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At least 415 records · Page 23

Report on local data recovery approaches suitable for weather and climate prediction (Deliverable 1.3) (V.1.0)

Numerical weather and climate prediction rates as one of the scientific applications whose accuracy improvements greatly depend on the growth of the available computing power. As the number of cores in top computing facilities pushes into the millions, increasing average frequency of hardware and software failures forces users to review their algorithms and systems in order to protect simulations from breakdown. This report surveys approaches for fault-tolerance in numerical algorithms and system resilience in parallel simulations from the perspective of numerical weather and climate prediction systems. A selection of existing strategies is analyzed, featuring interpolation-restart and compressed checkpointing for the numerics, in-memory checkpointing, user-level failure mitigation-based and backup-based methods for the systems. Numerical examples showcase the performance of the techniques in addressing faults, with particular emphasis on iterative solvers for linear systems, a staple of atmospheric fluid flow solvers. The potential impact of these strategies is discussed in relation to current development of numerical weather prediction algorithms and systems towards the exascale. Trade-offs between performance, efficiency and effectiveness of resiliency strategies are analyzed and some recommendations outlined for future developments.

97 MATHEMATICS AND COMPUTING↗

National Smart Manufacturing Strategic Plan: To Facilitate More Rapid Development, Deployment and Adoption of Smart Manufacturing Technologies

Smart manufacturing technologies provide real-time data and insight to improve the productivity, efficiency, and competitiveness of U.S. manufacturing, creating the potential for new jobs in the manufacturing sector. These technologies can support U.S. manufacturers’ ability to increase throughput and energy efficiency, and decrease waste, defects, and costs. A wide range of manufacturing and industrial subsectors, particularly energy-intensive and energy-dependent industries, have the potential to benefit from smart manufacturing technologies. There are technical improvements still needed to reduce the costs and barriers (trained workforce and upskilling, software-hardware integration, cost, and technical barriers to deployment of advanced sensors, computing, and communication technologies for existing manufacturing assets) to the adoption of smart manufacturing technologies, especially to small and medium-sized manufacturers, and subsequently, increase the overall adoption rate of smart manufacturing technologies. This report outlines the Department of Energy’s (DOE) strategic plan to accelerate the development and implementation of smart manufacturing technologies in the United States and the actions DOE has taken to use these technologies in smart manufacturing for the United States. DOE’s plan to facilitate more rapid development, deployment and widespread adoption of smart manufacturing technologies derive from the 2018 Strategy for American Leadership in Advanced Manufacturing. The strategy outlines a vision for America’s leadership in advanced manufacturing including the development of intelligent manufacturing systems to optimize manufacturing facilities and support the manufacturing of transformative materials. DOE’s Clean Energy Smart Manufacturing Innovation Institute (CESMII), a Manufacturing USA Institute, focuses on accelerating the development and adoption of advanced sensors, controls, platforms, and models needed for smart manufacturing. The objective is to enhance U.S. manufacturing productivity and global competitiveness through the research and development of these technologies. Smart manufacturing has the potential to improve the overall performance, energy productivity, and efficiency of manufacturing, fostering the economic competitiveness of the manufacturing sector.

99 GENERAL AND MISCELLANEOUS↗

TuckerMPI: A Parallel C++/MPI Software Package for Large-scale Data Compression via the Tucker Tensor Decomposition

