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At least 145 records · Page 8

Local respiratory motion correction for PET/CT imaging: Application to lung cancer

Purpose: Despite multiple methodologies already proposed to correct respiratory motion in the whole PET imaging field of view (FOV), such approaches have not found wide acceptance in clinical routine. An alternative can be the local respiratory motion correction (LRMC) of data corresponding to a given volume of interest (VOI: organ or tumor). Advantages of LRMC include the use of a simple motion model, faster execution times, and organ specific motion correction. The purpose of this study was to evaluate the performance of LMRC using various motion models for oncology (lung lesion) applications. Methods: Both simulated (NURBS based 4D cardiac-torso phantom) and clinical studies (six patients) were used in the evaluation of the proposed LRMC approach. PET data were acquired in list-mode and synchronized with respiration. The implemented approach consists first in defining a VOI on the reconstructed motion average image. Gated PET images of the VOI are subsequently reconstructed using only lines of response passing through the selected VOI and are used in combination with a center of gravity or an affine/elastic registration algorithm to derive the transformation maps corresponding to the respiration effects. Those are finally integrated in the reconstruction process to produce a motion free image over the lesion regions. Results: Although the center of gravity or affine algorithm achieved similar performance for individual lesion motion correction, the elastic model, applied either locally or to the whole FOV, led to an overall superior performance. The spatial tumor location was altered by 89% and 81% for the elastic model applied locally or to the whole FOV, respectively (compared to 44% and 39% for the center of gravity and affine models, respectively). This resulted in similar associated overall tumor volume changes of 84% and 80%, respectively (compared to 75% and 71% for the center of gravity and affine models, respectively). The application of the nonrigid deformation model in LRMC led to over an order of magnitude gain in computational efficiency of the correction relative to the application of the deformable model to the whole FOV. Conclusions: The results of this study support the use of LMRC as a flexible and efficient correction approach for respiratory motion effects for single lesions in the thoracic area.

60 APPLIED LIFE SCIENCES↗

Predicting Emission Source Terms in a Reduced-Order Fire Spread Model—Part 1: Particulate Emissions

A simple, easy-to-evaluate, surrogate model was developed for predicting the particle emission source term in wildfire simulations. In creating this model, we conceptualized wildfire as a series of flamelets, and using this concept of flamelets, we developed a one-dimensional model to represent the structure of these flamelets which then could be used to simulate the evolution of a single flamelet. A previously developed soot model was executed within this flamelet simulation which could produce a particle size distribution. Executing this flamelet simulation 1200 times with varying conditions created a data set of emitted particle size distributions to which simple rational equations could be tuned to predict a particle emission factor, mean particle size, and standard deviation of particle sizes. These surrogate models (the rational equation) were implemented into a reduced-order fire spread model, QUIC-Fire. Using QUIC-Fire, an ensemble of simulations were executed for grassland fires, southeast U.S. conifer forests, and western mountain conifer forests. Resulting emission factors from this ensemble were compared against field data for these fire classes with promising results. Also shown is a predicted averaged resulting particle size distribution with the bulk of particles produced to be on the order of 1 μm in size.

54 ENVIRONMENTAL SCIENCES↗

Validation for 233U-Fueled Systems in KENO V.a in SCALE 6.2

Validation of the KENO V.a Monte Carlo code has been performed in recent years using benchmark experiments contained in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. The models used in these recent validation efforts have been drawn from the Verified, Archived Library of Inputs and Data (VALID). Models must be generated and reviewed by qualified individuals to be added to the VALID library, which leads to high confidence in the models and reduces the probability that apparent validation issues are a result of modeling errors. The contents of the VALID library are somewhat limited because of the effort involved in generating and reviewing models, so no 233U-fueled experiments are included in VALID. A large number of models of 233U experiments have been modeled in the past in support of the criticality safety of 233U in storage at Oak Ridge National Laboratory (ORNL). In June 2016, two midshipmen from the United States Naval Academy were assigned to ORNL, and they reviewed and updated these models for execution in SCALE 6.2. The validation of 233U is of interest because some discrepancies in SCALE results were identified by a beta tester at the Nuclear Energy Agency modeling these systems. These discrepancies were related to a data thinning procedure in the continuous-energy nuclear data process, and had been resolved prior to the release of SCALE 6.2

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Validation for {sup 233}U-Fueled Systems in KENO V.a in SCALE 6.2

