Results for “proxy application” — Page 15

DOE OSTI2023

Practical Understanding of Cancer Model Identifiability in Clinical Applications

Mathematical models are a core component in the foundation of cancer theory and have been developed as clinical tools in precision medicine. Modeling studies for clinical applications often assume an individual’s characteristics can be represented as parameters in a model and are used to explain, predict, and optimize treatment outcomes. However, this approach relies on the identifiability of the underlying mathematical models. In this study, we build on the framework of an observing-system simulation experiment to study the identifiability of several models of cancer growth, focusing on the prognostic parameters of each model. Our results demonstrate that the frequency of data collection, the types of data, such as cancer proxy, and the accuracy of measurements all play crucial roles in determining the identifiability of the model. We also found that highly accurate data can allow for reasonably accurate estimates of some parameters, which may be the key to achieving model identifiability in practice. As more complex models required more data for identification, our results support the idea of using models with a clear mechanism that tracks disease progression in clinical settings. For such a model, the subset of model parameters associated with disease progression naturally minimizes the required data for model identifiability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Limitations of reanalysis data for wind power applications

Wind energy resource estimates commonly depend on simulated wind speed profiles generated by reanalysis or weather models due to the lack of long time series measurements with sufficient coverage at relevant heights (roughly 90 m above ground). However, modeled data, including reanalyses, can be noisy and display a wide range of biases and errors, variously attributed to terrain effects, poor coverage of assimilated inputs, and model resolution. Wind generation records, if available at high temporal and geographical resolution, can provide a proxy for wind measurements and allow for evaluation of reanalyses and weather model wind time series. We use a 7-year-long data set of hourly, plant-level generation records from over 100 wind plants across Texas to evaluate two commonly used reanalysis data sets (MERRA2 and ERA5). Additionally, we use 1-year of records (2019) to evaluate an operational, high-resolution regional weather modeling product (HRRR v3). We find that across the region, and across all modeling products, the modeled representation of wind generation (i.e., wind speeds at hub heights passed through a power curve) has relatively small mean errors when aggregated daily, but that accuracy and hourly correlation have a strong diurnal sensitivity. Accuracy and correlation systematically decline through the evening and markedly improve after sunrise. These diurnal patterns persist even in the highest resolution model tested (HRRR v3). We hypothesize the nighttime decline in accuracy is mostly due to poorly represented boundary layer conditions, perhaps related to model representation of stability, while other uncertainties (such as wake effects) play a secondary role.

17 WIND ENERGY↗

NASA NTRS2022

Merging of the Case 2 Regional Coast Colour and Maximum‑Peak Height Chlorophyll‑a Algorithms: Validation and Demonstration of Satellite‑derived Retrievals Across US Lakes

Water quality monitoring is relevant for protecting the designated, or beneficial uses, of water such as drinking, aquatic life, recreation, irrigation, and food supply that support the economy, human well-being, and aquatic ecosystem health. Managing finite water resources to support these designated uses requires information on water quality so that managers can make sustainable decisions. Chlorophyll-a (chl-a, µg L−1) concentration can serve as a proxy for phytoplankton biomass and may be used as an indicator of increased anthropogenic nutrient stress. Satellite remote sensing may present a complement to in situ measures for assessments of water quality through the retrieval of chl-a with in-water algorithms. Validation of chl-a algorithms across US lakes improves algorithm maturity relevant for monitoring applications. This study compares performance of the Case 2 Regional Coast Colour (C2RCC) chl-a retrieval algorithm, a revised version of the Maximum-Peak Height (MPH(P)) algorithm, and three scenarios merging these two approaches. Satellite data were retrieved from the MEdium Resolution Imaging Spectrometer (MERIS) and the Ocean and Land Colour Instrument (OLCI), while field observations were obtained from 181 lakes matched with U.S. Water Quality Portal chl-a data. The best performance based on mean absolute multiplicative error (MAEmult) was demonstrated by the merged algorithm referred to as C15−M10 (MAEmult = 1.8, biasmult = 0.97, n = 836). In the C15−M10 algorithm, the MPH(P) chl-a value was retained if it was > 10 µg L−1; if the MPH(P) value was ≤ 10 µg L−1, the C2RCC value was selected, as long as that value was < 15 µg L−1. Time-series and lake-wide gradients compared against independent assessments from Lake Champlain and long-term ecological research stations in Wisconsin were used as complementary examples supporting water quality reporting requirements. Trophic state assessments for Wisconsin lakes provided examples in support of inland water quality monitoring applications. This study presents and assesses merged adaptations of chl-a algorithms previously reported independently. Additionally, it contributes to the transition of chl-a algorithm maturity by quantifying error statistics for a number of locations and times.

