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At least 217 records · Page 12

SU-C-304-01: Investigation of Various Detector Response Functions and Their Geometry Dependence in a Novel Method to Address Ion Chamber Volume Averaging Effect

Purpose: A novel convolution-based approach has been proposed to address ion chamber (IC) volume averaging effect (VAE) for the commissioning of commercial treatment planning systems (TPS). We investigate the use of various convolution kernels and its impact on the accuracy of beam models. Methods: Our approach simulates the VAE by iteratively convolving the calculated beam profiles with a detector response function (DRF) while optimizing the beam model. At convergence, the convolved profiles match the measured profiles, indicating the calculated profiles match the “true” beam profiles. To validate the approach, beam profiles of an Elekta LINAC were repeatedly collected with ICs of various volumes (CC04, CC13 and SNC 125) to obtain clinically acceptable beam models. The TPS-calculated profiles were convolved externally with the DRF of respective IC. The beam model parameters were reoptimized using Nelder-Mead method by forcing the convolved profiles to match the measured profiles. We evaluated three types of DRFs (Gaussian, Lorentzian, and parabolic) and the impact of kernel dependence on field geometry (depth and field size). The profiles calculated with beam models were compared with SNC EDGE diode-measured profiles. Results: The method was successfully implemented with Pinnacle Scripting and Matlab. The reoptimization converged in ∼10 minutes. For all tested ICs and DRFs, penumbra widths of the TPS-calculated profiles and diode-measured profiles were within 1.0 mm. Gaussian function had the best performance with mean penumbra width difference within 0.5 mm. The use of geometry dependent DRFs showed marginal improvement, reducing the penumbra width differences to less than 0.3 mm. Significant increase in IMRT QA passing rates was achieved with the optimized beam model. Conclusion: The proposed approach significantly improved the accuracy of the TPS beam model. Gaussian functions as the convolution kernel performed consistently better than Lorentzian and parabolic functions. Further improvement of using geometry-dependent kernels was marginal.

60 APPLIED LIFE SCIENCES↗

astroABC : An Approximate Bayesian Computation Sequential Monte Carlo sampler for cosmological parameter estimation

Given the complexity of modern cosmological parameter inference where we arefaced with non-Gaussian data and noise, correlated systematics and multi-probecorrelated data sets, the Approximate Bayesian Computation (ABC) method is apromising alternative to traditional Markov Chain Monte Carlo approaches in thecase where the Likelihood is intractable or unknown. The ABC method is called"Likelihood free" as it avoids explicit evaluation of the Likelihood by using aforward model simulation of the data which can include systematics. Weintroduce astroABC, an open source ABC Sequential Monte Carlo (SMC) sampler forparameter estimation. A key challenge in astrophysics is the efficient use oflarge multi-probe datasets to constrain high dimensional, possibly correlatedparameter spaces. With this in mind astroABC allows for massive parallelizationusing MPI, a framework that handles spawning of jobs across multiple nodes. Akey new feature of astroABC is the ability to create MPI groups with differentcommunicators, one for the sampler and several others for the forward modelsimulation, which speeds up sampling time considerably. For smaller jobs thePython multiprocessing option is also available. Other key features include: aSequential Monte Carlo sampler, a method for iteratively adapting tolerancelevels, local covariance estimate using scikit-learn's KDTree, modules forspecifying optimal covariance matrix for a component-wise or multivariatenormal perturbation kernel, output and restart files are backed up everyiteration, user defined metric and simulation methods, a module for specifyingheterogeneous parameter priors including non-standard prior PDFs, a module forspecifying a constant, linear, log or exponential tolerance level,well-documented examples and sample scripts. This code is hosted online athttps://github.com/EliseJ/astroABC

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

SELF-GRAVITATIONAL FORCE CALCULATION OF INFINITESIMALLY THIN GASEOUS DISKS ON NESTED GRIDS

We extend the work of Yen et al. and develop second-order formulae to accommodate a nested grid discretization for the direct self-gravitational force calculation for infinitesimally thin gaseous disks. This approach uses a two-dimensional kernel that is derived for infinitesimally thin disks and is free of artificial boundary conditions. The self-gravitational force calculation is presented in generalized convolution forms for a nested grid configuration. A numerical technique derived from a fast Fourier transform is employed to reduce the computational complexity to be nearly linear. By comparing with analytic potential–density pairs associated with the generalized Maclaurin disks, the extended approach is verified to be of second-order accuracy when using numerical simulations. The proposed method is accurate, computationally fast, and has the potential to be applied to studies of planetary migration and the gaseous morphology of disk galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,‘bottom-up’ and ‘top-down’, are illustrated. Here, preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.