Validation of the KENO V.a Monte Carlo code has been performed in recent years using benchmark experiments contained in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. The models used in these recent validation efforts have been drawn from the Verified, Archived Library of Inputs and Data (VALID). Models must be generated and reviewed by qualified individuals to be added to the VALID library, which leads to high confidence in the models and reduces the probability that apparent validation issues are a result of modeling errors. The contents of the VALID library are somewhat limited because of the effort involved in generating and reviewing models, so no {sup 233}U-fueled experiments are included in VALID. A large number of models of {sup 233}U experiments have been modeled in the past in support of the criticality safety of {sup 233}U in storage at Oak Ridge National Laboratory (ORNL). In June, 2016, two midshipmen from the United States Naval Academy were assigned to ORNL, and they reviewed and updated these models for execution in SCALE 6.2. The validation of {sup 233}U is of interest because some discrepancies in SCALE results were identified by a beta tester at the Nuclear Energy Agency modeling these systems. These discrepancies were related to a data thinning procedure in the continuous-energy nuclear data process, and had been resolved prior to the release of SCALE 6.2. (authors)

07 ISOTOPE AND RADIATION SOURCES↗

Computer-implemented security evaluation methods, security evaluation systems, and articles of manufacture

Computer-implemented security evaluation methods, security evaluation systems, and articles of manufacture are described. According to one aspect, a computer-implemented security evaluation method includes accessing information regarding a physical architecture and a cyber architecture of a facility, building a model of the facility comprising a plurality of physical areas of the physical architecture, a plurality of cyber areas of the cyber architecture, and a plurality of pathways between the physical areas and the cyber areas, identifying a target within the facility, executing the model a plurality of times to simulate a plurality of attacks against the target by an adversary traversing at least one of the areas in the physical domain and at least one of the areas in the cyber domain, and using results of the executing, providing information regarding a security risk of the facility with respect to the target.

97 MATHEMATICS AND COMPUTING↗

Sensitivity and Uncertainty Workflow of Full System SIERRA Models Supporting High Consequence Applications

Credibility of end-to-end CompSim (Computational Simulation) models and their agile execution requires an expressive framework to describe, communicate and execute complex computational tool chains representing the model. All stakeholders from system engineering and customers through model developers and V&V partners need views and functionalities of the workflow representing the model in a manner that is natural to their discipline. In the milestone and in this report we define workflow as a network of computation simulation activities executed autonomously on a distributed set of computational platforms. The FY19 ASC L2 Milestone (6802) for the Integrated Workflow (IWF) project was designed to integrate and improve existing capabilities or develop new functionalities to provide a wide range of stakeholders a coherent and intuitive platform capable of defining and executing CompSim modeling from analysis workflow definition to complex ensemble calculations. The main goal of the milestone was to advance the integrated workflow capabilities to support the weapon system analysts with a production deployment in FY20. Ensemble calculations supporting program decisions include sensitivity analysis, optimization and uncertainty quantification. The goal of the L2 milestone aligned with the ultimate goal of the IWF project is to foster cultural and technical shift toward and integrated CompSim capability based on automated workflows. Specific deliverables were defined in five broad categories: 1) Infrastructure, including development of distributed-computing workflow capability, 2) integration of Dakota (Sandia's sensitivity, optimization and UQ engine) with SAW (Sandia Analysis Workbench), 3) ARG (Automatic Report Generator introspecting analysis artifacts and generating human-readable extensible and archivable reports), 4) Libraries and Repositories aiding capability reuse, and 5) Exemplars to support training, capturing best practices and stress testing of the platform. A set of exemplars was defined to represent typical weapon system qualification CompSim projects. Analyzing the required capabilities and using the findings to plan implementation of required capabilities ensured optimal allocation of development resources focused on production deployment after the L2 is completed. It was recognized early that the end-to-end modeling applications pose a considerable number of diverse risks, and a formal risk tracking process was implemented. The project leveraged products, capabilities and development tasks of IWF partners. SAW, Dakota, Cubit, Sierra, Slycat, and NGA (NexGen Analytics, a small business) contributed to the integrated platform developed during this milestone effort. New products delivered include: a) NGW (Next Generation Workflow) for robust workflow definition and execution, b) Dakota wizards, editor and results visualization, and c) the automatic report generator ARG. User engagement was initiated early in the development process eliciting concrete requirements and actionable feedback to assure that the integrated CompSim capability will have high user acceptance and impact. The current integrated capabilities have been demonstrated and are continually being tested by a set of exemplars ranging from training scenarios to computationally demanding uncertainty analyses. The integrated workflow platform has been deployed on both SRN (Sandia Restricted Network) and SCN (Sandia Classified Network). Computational platforms where the system has been demonstrated span from Windows (Creo the CAD platform chosen by Sandia) to Trinity HPC (Sierra and CTH solvers). Follow up work will focus on deployment at SNL and other sites in the nuclear enterprise (LLNL, KCNSC), training and consulting support to democratize the analysis agility, process health and knowledge management benefits the NGW platform provides.