Satellite↗

DOE OSTI2016

Application of distance correction to ChemCam laser-induced breakdown spectroscopy measurements

Laser-induced breakdown spectroscopy (LIBS) provides chemical information from atomic, ionic, and molecular emissions from which geochemical composition can be deciphered. Analysis of LIBS spectra in cases where targets are observed at different distances, as is the case for the ChemCam instrument on the Mars rover Curiosity, which performs analyses at distances between 2 and 7.4 m is not a simple task. Previously, we showed that spectral distance correction based on a proxy spectroscopic standard created from first-shot dust observations on Mars targets ameliorates the distance bias in multivariate-based elemental-composition predictions of laboratory data. In this work, we correct an expanded set of neutral and ionic spectral emissions for distance bias in the ChemCam data set. By using and testing different selection criteria to generate multiple proxy standards, we find a correction that minimizes the difference in spectral intensity measured at two different distances and increases spectral reproducibility. When the quantitative performance of distance correction is assessed, there is improvement for SiO 2 , Al 2 O 3 , CaO, FeOT, Na 2 O, K 2 O, that is, for most of the major rock forming elements, and for the total major-element weight percent predicted. But, for MgO the method does not provide improvements while for TiO 2 , it yields inconsistent results. Additionally, we observed that many emission lines do not behave consistently with distance, evidenced from laboratory analogue measurements and ChemCam data. This limits the effectiveness of the method.

36 MATERIALS SCIENCE↗

DOE OSTI2016

CoMD Implementation Suite in Emerging Programming Models

CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended to support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.

Haque, Riyaz↗

DOE OSTI2014

CoMD Implementation Suite in Emerging Programming Models

CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended to support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.

Haque, Riyaz↗

DOE OSTI2025

Subhaloes are anisotropically distributed and aligned with the smooth matter distribution of their host haloes

ABSTRACT We investigate the distributions of subhaloes about their hosts in two suites of zoom-in N-body simulations of halo growth – one suite focused on Milky Way-Mass haloes ($\sim 10^{12} \, \mathrm{M}_{\odot }$) and another focused on cluster-mass haloes ($\sim 10^{15} \, \mathrm{M}_{\odot }$) in the Symphony simulation suite. We find, in agreement with previous work on this subject, that subhaloes are distributed anisotropically about their host haloes. In particular, the positions of subhaloes lie preferentially near the major axes of their host haloes, possibly implying that satellite galaxies will exhibit a similar alignment. Furthermore, we show that in two-dimensional projection subhaloes are more likely to be observed near the halo centre (where the central galaxy presumably resides) when the host halo is projected nearly along its major axis. This projection effect is significant. Within projected radii of a few per cent of the virial radius of the host halo, the fraction of mass in subhaloes is $\sim 175~{{\ \rm per\ cent}}$ larger for Milky Way-mass haloes and as much as $\sim 195~{{\ \rm per\ cent}}$ larger for cluster haloes when projected along the major axis as compared to the average from a random projection. This result has consequences for many applications including the interpretation of gravitational lenses. Finally, we find that the orbital angular momentum vector of subhaloes is aligned with the angular momentum vector of their host halo, indicating that a significant component of a halo’s angular momentum may be carried in its subhaloes. This has consequences for galaxy formation models which use host halo angular momentum as a proxy for galaxy momentum.

Mezini, Lorena (ORCID:0000000300053973)↗

NASA NTRS2012

Lightning Jump Algorithm and Relation to Thunderstorm Cell Tracking, GLM Proxy and Other Meteorological Measurements

The lightning jump algorithm has a robust history in correlating upward trends in lightning to severe and hazardous weather occurrence. The algorithm uses the correlation between the physical principles that govern an updraft's ability to produce microphysical and kinematic conditions conducive for electrification and its role in the development of severe weather conditions. Recent work has demonstrated that the lightning jump algorithm concept holds significant promise in the operational realm, aiding in the identification of thunderstorms that have potential to produce severe or hazardous weather. However, a large amount of work still needs to be completed in spite of these positive results. The total lightning jump algorithm is not a stand-alone concept that can be used independent of other meteorological measurements, parameters, and techniques. For example, the algorithm is highly dependent upon thunderstorm tracking to build lightning histories on convective cells. Current tracking methods show that thunderstorm cell tracking is most reliable and cell histories are most accurate when radar information is incorporated with lightning data. In the absence of radar data, the cell tracking is a bit less reliable but the value added by the lightning information is much greater. For optimal application, the algorithm should be integrated with other measurements that assess storm scale properties (e.g., satellite, radar). Therefore, the recent focus of this research effort has been assessing the lightning jump's relation to thunderstorm tracking, meteorological parameters, and its potential uses in operational meteorology. Furthermore, the algorithm must be tailored for the optically-based GOES-R Geostationary Lightning Mapper (GLM), as what has been observed using Very High Frequency Lightning Mapping Array (VHF LMA) measurements will not exactly translate to what will be observed by GLM due to resolution and other instrument differences. Herein, we present some of the promising aspects and challenges encountered in utilizing objective tracking and GLM proxy data, as well as recent results that demonstrate the value added information gained by combining the lightning jump concept with traditional meteorological measurements.