With this study, our goal is compression of massive-scale grid-structured data, such as the multi-terabyte output of a high-fidelity computational simulation. For such data sets, we have developed a new software package called TuckerMPI, a parallel C++/MPI software package for compressing distributed data. The approach is based on treating the data as a tensor, i.e., a multidimensional array, and computing its truncated Tucker decomposition, a higher-order analogue to the truncated singular value decomposition of a matrix. The result is a low-rank approximation of the original tensor-structured data. Compression efficiency is achieved by detecting latent global structure within the data, which we contrast to most compression methods that are focused on local structure. In this work, we describe TuckerMPI, our implementation of the truncated Tucker decomposition, including details of the data distribution and in-memory layouts, the parallel and serial implementations of the key kernels, and analysis of the storage, communication, and computational costs. We test the software on 4.5 and 6.7 terabyte data sets distributed across 100 s of nodes (1,000 s of MPI processes), achieving compression ratios between 100 and 200,000×, which equates to 99--99.999% compression (depending on the desired accuracy) in substantially less time than it would take to even read the same dataset from a parallel file system. Moreover, we show that our method also allows for reconstruction of partial or down-sampled data on a single node, without a parallel computer so long as the reconstructed portion is small enough to fit on a single machine, e.g., in the instance of reconstructing/visualizing a single down-sampled time step or computing summary statistics. The code is available at https://gitlab.com/tensors/TuckerMPI.

97 MATHEMATICS AND COMPUTING↗

Impact of control blade insertion on the deformation behavior of SiC-SiC channel boxes in BWRs

This article describes the analysis of distortion of a silicon carbide fiber-reinforced, silicon carbide matrix (SiC-SiC) composite channel box under in-reactor conditions of a boiling water reactor (BWR). The BWR core has significant gradients in the fast neutron flux across the channel box due to the presence of water rods within the fuel assemblies, and these gradients increase further with the insertion of control blades. As a result of the temperature and neutron flux dependent irradiation-induced swelling of SiC, the SiC-SiC composite channel box can undergo distortion. In this work, we evaluate the SiC-SiC channel box distortion for three different control blade positions. This analysis is based on the neutron flux and temperature distributions in the BWR core calculated using the neutronics code MPACT and thermal-hydraulics code CTF. This calculation is coupled through temperature feedback. Subsequently, we have performed structural analysis based on the calculated neutron flux and temperature distributions to determine the deformation and stress development in the channel box. The structural analysis was performed using the fuel performance modeling code BISON and the commercial finite element analysis software Abaqus. The results indicate that large gradients in fast neutron flux (up to 35–40% across a single axial level) will develop across the channel box. Due to these gradients, the channel box will undergo time-dependent bending for all the control blade positions in the assembly. The time-dependent bowing behavior is dominated by the transient swelling of SiC-SiC material under non-uniform neutron flux, and changes with variation in the control blade position. The bending will cause temporary interference between the channel box and control blade, and the interference is expected to be most severe for the fully inserted control blade position. The developed stresses due to differential swelling in the channel box exceed the proportional limit stress of the material, which may cause matrix microcracking in the channel box. However, the stresses remain below the tensile strength of the material, and therefore, development of a full, through-thickness crack in the channel box is not expected. Finally, further work is recommended to explore and evaluate the mitigation strategies.

42 ENGINEERING↗

Data from Adopting Bioenergy Crops: Does Farmers’ Attitude Toward Loss Matter?

We apply prospect theory to examining farmers’ economic incentives to divert a share of their land to bioenergy crops (miscanthus and switchgrass in this study). Numerical simulation is conducted for 1,919 rain‐fed U.S. counties to identify the impact of loss aversion on bioenergy crop adoption, and how this impact is influenced by biomass price, discount rate, credit constraint status, and policy instruments. Results show that ignoring farmer’s loss aversion causes overestimation of miscanthus production but underestimation of switchgrass production, particularly when farmers are credit constrained and have a high discount rate. We find that establishment cost subsidy induces more miscanthus production whereas subsidized energy crop insurance induces more switchgrass production. The efficacy of these two policy instruments, measured by biomass production increased by per dollar of government outlay, depends on the magnitude of farmers’ loss aversion and discount rate.