97 MATHEMATICS AND COMPUTING↗

Dynamic Modeling of Adjustable-Speed Pumped Storage Hydropower Plant: Preprint

Hydropower is the largest producer of renewable energy in the U.S. More than 60% of the total renewable generation comes from hydropower. There is also approximately 22 GW of pumped storage hydropower (PSH). Conventional PSH uses a synchronous generator, and thus the rotational speed is constant at synchronous speed. This work details a hydrodynamic model and generator/power converter dynamic model. The optimization of the hydrodynamic model is executed by the hydro-turbine controller, and the electrical output real/reactive power is controlled by the power converter. All essential controllers to perform grid-interface functions and provide ancillary services are included in the model.

13 HYDRO ENERGY↗

Outcomes of the 2013 GTO Workshop on Geothermal Code Comparison

Pacific Northwest National Laboratory (PNNL) is supporting the Department of Energy (DOE) Geothermal Technologies Office (GTO) in organizing and executing a model comparison activity. This project is directed at testing, diagnosing differences, and demonstrating modeling capabilities of a worldwide collection of numerical simulators for evaluating geothermal technologies. A key element of the project was the planning and implementation of a one-day project kickoff workshop, held February 14, 2013 in Palo Alto, CA. The primary goals of the workshop were to 1) introduce the project and its objectives to potential participating team members, and 2) develop an initial set of test problem descriptions for use in the execution stage. This report summarizes the outcomes of the workshop.

15 GEOTHERMAL ENERGY↗

Machine Learning-Based Temperature Prediction for Runtime Thermal Management Across System Components

Elevated temperatures limit the peak performance of systems because of frequent interventions by thermal throttling. Non-uniform thermal states across system nodes also cause performance variation within seemingly equivalent nodes leading to significant degradation of overall performance. In this paper we present a framework for creating a lightweight thermal prediction system suitable for run-time management decisions. We pursue two avenues to explore optimized lightweight thermal predictors. First, we use feature selection algorithms to improve the performance of previously designed machine learning methods. Second, we develop alternative methods using neural network and linear regression-based methods to perform a comprehensive comparative study of prediction methods. We show that our optimized models achieve improved performance with better prediction accuracy and lower overhead as compared with the Gaussian process model proposed previously. Specifically we present a reduced version of the Gaussian process model, a neural network-based model, and a linear regression-based model. Using the optimization methods, we are able to reduce the average prediction errors in the Gaussian process from 4: 2 degrees C to 2: 9 degrees C. We also show that the newly developed models using neural network and Lasso linear regression have average prediction errors of 2: 9 degrees C and 3: 8 degrees C respectively. The prediction overheads are 0.22, 0.097, and 0.026 ms per prediction for reduced Gaussian process, neural network, and Lasso linear regression models, respectively, compared with 0.57 ms per prediction for the previous Gaussian process model. We have implemented our proposed thermal prediction models on a two-node system configuration to help identify the optimal task placement. The task placement identified by the models reduces the average system temperature by up to 11: 9 degrees C without any performance degradation. Furthermore, these models respectively achieve 75, 82.5, and 74.17 percent success rates in correctly pointing to those task placements with better thermal response, compared with 72.5 percent success for the original model in achieving the same objective. Lastly, we extended our analysis to a 16-node system and we were able to train models and execute them in real time to guide task migration and achieve on average 17 percent reduction in the overall system cooling power.

