete tomographic pipeline from measurement to 3D visualization can occur rapidly. The project was extended to offer capabilities for micro-CT, X-ray, neutron, focused ion beam, atomic electron tomography and atom probe tomography. With over 600 transmission electron microscopes worldwide and approximately 50 coming online each year, the demand and impact of an open-source tomography tool is large. Significant opportunities exist in high-tech industry, universities, and national labs to enable or enhance three-dimensional imaging at the nanoscale and bring automated high-throughput approaches that will accelerate progress in materials characterization and metrology. The project supports a service based business model by enabling lab-specific acquisition and processing customization and integration-support and development that will be provided into Phase III and beyond.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Simulation-Based Analysis of Impacts of Reduced Envelope and Duct Air Leakage on Indoor Air Pollutant Concentrations in Occupied Manufactured Homes

This report presents a simulation-based analysis that estimates the magnitude of indoor air pollutant concentration changes that could result from the proposed energy conservation standards. The analysis was conducted for a 1568 ft 2 , double-wide MH with variations in heating and cooling equipment (either furnace + air conditioner or heat pump) and various types of whole-house mechanical ventilation (continuous exhaust fan or central fan integrated supply), in three locations with varying climate conditions: Chicago IL, Fresno, CA; and Houston TX. The simulations tracked four air pollutants that can reach levels exceeding established safe target levels in homes: acrolein, formaldehyde, fine particulate matter (PM 2.5 ), and nitrogen dioxide (NO 2 ). The simulations considered acrolein and formaldehyde emitted from continuous indoor sources; acrolein, NO 2 and PM 2.5 from cooking; PM 2.5 from dispersed occupant activities; and NO 2 and PM 2.5 from outdoors, using historical data to identify typical levels. The impacts in homes operating or not operating whole-house mechanical ventilation equipment, kitchen and bath exhaust fans, and window opening as ventilation approaches were examined.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Alteration trends and geochemical source region characteristics preserved in the fluviolacustrine sedimentary record of Gale crater, Mars

The Mars Science Laboratory’s Chemistry and Camera (ChemCam) instrument suite on-board the Curiosity rover has analysed ~1200 sedimentary targets during the mission up to sol 1482. These targets have included sedimentary rock, diagenetic features (e.g., fracture-associated alteration halos, mineral veins, nodules, and erosion resistant raised ridges), active aeolian fines, soils and float. We have isolated ChemCam geochemical trends relating to diagenetic features and alteration products from those of the sedimentary rock in order to identify the compositional characteristics of Gale crater’s sediment source regions. The effects of grain size variation on sedimentary unit geochemistry have been taken into account by grouping and analysing geological units according to grain size. With obvious diagenetic features removed from the database, and predominately isochemical aqueous alteration inferred for the Mt Sharp Group samples, we propose that source region composition is a stronger source of geochemical change between the Bradbury and Mt Sharp Groups than open-system alteration. Additionally, a lack of correlation between the Chemical Index of Alteration (CIA) values and SiO 2 , MgO or FeO T indicates that the slight increase in chemical weathering of the Mt Sharp Group sediments was insufficient to overprint sediment source compositional signatures. This has led to the identification of five unique igneous endmember compositions which we hypothesise to have contributed to Gale crater’s stratigraphic record. These endmembers are: (1) a subalkaline basalt, compositionally similar to the tholeiitic Adirondack Class basalts of Gusev crater, and dominant within the finer grained units up to the base of Mt Sharp; (2) a trachybasalt, mostly identified within conglomerate units from the Darwin waypoint to the base of Mt Sharp; (3) a potassium-rich volcanic source, determined from strong potassium enrichment and a high abundance of sanidine that is most dominant in the fluvial sandstones and conglomerates of the Kimberley formation; (4) a highly evolved, silica-rich igneous source that correlates with the presence of tridymite, and is recorded in the lacustrine mudstone of Mt Sharp’s Marias Pass locality; and, (5) a fractionated, relatively SiO 2 -rich subalkaline basalt, seen to have influenced the composition of mudstone deposited in the lower part of the Mt Sharp Group. Endmembers (1), (2), (3), and (4) have previously been identified at specific waypoints along the rover’s traverse, but we show that their influence extends throughout Gale’s stratigraphic record. The occurrence of detected endmembers is also strongly correlated with stratigraphic position, which suggests changing sediment source regions with time. We conclude that Gale sediment provenances were much more varied than suggested by the largely homogenous, globally-distributed Martian basalt inferred from orbit, showing that complex magmatic assemblages exist within the ancient highland crust surrounding Gale.