Economics↗

TU-F-CAMPUS-I-01: Investigation of the Effective Dose From Bolus Tracking Acquisitions at Different Anatomical Locations in the Chest for CT

Purpose: Stationary table acquisitions (Bolus tracking) in X-ray Computed Tomography (CT) can Result in dose length products (DLP) comparable to spiral scans. It is today unclear whether or not the effective dose (E) for Bolus Tracking can be approximated using target region specific conversion factors (E/DLP). The purpose of this study was to investigate how E depends on the anatomical location of the Bolus Tracking in relation to Chest CT scans with the same DLP. Methods: Effective doses were approximated for the ICRP 110 adult Reference Male (AM) and adult Reference Female (FM) computational voxel phantoms using software for CT dose approximations (pre-simulated MC data). The effective dose was first approximated for a Chest CT scan using spiral technique and a CTDIvol (32 cm) of 6 mGy. The effective dose from the spiral scan was then compared to E approximated for contiguous Bolus Tracking acquisitions (1 cm separation), with a total collimation of 1 cm, over different locations of the chest of the voxel phantoms. The number of rotations used for the Bolus Tracking acquisitions was adjusted to yield the same DLP (32 cm) as the spiral scan. Results: Depending on the anatomical location of the Bolus Tracking, E ranged by factors of 1.3 to 6.8 for the AM phantom and 1.4 to 3.3 for the AF phantom, compared to the effective dose of the spiral scans. The greatest E for the Bolus Tracking acquisitions was observed for anatomical locations coinciding with breast tissue. This can be expected as breast tissue has a high tissue weighting factor in the calculation of E. Conclusion: For Chest CT scans, the effective dose from Bolus Tracking is highly dependent on the anatomical location where the scan is administered and will not always accurately be represented using target region specific conversion factors.

60 APPLIED LIFE SCIENCES↗

ProvSec: Open Cybersecurity System Provenance Analysis Benchmark Dataset with Labels

System provenance forensic analysis has been studied by a large body of research work. This area needs fine granularity data such as system calls along with event fields to track the dependencies of events. While prior work on security datasets has been proposed, we found a useful dataset of realistic attacks and details that are needed for high-quality provenance tracking is lacking. We created a new dataset of eleven vulnerable cases for system forensic analysis. It includes the full details of system calls including syscall parameters. Realistic attack scenarios with real software vulnerabilities and exploits are used. For each case, we created two sets of benign and adversary scenarios which are manually labeled for supervised machine-learning analysis. In addition, we present an algorithm to improve the data quality in the system provenance forensic analysis. We demonstrate the details of the dataset events and dependency analysis of our dataset cases.

97 MATHEMATICS AND COMPUTING↗

ITS Version 6.7: The Integrated TIGER Series of Coupled Electron/Photon Monte Carlo Transport Codes User's Manual

ITS is a powerful software package permitting state-of-the-art Monte Carlo solution of linear time-independent coupled electron/photon radiation transport problems, with or without the presence of macroscopic electric and magnetic fields of arbitrary spatial dependence. Our goal has been to simultaneously maximize operational simplicity and physical accuracy. Through a set of preprocessor directives, the user selects one of the many ITS codes. The ease with which the make system is applied combines with an input scheme based on order-independent descriptive keywords that makes maximum use of defaults and internal error checking to provide experimentalists and theorists alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Physical rigor is provided by employing accurate cross sections, sampling distributions, and physical models for describing the production and transport of the electron/photon cascade from 1.0 GeV down to 1.0 keV. The availability of source code permits the more sophisticated user to tailor the codes to specific applications and to extend the capabilities of the codes to more complex applications. Version 6, the latest version of ITS, contains (1) improvements to the ITS 5.0 codes, and (2) conversion to Fortran 95. The general user friendliness of the software has been enhanced through memory allocation to reduce the need for users to modify and recompile the code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SU-E-T-195: Gantry Angle Dependency of MLC Leaf Position Error