97 MATHEMATICS AND COMPUTING↗

Universal Method of Modeling Linear Stationary Physical Fields

The aim of this paper is to develop a method, described earlier, of solving quantum-mechanical problems into a universal numerical method of modeling fields of various physical nature. This method is based on reducing the initial equation of mathematical physics describing a given physical field to a simpler inhomogeneous equation with a known fundamental solution. This equation is then transformed into an inhomogeneous integral equation with a kernel expressed in terms of the known fundamental solution. The obtained integral equation with boundary conditions is solved numerically. To confirm the efficiency of the proposed numerical method, a two-dimensional and a three-dimensional boundary value problem with known solutions have been solved. Another important illustration of the efficiency of the proposed method is the solution of quantum-mechanical problems for one-dimensional and two-dimensional quantum oscillators. It is shown that the considered method allows one to find the energy eigenvalues and the eigenfunctions with acceptable accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Collinear dual-pulse laser optical breakdown and energy deposition

A non-equilibrium model for laser-generated plasmas is used to represent collinear dual nano-second-pulse interactions. In the specific case considered, the breakdown is initiated with an ultraviolet (UV) laser pulse at 266 nm, which pre-ionizes the gas, and it is followed by a near-infrared (NIR) pulse at 1064 nm, which deposits significant energy into the ionized mixture. The model is validated against corresponding experiments, and simulation results are interrogated to understand key features of the plasma-kernel dynamics and the post-discharge hydrodynamics. The hydrodynamics of the non-equilibrium plasma is governed by the two-temperature Navier–Stokes equations accounting for both multiphoton ionization and inverse bremsstrahlung. The interaction between the laser beam and the plasma is modeled based on the radiative transfer equation. The temporal and spatial offsets of the two pulses can generate ionization kernels with different topology and dynamics. It is shown that the UV pre-ionization pulse can tailor the plasma region, leading to a larger ionized volume than would occur for a single-pulse breakdown, and it increases the efficiency of the energy deposition for the following NIR discharge. Vorticity in the early post-discharge phase is generated via baroclinic torque from the misalignment of the radial gradient of density (sudden gas expansion) and the strong pressure gradient (initiated by energy deposition from the laser beam). It is predicted that the collinear dual pulse can be designed to specify the plasma kernel size, shape, and maximum temperature in the breakdown phase, and the initial post-breakdown vorticity and plasma-core decay.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Triple collinear emissions in parton showers

A framework to include triple collinear splitting functions into parton showers is presented, and the implementation of flavor-changing next-to-leading-order (NLO) splitting kernels is discussed as a first application. The correspondence between the Monte Carlo integration and the analytic computation of NLO DGLAP evolution kernels is made explicit for both timelike and spacelike parton evolution. Numerical simulation results are obtained with two independent implementations of the new algorithm, using the two independent event generation frameworks PYTHIA and SHERPA.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Semiclassical dynamics of spin density waves

Here, we present a theoretical framework for equilibrium and nonequilibrium dynamical simulation of quantum states with spin-density-wave (SDW) order. Within a semiclassical adiabatic approximation that retains electron degrees of freedom, we demonstrate that the SDW order parameter obeys a generalized Landau-Lifshitz equation. With the aid of an enhanced kernel polynomial method, our linear-scaling quantum Landau-Lifshitz dynamics (QLLD) method enables dynamical SDW simulations with N ≃ 10 5 lattice sites. Our real-space formulation can be used to compute dynamical responses, such as the dynamical structure factor, of complex and even inhomogeneous SDW configurations at zero or finite temperatures. Applying the QLLD to study the relaxation of a noncoplanar topological SDW under the excitation of a short pulse, we further demonstrate the crucial role of spatial correlations and fluctuations in the SDW dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Parallel DTFE Surface Density Field Reconstruction

We improve the interpolation accuracy and efficiency of the Delaunay tessellation field estimator (DTFE) for surface density field reconstruction by proposing an algorithm that takes advantage of the adaptive triangular mesh for line-of-sight integration. The costly computation of an intermediate 3D grid is completely avoided by our method and only optimally chosen interpolation points are computed, thus, the overall computational cost is significantly reduced. The algorithm is implemented as a parallel shared-memory kernel for large-scale grid rendered field reconstructions in our distributed-memory framework designed for N-body gravitational lensing simulations in large volumes. We also introduce a load balancing scheme to optimize the efficiency of processing a large number of field reconstructions. Our results show our kernel outperforms existing software packages for volume weighted density field reconstruction, achieving ~ 10x speedup, and our load balancing algorithm gains an additional ~ 3.6x speedup at scales with ~ 16k processes.