Schultz, Christopher J.↗

NASA NTRS2004

Advances in Scientific Balloon Thermal Modeling

The National Aeronautics and Space Administration's Balloon Program office has long acknowledged that the accurate modeling of balloon performance and flight prediction is dependant on how well the balloon is thermally modeled. This ongoing effort is focused on developing accurate balloon thermal models that can be used to quickly predict balloon temperatures and balloon performance. The ability to model parametric changes is also a driver for this effort. This paper will present the most recent advances made in this area. This research effort continues to utilize the "Thrmal Desktop" addition to AUTO CAD for the modeling. Recent advances have been made by using this analytical tool. A number of analyses have been completed to test the applicability of this tool to the problem with very positive results. Progressively detailed models have been developed to explore the capabilities of the tool as well as to provide guidance in model formulation. A number of parametric studies have been completed. These studies have varied the shape of the structure, material properties, environmental inputs, and model geometry. These studies have concentrated on spherical "proxy models" for the initial development stages and then to transition to the natural shaped zero pressure and super pressure balloons. An assessment of required model resolution has also been determined. Model solutions have been cross checked with known solutions via hand calculations. The comparison of these cases will also be presented. One goal is to develop analysis guidelines and an approach for modeling balloons for both simple first order estimates and detailed full models. This papa presents the step by step advances made as part of this effort, capabilities, limitations, and the lessons learned. Also presented are the plans for further thermal modeling work.

Bohaboj, T.↗

NASA NTRSDate not supplied

Considerations on Electrolytic Conductivity Measurement for Monitoring of Ionic Silver Biocide Dosing

NASA interest in ionic silver (Ag+) as a biocide for spacecraft potable water systems motivates the development of Ag+ concentration sensors to ensure nominal dosing. The electrolytic conductivity change of highly-purified potable water is linearly related to the concentration of chemically-dosed Ag+ and could serve as a useful proxy measurement, while the conductivity change during electrolytic dosing may be less so, depending on the influent water chemistry and electrolytic efficiency. Understanding and mitigating the potentially deleterious effects of Ag+ interaction with conductivity measurement systems requires investigation. Issues associated with traditional conductivity cells, which rely on wetted(typically metal or graphite) electrodes, and capacitively-coupled contactless conductivity detection (C4D) for this application are considered. Traditional conductivity cells may potentially be subject to significant excitation-induced or auto-galvanic reduction of Ag+. These may result in Ag+ depletion or electrode fouling and associated measurement error. Proper selection of electrode material, excitation parameters, and cell geometry may limit such effects. C4D uses electrodes placed outside an inert, insulating material, with dielectric polarization enabling the production of an electric field and resultant current across the analyte solution. This approach could potentially mitigate problems with Ag+ depletion and fouling by eliminating the possibility of auto-galvanic deposition and reducing the Faradaic current density. However, it is necessary to confirm C4D performance at very low conductivity levels and to determine if long-term operation produces conductive deposits, which could result in measurement error. A commercial C4D system with 1/16” (1.59 mm)outer diameter flow tubing and claimed performance in the conductivity range appropriate for this application was identified, and its sensitivity in the upper parts of this range was confirmed in a preliminary experiment. A concept for a C4D detector that could allow for full rate flow-through using planar electrodes and thin-film dielectric layers is discussed.