Purpose: The aim of this study was to investigate the gantry angle dependency of the multileaf collimator (MLC) leaf position error. Methods: An automatic MLC quality assurance system (AutoMLCQA) was developed to evaluate the gantry angle dependency of the MLC leaf position error using an electronic portal imaging device (EPID). To eliminate the EPID position error due to gantry rotation, we designed a reference maker (RM) that could be inserted into the wedge mount. After setting up the EPID, a reference image was taken of the RM using an open field. Next, an EPID-based picket-fence test (PFT) was performed without the RM. These procedures were repeated at every 45° intervals of the gantry angle. A total of eight reference images and PFT image sets were analyzed using in-house software. The average MLC leaf position error was calculated at five pickets (-10, -5, 0, 5, and 10 cm) in accordance with general PFT guidelines using in-house software. This test was carried out for four linear accelerators. Results: The average MLC leaf position errors were within the set criterion of <1 mm (actual errors ranged from -0.7 to 0.8 mm) for all gantry angles, but significant gantry angle dependency was observed in all machines. The error was smaller at a gantry angle of 0° but increased toward the positive direction with gantry angle increments in the clockwise direction. The error reached a maximum value at a gantry angle of 90° and then gradually decreased until 180°. In the counter-clockwise rotation of the gantry, the same pattern of error was observed but the error increased in the negative direction. Conclusion: The AutoMLCQA system was useful to evaluate the MLC leaf position error for various gantry angles without the EPID position error. The Gantry angle dependency should be considered during MLC leaf position error analysis.

07 ISOTOPE AND RADIATION SOURCES↗

Metrics for the Complexity of Material Models

Quantitative measures are proposed for characterizing the complexity of material models used in computational mechanics. The algorithms for evaluating these metrics operate on the mathematical equations in the model rather than a code implementation and are different from software complexity measures. The metrics do not rely on a physical understanding of the model, using instead only a formal statement of the equations. A new algorithm detects the dependencies, whether explicit or implicit, between all the variables. The resulting pattern of dependencies is expressed in a set of pathways, each of which represents a chain of dependence between the variables. These pathways provide the raw data used in the metrics, which correlate with the expected ease of understanding, coding, and applying the model. Usage of the ComplexityMetrics code is described, with examples.

97 MATHEMATICS AND COMPUTING↗

Determining the Concentration of Free Electrons in n-InSb from Far-Infrared Reflectance Spectra with Allowance for Plasmon–Phonon Coupling

Contactless nondestructive testing is a means for determining the concentration of free electrons N in indium antimonide (InSb) samples from far-infrared reflectance spectra recorded at room temperature. A computer program capable of determining the characteristic wave number from the Kramers–Kronig relation is developed. The calculated calibration dependence makes it possible to determine the electron concentration from the known characteristic wave number. It is shown that this dependence is described by a cubic polynomial. In the calculations, the energy dependence of the electron effective mass is taken into account. It is established that, in determining the electron concentration, account must be taken of plasmon–phonon coupling, specifically at N ≤ 5 × 10{sup 17} cm{sup –3}. The systematic error introduced into the determination of N by disregard of plasmon–phonon coupling is estimated. The software elaborated here makes it possible to calculate the electron concentration N from experimental reflectance spectra and to store and process the results. The software is tested by the example of the reflectance spectrum of heavily doped n-InSb.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

SU-E-T-644: Evaluation of Angular Dependence Correction for 2D Array Detector Using for Quality Assurance of Volumetric Modulated Arc Therapy