97 MATHEMATICS AND COMPUTING↗

JACC: Leveraging HPC Meta-Programming and Performance Portability with the Just-in-Time and LLVM-based Julia Language

We present JACC (Julia for Accelerators), the first high-level, and performance-portable model for the just-in-time and LLVM-based Julia language. JACC provides a unified and lightweight front end across different back ends available in Julia, enabling the same Julia code to run efficiently on many HPC CPU and GPU targets. We evaluated the performance of JACC for common HPC kernels as well as for the most computationally demanding kernels used in applications, HPCCG, a supercomputing benchmark test for sparse domains, and HARVEY, a blood flow simulator to assist in the diagnosis and treatment of patients suffering from vascular diseases. We carried out the performance analysis on the most advanced US DOE supercomputers: Aurora, Frontier, and Perlmutter. Overall, we show that JACC has a negligible overhead versus vendor-specific solutions, reporting GPU speedups with no extra cost to programmability.

Valero-Lara, Pedro↗

Simulation of macromolecule self-assembly in solution: A multiscale approach

One of the most common processes to produce polymer nanoparticles is to induce self-assembly by using the solvent-displacement method, in which the polymer is dissolved in a “good” solvent and the solution is then mixed with an “anti-solvent”. The polymer ability to self-assemble in solution is therefore determined by its structural and transport properties in solutions of the pure solvents and at the intermediate compositions. In this work, we focus on poly-ε-caprolactone (PCL) which is a biocompatible polymer that finds widespread application in the pharmaceutical and biomedical fields, performing simulation at three different scales using three different computational tools: full atomistic molecular dynamics (MD), population balance modeling (PBM) and computational fluid dynamics (CFD). Simulations consider PCL chains of different molecular weight in solution of pure acetone (good solvent), of pure water (anti-solvent) and their mixtures, and mixing at different rates and initial concentrations in a confined impinging jets mixer (CIJM). Our MD simulations reveal that the nano-structuring of one of the solvents in the mixture leads to an unexpected identical polymer structure irrespectively of the concentration of the two solvents. In particular, although in pure solvents the behavior of the polymer is, as expected, very different, at intermediate compositions, the PCL chain shows properties very similar to those found in pure acetone as a result of the clustering of the acetone molecules in the vicinity of the polymer chain. We derive an analytical expression to predict the polymer structural properties in solution at different solvent compositions and use it to formulate an aggregation kernel to describe the self-assembly in the CIJM via PBM and CFD. Simulations are eventually validated against experiments.

36 MATERIALS SCIENCE↗

Collaborating CPU and GPU for large-scale high-order CFD simulations with complex grids on the TianHe-1A supercomputer

Programming and optimizing complex, real-world CFD codes on current many-core accelerated HPC systems is very challenging, especially when collaborating CPUs and accelerators to fully tap the potential of heterogeneous systems. In this paper, with a tri-level hybrid and heterogeneous programming model using MPI + OpenMP + CUDA, we port and optimize our high-order multi-block structured CFD software HOSTA on the GPU-accelerated TianHe-1A supercomputer. HOSTA adopts two self-developed high-order compact definite difference schemes WCNS and HDCS that can simulate flows with complex geometries. We present a dual-level parallelization scheme for efficient multi-block computation on GPUs and perform particular kernel optimizations for high-order CFD schemes. The GPU-only approach achieves a speedup of about 1.3 when comparing one Tesla M2050 GPU with two Xeon X5670 CPUs. To achieve a greater speedup, we collaborate CPU and GPU for HOSTA instead of using a naive GPU-only approach. We present a novel scheme to balance the loads between the store-poor GPU and the store-rich CPU. Taking CPU and GPU load balance into account, we improve the maximum simulation problem size per TianHe-1A node for HOSTA by 2.3×, meanwhile the collaborative approach can improve the performance by around 45% compared to the GPU-only approach. Further, to scale HOSTA on TianHe-1A, we propose a gather/scatter optimization to minimize PCI-e data transfer times for ghost and singularity data of 3D grid blocks, and overlap the collaborative computation and communication as far as possible using some advanced CUDA and MPI features. Scalability tests show that HOSTA can achieve a parallel efficiency of above 60% on 1024 TianHe-1A nodes. With our method, we have successfully simulated an EET high-lift airfoil configuration containing 800M cells and China's large civil airplane configuration containing 150M cells. To our best knowledge, those are the largest-scale CPU–GPU collaborative simulations that solve realistic CFD problems with both complex configurations and high-order schemes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantitative Monte Carlo-based holmium-166 SPECT reconstruction