silver↗

DOE OSTI2021

Milestone M6 Report: Reducing Excess Data Movement Part 1

This is the second in a sequence of three Hardware Evaluation milestones that provide insight into the following questions: What are the sources of excess data movement across all levels of the memory hierarchy, going out to the network fabric? What can be done at various levels of the hardware/software hierarchy to reduce excess data movement? How does reduced data movement track application performance? The results of this study can be used to suggest where the DOE supercomputing facilities, working with their hardware vendors, can optimize aspects of the system to reduce excess data movement. Quantitative analysis will also benefit systems software and applications to optimize caching and data layout strategies. Another potential avenue is to answer cost-benefit questions, such as those involving memory capacity versus latency and bandwidth. This milestone focuses on techniques to reduce data movement, quantitatively evaluates the efficacy of the techniques in accomplishing that goal, and measures how performance tracks data movement reduction. We study a small collection of benchmarks and proxy mini-apps that run on pre-exascale GPUs and on the Accelsim GPU simulator. Our approach has two thrusts: to measure advanced data movement reduction directives and techniques on the newest available GPUs, and to evaluate our benchmark set on simulated GPUs configured with architectural refinements to reduce data movement.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Containers on Switches: A Cluster School Experience

Network switches, such as those from Arista and Mellanox, often have underutilized computational resources in the form of built-in processors and memory. By leveraging these untapped resources, we can optimize functionality and efficiency of computational cluster networks. Our research focuses on deploying containers directly onto these switches to execute various auxiliary tasks ranging from metric logging to system-wide management via post-boot configuration. By doing so, we can significantly enchance the capabilities of the cluster without the need for additional dedicated hardware. Our research involved five distinct scenarios where switch utilization could have a profound impact on HPC Clusters: run cloud-init services via link-local connection; configuring a Telegraf container to export metrics; deploying a caching proxy; creating a reconfigurable IPv6 DHCP/DNS provider for VLAN; and implementing a client detection with Magellan discovery. These scenarios were containerized with podman and docker, and tested both physically on the switch virtually on a QEMU VM both running SONiC OS. Testing and findings indicate that network switches can indeed be used for these scenarios. They offer a wide range of possibilities beyond these applications. They run as expected as containers on the switches, and although there were some minor issues, work-arounds were implemented. Overall, this is a positive result that can be further explored with more scenarios.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Particle In Cell Scalable Application Resource (PICSAR) v2

PICSAR, for Particle-In-Cell Scalable Application Resource, is a high-performance Particle-in-Cell library developed in Fortran 90 and Python. This library was first developed to be coupled with WARP and provide efficient subroutines optimized for Many-Integrated Core (MIC) architectures such as the forthcoming system Cori Phase II that will be equipped with Intel Xeon Phi KNL processors. It is a compact self-contained proxy that adequately portrays the computational loads and dataflow of the more complex WARP code but can also be used by other PIC codes. PICSAR also contains a Fortran stand-alone Particle-In-Cell "mini-app" that includes the key functionalities of a PIC code. This stand-alone code is used for testing implementation performances and to do some benchmarks.

VINCENTI, HENRI↗

DOE OSTI2022

Irradiation-induced Degradation of Surface Acoustic Wave Devices Fabricated on Bulk AlN

Here, recent work to evaluate the prospects for surface acoustic wave (SAW) devices fabricated on bulk aluminum nitride (AlN) for elevated temperature and radiation environments is reported and discussed. The design and fabrication of an array of SAW devices using commercial wafers is described, including the non-standard fabrication approach taken to overcome the stress-induced warpage of the 50 mm diameter AlN substrates. Radio frequency performance characterization of the SAW devices, with resonance frequencies ranging from 0.5 GHz to 1.5 GHz, is described. The linear temperature coefficient of frequency (TCF) near room temperature was measured and is compared to theoretical results from other investigators. Further, the effects of 8 MeV Al ion irradiation at 300°C and 500°C to damage levels of 0.01, 0.1 and 1 displacements per atom (dpa), as a proxy for neutron irradiation, was investigated. The ion irradiation damage was observed to decrease the SAW resonant frequency, and this effect is characterized and discussed. Significant degradation in the conductivity of the Ti/Al electrodes of the SAW devices was also observed and characterized. These experimental results provide a basis for further investigation of the prospects for development of SAW sensor devices in bulk AlN material for application in elevated temperature and radiation environments.

36 MATERIALS SCIENCE↗

DOE OSTI2015

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem (Mid-year report FY15 Q2)

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressing four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem: Year-end report FY15 Q4.

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressing four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem. Mid-year report FY16 Q2

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressing four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

XVis: Visualization for the Extreme-Scale Scientific-Computation Ecosystem: Mid-year report FY17 Q2

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. This project provides the necessary research and infrastructure for scientific discovery in this new computational ecosystem by addressing four interlocking challenges: emerging processor technology, in situ integration, usability, and proxy analysis.

97 MATHEMATICS AND COMPUTING↗