Purpose: To evaluate the angular dependence correction for Matrix Evolution 2D array detector in quality assurance of volumetric modulated arc therapy(VMAT). Methods: Total ten patients comprising of different sites were planned for VMAT and taken for the study. Each plan was exposed on Matrix Evolution 2D array detector with Omnipro IMRT software based on the following three different methods using 6MV photon beams from Elekta Synergy linear accelerator. First method, VMAT plan was delivered on Matrix Evolution detector as it gantry mounted with dedicated holder with build-up of 2.3cm. Second, the VMAT plan was delivered with the static gantry angle on to the table mounted setup. Third, the VMAT plan was delivered with actual gantry angle on Matrix Evolution detector fixed in Multicube phantom with gantry angle sensor and angular dependence correction were applied to quantify the plan quality. For all these methods, the corresponding QA plans were generated in TPS and the dose verification was done for both point and 2D fluence analysis with pass criteria of 3% dose difference and 3mm distance to agreement. Results: The measured point dose variation for the first method was observed as 1.58±0.6% of mean and SD with TPS calculated. For second and third method, the mean and standard deviation(SD) was observed as 1.67±0.7% and 1.85±0.8% respectively. The 2D fluence analysis of measured and TPS calculated has the mean and SD of 97.9±1.1%, 97.88±1.2% and 97.55±1.3% for first, second and third methods respectively. The calculated two-tailed Pvalue for point dose and 2D fluence analysis shows the insignificance with values of 0.9316 and 0.9015 respectively, among the different methods of QA. Conclusion: The qualitative evaluation of angular dependence correction for Matrix Evolution 2D array detector shows its competency in accuracy of quality assurance measurement of composite dose distribution of volumetric modulated arc therapy.

07 ISOTOPE AND RADIATION SOURCES↗

TH-CD-207B-11: Multi-Vendor Phantom Study of CT Lung Density Metrics: Is a Reproducibility of Less Than 1 HU Achievable?

Purpose: To standardize the calibration procedures of CT lung density measurements using low-density reference foams in a phantom, and to demonstrate a reproducibility of less than 1 HU for lung equivalent foam densities measured across CT vendor platforms and protocols. Methods: A phantom study was conducted on CT scanner models from 4 vendors at 100, 120, and 135/140 kVp and 1.5, 3, and 6 mGy dose settings, using a lung density phantom containing air, water, and 3 reference foams (indirectly calibrated) with discrete densities simulating a 5-cm slice of the human chest. Customized segmentation software was used to analyze the images and generate a mean HU and variance for each of the density for the 22 vendor/protocols. A 3-step calibration process was devised to remove a scanner-dependent parameter using linear regression of the HU value vs the relative electron density. The results were mapped to a single energy (80 keV) for final comparison. Results: The heterogeneity across vendor platforms for each density assessed by a random effects model was reduced by 50% after re-calibration, while the standard deviation of the mean HU values also improved by about the same amount. The 95% CI of the final HU value was within +/−1 HU for all 3 reference foam densities. For the backing lung foam in the phantom (served as an “unknown”), this CI is +/− 1.6 HU. The kVp and dose settings did not appear to have significant contributions to the variability. Conclusion: With the proposed calibration procedures, the inter-scanner reproducibility of better than 1 HU is demonstrated in the current phantom study for the reference foam densities, but not yet achieved for a test density. The sources of error are being investigated in the next round of scanning with a certified Standard Reference Material for direct calibration. Fain: research funding from GE Healthcare to develop pulmonary MRI techniques. Hoppel: employee of Toshiba Medical Research Institute USA/financial interest with GE Healthcare. M. Fuld: employee of Siemens Healthcare for medical device equipment and software. This project is supported partially by RSNA QIBA Concept Award (Fain), NIH/NIBIB, HHSN268201300071C (Y).

60 APPLIED LIFE SCIENCES↗

MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics

General proteomics research for fundamental science typically addresses laboratory- or patient-derived samples of known origin and composition. However, in a few research areas, such as environmental proteomics, clinical identification of infectious organisms, archeology, art/cultural history, and forensics, attributing the origin of a protein-containing sample to the organisms that produced it is a central focus. A small number of groups have approached this problem and developed software tools for taxonomic characterization and/or identification using bottom-up proteomics. Most such tools identify peptides via database search, and many rely on organism-specific peptides as markers. Our group recently introduced MARLOWE, a software tool for taxonomic characterization of unknown samples based on de novo peptide identification and signal-erosion-resistant strong peptides, which are shared peptides distributed in a taxonomy-dependent manner. In the current work, we further characterize the utility of MARLOWE using publicly available proteomics data from forensically-relevant samples. MARLOWE characterizes samples based on their protein profile, and returns ranked organism lists of potential contributors and taxonomic scores based on shared strong peptides between organisms. Overall, the correct characterization rate ranges between 44 and 100%, depending on the sample type and data acquisition parameters (with lower numbers associated with lower-quality data sets). MARLOWE demonstrates successful characterization of true contributors and close relatives, and provides sufficient specificity to distinguish certain microbial species. MARLOWE demonstrates its ability to provide insight into potential taxonomic sources for a wide range of sample types without prior assumptions about sample contents. As a result, this approach can find utility in forensic science and also broadly in bioanalytical applications that utilize proteomics approaches for taxonomic characterization.