97 MATHEMATICS AND COMPUTING↗

Achieving Energy Efficiency In Small Businesses In Low-Income Areas

Lime Energy, with funding from the Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE), recently concluded a project demonstrating a new business model for executing energy efficiency for small businesses, in which we aspired to focus on low-income urban areas. As initially conceived, the Project would advance beyond the current best practices used to foster energy efficiency action in small and midsized commercial buildings (under 25,000 square feet), which represent 95% of all commercial customers in the United States. As the project proceeded, Lime Energy discovered that the business model needed to be further refined in areas where Lime already had a presence in the community and the benefit of a relationship with the known utility. The need for this intermediate step – of deploying the business model in an established region – has since been validated.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗

High-Performance Accelerator Modeling: Toward Improving Controls and Diagnostics for High-Brightness Beams in Experiment

One of the main charges of beam physics is to improve the overall beam quality delivered to experiments and applications, which is generally quantified by the beam brightness. High brightness beams have numerous applications, including x-ray free electron lasers and ultrafast electron diffraction (UED). To these ends, this thesis details efforts to use high-performance models --- high-fidelity models that execute quickly --- for controls and diagnostics. To demonstrate the generality of these techniques, this thesis focuses on three of the most successful photoinjector designs currently used worldwide: the UCLA/SLAC/BNL-type high-gradient S-band gun, the continuous-wave high-repetition rate VHF APEX gun and the L-band DESY-PITZ-type gun. Work will be shown from Pegasus (UCLA), HiRES (LBNL) and FAST (FNAL).Specifically, data-driven models for online virtual diagnostics are presented, in this case, in the context of UED at HiRES, leading to a temporal resolution improvement. Methods for improving the fidelity of physics-based models are discussed, with examples at HiRES, Pegasus and FAST. Markov-chain Monte Carlo analysis is applied to match simulations, in the context of photocathode studies at HiRES and Pegasus. Lastly, the augmentation of online model-based predictions with model-independent optimization is explored in a fluctuating environment at Pegasus and HiRES. A central theme of this dissertation is working with parameter fluctuations when modeling an accelerator beamline. Long-term drifts and shot-to-shot jitter exist in every accelerator to a varying degree and therefore play an important role in every chapter of this dissertation. This thesis attempts to address the issues associated with these fluctuations when trying to develop faithful model representations of the system.

43 PARTICLE ACCELERATORS↗

Theoretical Study of Structural, Magnetic, Elastic, Phonon, and Thermodynamic Properties of Heusler Alloys Fe{sub 2}CrX (X = Al, Ga)

First-principle calculations based on generalized gradient approximation and quasi-harmonic Debye model were executed to analyze the structural, magnetic, elastic, phonon, and thermodynamic properties of Fe{sub 2}CrX (X = Al, Ga) Heusler alloys. The computed lattice parameters concurred well with available experimental and theoretical data. The calculated elastic constants reveal that the Fe{sub 2}CrAl is brittle and Fe{sub 2}CrGa is ductile. The phonon dispersion relation of Fe{sub 2}CrX (X = Al, Ga) are calculated using finite displacement method with a cutoff radius of 5 Å. We likewise explored the thermodynamic properties by utilizing quasi-harmonic Debye model in which bulk modulus, heat capacity, Debye temperature, Grüneisen parameter, and thermal expansion coefficient are resolved at 0–30 Gpa pressure and 0–900 K temperature from the non-equilibrium Gibbs functions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and execution strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.

97 MATHEMATICS AND COMPUTING↗

Application Characterization at Scale: Lessons learned from developing a distributed Open Community Runtime system for High Performance Computing

Since 2012, the U.S. Department of Energy’s X-Stack program has been developing solutions including runtime systems, programming models, languages, compilers, and tools for the Exascale system software to address crucial performance and power requirements. Fine grain programming models and runtime systems show a great potential to efficiently utilize the underlying hardware. Thus, they are essential to many X-Stack efforts. An abundant amount of small tasks can better utilize the vast parallelism available on current and future machines. Moreover, finer tasks can recover faster and adapt better, due to a decrease in state and control. Nevertheless, current applications have been written to exploit old paradigms (such as Communicating Sequential Processor and Bulk Synchronous Parallel processing). To fully utilize the advantages of these new systems, applications need to be adapted to these new paradigms. As part of the applications’ porting process, in-depth characterization studies, focused on both application characteristics and runtime features, need to take place to fully understand the application performance bottlenecks and how to resolve them. This paper presents a characterization study for a novel high performance runtime system, called the Open Community Runtime, using key HPC kernels as its vehicle. This study has the following contributions: one of the first high performance, fine grain, distributed memory runtime system implementing the OCR standard (version 0.99a); and a characterization study of key HPC kernels in terms of runtime primitives running on both intra and inter node environments. Running on a general purpose cluster, we have found up to 1635x relative speed-up for a parallel tiled Cholesky Kernels on 128 nodes with 16 cores each and a 1864x relative speed-up for a parallel tiled Smith-Waterman kernel on 128 nodes with 30 cores.