58 GEOSCIENCES↗

DOE OSTI2021

Reliability metrics and their management implications for open pond algae cultivation

The prevalence of contaminating organisms in outdoor algae cultivation, with the often-associated dramatic crop failures, necessitates the need for metrics describing production system reliability. Standard metrics for algae cultivation reliability are critically needed to be able to map improvements in operational parameters, but do not currently exist. In this work, we present a set of standard metrics including mean time to failure (MTTF) and mean time between failures (MTBF) as the basis for the calculation of pond failure rate (FR) and reliability coefficient (RC). Metrics associated with the numbers of contaminating organisms such as abundance ratio (AR), prevalence of infection (PI), and mean intensity of infection (MII) are also relevant. These metrics, based on measured experimental values of outdoor pond performance during the Algae Testbed Public-Private Partnership (ATP3) Unified Field Studies (UFS), provide a basis for quantifying pond failure and provide insight into potential pond management and contaminant mitigation strategies. From these reliability metrics applied to this dataset, we are able to link operational parameters, such as harvest frequency and inoculum source, to pond reliability for different algae strains and seasons, and from an assessment of AR, provide contamination thresholds beyond which a culture may be unrecoverable. Ultimately, the implementation of widely-practiced and simple-to-calculate algae pond reliability metrics calculated from rapid and easy to collect data or observations will reduce risk and uncertainty in large-scale algae deployment and aid in the development of integrated pest management (IPM) strategies.

09 BIOMASS FUELS↗

DOE OSTI2017

Design and performance of an X-ray scanning microscope at the Hard X-ray Nanoprobe beamline of NSLS-II

A hard X-ray scanning microscope installed at the Hard X-ray Nanoprobe beamline of the National Synchrotron Light Source II has been designed, constructed and commissioned. The microscope relies on a compact, high stiffness, low heat dissipation approach and utilizes two types of nanofocusing optics. It is capable of imaging with ~15 nm × 15 nm spatial resolution using multilayer Laue lenses and 25 nm × 26 nm resolution using zone plates. Fluorescence, diffraction, absorption, differential phase contrast, ptychography and tomography are available as experimental techniques. The microscope is also equipped with a temperature regulation system which allows the temperature of a sample to be varied in the range between 90 K and 1000 K. The constructed instrument is open for general users and offers its capabilities to the material science, battery research and bioscience communities.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Factors affecting variability in PM2.5 exposure concentrations in a metro system

Highlights: • Door-side PM{sub 2.5} concentrations typically increase when train doors open. • Train in-cabin PM{sub 2.5} concentrations are lower than ambient PM{sub 2.5} concentration. • Underground metro train in-cabin PM{sub 2.5} concentrations are higher than above-ground. • Ambient PM{sub 2.5} infiltration into cabins is higher for above-ground than underground. • Non-ambient sources contributed around half of PM{sub 2.5} inside the underground metro. The objectives of this study were to: (1) evaluate PM{sub 2.5} inflow to metro train cabins when doors open at stations; (2) assess the spatial and temporal variability in PM{sub 2.5} exposure concentration; and (3) quantify the relationship between in-cabin concentration versus outdoor and non-ambient PM{sub 2.5}. We measured in-cabin PM{sub 2.5} concentrations using portable monitors at the door-side and center of a train cabin simultaneously on a Hong Kong metro line. In addition, platform and in-cabin pollutant concentrations near a train door were simultaneously measured. Short-term spikes in PM{sub 2.5} concentrations typically occur near train doors when doors open, related to inflow of ambient air aboveground and tunnel air underground. In-cabin PM{sub 2.5} exposure concentrations are typically lower away from the doors when the doors open. PM{sub 2.5} concentrations inside train cabins and on station platform operating above-ground are more influenced, compared to underground, by outdoor PM{sub 2.5}. Moreover, non-ambient sources contribute approximately 50% of train in-cabin and station platform PM{sub 2.5} concentrations during underground operation. The results help more accurately quantify commuting PM{sub 2.5} exposure on a metro system, and can be used to improve population-based exposure simulation models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Quantifying vegetation and canopy structural complexity from terrestrial LiDAR data using the FORESTR R package

Terrestrial LiDAR (light detection and ranging) technologies have created new means of quantifying forest canopy structure, allowing not only the estimation of biomass, but also descriptions of the position and variability in canopy elements in space. Such measures provide novel structural information broadly useful to ecologists. There is a growing need for both a detailed taxonomy of forest canopy structural complexity (CSC) and open, transparent, and flexible tools to quantify complexity in ways that will advance foundational ecological knowledge of structure-function relationships. The CSC taxonomy we present groups structural descriptors into five categories: leaf area and density, canopy height, canopy arrangement, canopy openness, and canopy variability. This paper also introduces the r package forestr, the first open-source r package for the calculation of CSC metrics from terrestrial LiDAR data. The r package forestr is an analysis toolbox that works with portable canopy LiDAR (PCL) data and other pixelated/voxelized point clouds derived from terrestrial LiDAR scanning (TLS) data to calculate CSC metrics of interest to ecologists, modellers, forest managers, and remote sensing scientists.

52 ecosystem↗