Bacteria↗

Statistical Uncertainty of Inhalation Dose Coefficients: Impact of Particle Deposition in ICRP 66 Human Respiratory Tract Model

Inhaled radioactive materials can pose a long-term health concern, as the material can be incorporated into the body’s metabolic pathways and remain in organs and tissues for extended durations. During the retention period, the radioactive material may localize in a source organ and irradiate adjacent target organs and tissues. Distribution of these materials changes over time, requiring biokinetic modeling to evaluate their movement through various tissues and organs. The evolving distribution depends on multiple inputs characterizing the inhaled material, such as particle size and size distribution, particle density, aspect ratio, specific radionuclide, the chemical form, and solubility. In addition, biological parameters such as breathing rate, breathing type (nasal or nasal/oral), respiratory system morphometry, tidal volume, functional residual capacity, and anatomical dead space all influence material transport. These aerosol properties and physiological characteristics of the respiratory tract jointly define a range of initial conditions that influence the time-dependent distribution of radioactive material. To evaluate both uncertainty in the initial conditions of inhalation exposure and the final output (committed effective dose) from biokinetic models, a Python-based software tool, Radiological Exposure Dose Calculator (REDCAL), was developed to propagate uncertainty within the human respiratory tract model. Focusing on deposition fraction uncertainty, the primary objective was to characterize the initial activity distribution across respiratory regions as a function of anticipated particle sizes and distributions. The impact of the deposition fraction uncertainty was propagated to committed effective dose coefficients for selected radionuclides in a companion publication. For each particle size, a lognormal distribution, characterized by its geometric mean as defined within ICRP Publication 66, serves as the basis for introducing uncertainty into the physical processes governing deposition in various lung regions. Finally, this study addresses the deposition process and examines how uncertainty in deposition mechanisms affects activity distribution in the airways, ultimately presenting the expected range and standard deviation of deposited activity as a function of particle size.

International Commission on Radiological Protectio↗

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↗

Xavier: High-Performance X-Drop Adaptive Banded Pairwise Alignment (Xavier) v1.0

Pairwise sequence alignment is one of the most compute-intense challenges for the analysis of genomics data and it can account for more than 90% of the runtime depending on the application. Despite the effort to reduce the computational cost introducing heuristics such as banded and x-drop alignment, the performance of state-of-the-art software is often unsatisfactory for long sequences. Recent advances in single-molecule sequencing technologies keep increasing the length of the sequences to align at the cost of higher error rates b ranging from 5% to 15% b, emphasizing the need for fast and accurate software. Our long-read alignment software, named Xavier, computes high-performance x-drop adaptive banded pairwise alignment exploiting instruction-level parallelism via Single-Instruction-Multiple-Data (SIMD) operations. Xavier uses a narrow bandwidth that appreciably improves performance reducing the search space for the optimal alignment. In our experiment, the adaptive mechanism enables Xavier to find the optimal alignment between related sequences even when the error rate is as high as 50%. Xavier achieves speed-up up to 5X over competitor software when enabling the x-drop termination and up to 415X when disabling it, with negligible accuracy loss.

Guidi, Giulia↗

Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data

The particular challenge of the analysis of optical absorption and Raman spectroscopic data measured from protein crystals and how the SLS-APE software toolbox supports scientists in dealing with such data is described. Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APEin situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