Application characterization↗

Uniaxial, Pure Bending, and Column Buckling Experiments on Superelastic NiTi Rods and Tubes

Many existing shape memory alloy (SMA) devices consist of slender beams and frames. To better understand SMA beam behavior, we experimentally examined the isothermal, room temperature response of superelastic NiTi rods and tubes, of similar outer diameters, subjected to four different modes of loading. Pure tension, pure compression, and pure bending experiments were first performed to establish and compare the baseline uniaxial and bending behaviors of rods and tubes. Column buckling experiments were then performed on rod and tube columns of several slenderness ratios to investigate their mechanical responses, phase transformation kinetics under combined uniaxial and bending deformation, and the interaction between material and structural instabilities. In all experiments, stereo digital image correlation measured local displacement fields in order to capture phenomena such as strain localization and propagating phase boundaries. Superelastic mechanical behavior and the nature of stress-induced phase transformation were found to be strongly affected by specimen geometry and the deformation mode. Under uniaxial tension, both the rod and tube had well-defined loading and unloading plateaus in their superelastic responses, during which stress-induced phase transformation propagated along the length of the specimen in the form of a high/low strain front. Due to the dependence of strain localization on kinematic compatibility, the high/low strain front morphologies differed between the rod and tube: for the rod, the high/low strain front consisted of a diffuse “neck”, while the high/low strain front in the tube consisted of distinct, criss-crossing “fingers.” During uniaxial compression, both cross-sectional forms exhibited higher transformation stresses and smaller transformation strains than uniaxial tension, highlighting the now well-known tension-compression asymmetry of SMAs. Additionally, phase transformation localization and propagation were absent under compressive loading. During pure bending, the moment-curvature response of both forms exhibited plateaus and strain localization during forward and reverse transformations. Rod specimens developed localized, high-curvature regions that propagated along the specimen axis and caused shear strain near the high/low curvature interface; whereas, the tube specimens exhibited finger/wedge-like high strain regions over the tensile side of the tube which caused nonlinear strain profiles through the thickness of the specimen that did not propagate. Here, it was therefore found that classical beam theory assumptions did not hold in the presence of phase transformation localization (although, the assumptions did hold on average for the tube). During column buckling, the structures were loaded into the post-buckling regime yet recovered nearly-straight forms upon unloading. Strain localization was observed only for high aspect ratio (slender) tubes, but the mechanical responses were similar to that of rods of the same slenderness ratio. Also, an interesting “unbuckling” phenomenon was discovered in certain low aspect ratio (stout) columns, where late post-buckling straightening was observed despite continuous monotonic loading. Thus, these behaviors are some of the challenging phenomena which must be captured when developing SMA constitutive models and executing structural simulations.

36 MATERIALS SCIENCE↗

Quantum Annealing for Prime Factorization

We have developed a framework to convert an arbitrary integer factorization problem to an executable Ising model by first writing it as an optimization function then transforming the k-bit coupling (k ≥ 3) terms to quadratic terms using ancillary variables. Our resource-efficient method uses O (log 2 ( N )) binary variables (qubits) for finding the factors of an integer N. We present how to factorize 15, 143, 59989, and 376289 using 4, 12, 59, and 94 logical qubits, respectively. This method was tested using the D-Wave 2000Q for finding an embedding and determining the prime factors for a given composite number. The method is general and could be used to factor larger integers as the number of available qubits increases, or combined with other ad hoc methods to achieve better performances for specific numbers.

97 MATHEMATICS AND COMPUTING↗

Quasi-Optimal Elimination Trees for 2D Grids with Singularities

We construct quasi-optimal elimination trees for 2D finite element meshes with singularities. These trees minimize the complexity of the solution of the discrete system. The computational cost estimates of the elimination process model the execution of the multifrontal algorithms in serial and in parallel shared-memory executions. Since the meshes considered are a subspace of all possible mesh partitions, we call these minimizers quasi-optimal. We minimize the cost functionals using dynamic programming. Finding these minimizers is more computationally expensive than solving the original algebraic system. Nevertheless, from the insights provided by the analysis of the dynamic programming minima, we propose a heuristic construction of the elimination trees that has cost O N e log ⁡ N e , where N e is the number of elements in the mesh. We show that this heuristic ordering has similar computational cost to the quasi-optimal elimination trees found with dynamic programming and outperforms state-of-the-art alternatives in our numerical experiments.

Paszyńska, A.↗