Purpose: Quantitative imaging of the radionuclide distribution is of increasing interest for microsphere radioembolization (RE) of liver malignancies, to aid treatment planning and dosimetry. For this purpose, holmium-166 ({sup 166}Ho) microspheres have been developed, which can be visualized with a gamma camera. The objective of this work is to develop and evaluate a new reconstruction method for quantitative {sup 166}Ho SPECT, including Monte Carlo-based modeling of photon contributions from the full energy spectrum.Methods: A fast Monte Carlo (MC) simulator was developed for simulation of {sup 166}Ho projection images and incorporated in a statistical reconstruction algorithm (SPECT-fMC). Photon scatter and attenuation for all photons sampled from the full {sup 166}Ho energy spectrum were modeled during reconstruction by Monte Carlo simulations. The energy- and distance-dependent collimator-detector response was modeled using precalculated convolution kernels. Phantom experiments were performed to quantitatively evaluate image contrast, image noise, count errors, and activity recovery coefficients (ARCs) of SPECT-fMC in comparison with those of an energy window-based method for correction of down-scattered high-energy photons (SPECT-DSW) and a previously presented hybrid method that combines MC simulation of photopeak scatter with energy window-based estimation of down-scattered high-energy contributions (SPECT-ppMC+DSW). Additionally, the impact of SPECT-fMC on whole-body recovered activities (A{sup est}) and estimated radiation absorbed doses was evaluated using clinical SPECT data of six {sup 166}Ho RE patients.Results: At the same noise level, SPECT-fMC images showed substantially higher contrast than SPECT-DSW and SPECT-ppMC+DSW in spheres ≥17 mm in diameter. The count error was reduced from 29% (SPECT-DSW) and 25% (SPECT-ppMC+DSW) to 12% (SPECT-fMC). ARCs in five spherical volumes of 1.96–106.21 ml were improved from 32%–63% (SPECT-DSW) and 50%–80% (SPECT-ppMC+DSW) to 76%–103% (SPECT-fMC). Furthermore, SPECT-fMC recovered whole-body activities were most accurate (A{sup est}= 1.06 × A − 5.90 MBq, R{sup 2}= 0.97) and SPECT-fMC tumor absorbed doses were significantly higher than with SPECT-DSW (p = 0.031) and SPECT-ppMC+DSW (p = 0.031).Conclusions: The quantitative accuracy of {sup 166}Ho SPECT is improved by Monte Carlo-based modeling of the image degrading factors. Consequently, the proposed reconstruction method enables accurate estimation of the radiation absorbed dose in clinical practice.

61 RADIATION PROTECTION AND DOSIMETRY↗

Smoothing Lexis diagrams using kernel functions: A contemporary approach

Lexis diagrams are rectangular arrays of event rates indexed by age and period. Analysis of Lexis diagrams is a cornerstone of cancer surveillance research. Typically, population-based descriptive studies analyze multiple Lexis diagrams defined by sex, tumor characteristics, race/ethnicity, geographic region, etc. Inevitably the amount of information per Lexis diminishes with increasing stratification. Several methods have been proposed to smooth observed Lexis diagrams up front to clarify salient patterns and improve summary estimates of averages, gradients, and trends. In this article, we develop a novel bivariate kernel-based smoother that incorporates two key innovations. First, for any given kernel, we calculate its singular values decomposition, and select an optimal truncation point—the number of leading singular vectors to retain—based on the bias-corrected Akaike information criterion. Second, we model-average over a panel of candidate kernels with diverse shapes and bandwidths. The truncated model averaging approach is fast, automatic, has excellent performance, and provides a variance-covariance matrix that takes model selection into account. We present an in-depth case study (invasive estrogen receptor-negative breast cancer incidence among non-Hispanic white women in the United States) and simulate operating characteristics for 20 representative cancers. The truncated model averaging approach consistently outperforms any fixed kernel. Our results support the routine use of the truncated model averaging approach in descriptive studies of cancer.

60 APPLIED LIFE SCIENCES↗

Landrush: Rethinking In-Situ Analysis for GPGPU Workflows

In-situ analysis on the output data of scientific simulations has been made necessary by ever-growing output data volumes and increasing costs of data movement as supercomputing is moving towards exascale. With hardware accelerators like GPUs becoming increasingly common in high end machines, new opportunities arise to co-locate scientific simulations and online analysis performed on the scientific data generated by the simulations. However, the asynchronous nature of GPGPU programming models and the limited context-switching capabilities on the GPU pose challenges to co-locating the scientific simulation and analysis on the same GPU. This paper dives deeper into these challenges to understand how best to co-locate analysis with scientific simulations on the GPUs in HPC clusters. Specifically, our 'Landrush' approach to GPU sharing proposes a solution that utilizes idle cycles on the GPU to provide an improved time-to-answer, that is, the total time to run the scientific simulation and analysis of the generated data. Landrush is demonstrated with experimental results obtained from leadership high-end applications on ORNL's Titan supercomputer, which show that (i) GPU-based scientific simulations have varying degrees of idle cycles to afford useful analysis task co-location, and (ii) the inability to context switch on the GPU at instruction granularity can be overcome by careful control of the analysis kernel launches and software-controlled early completion of analysis kernel executions. Results show that Landrush is superior in terms of time-to-answer compared to serially running simulations followed by analysis or by relying on the GPU driver and hardwired thread dispatcher to run analysis concurrently on a single GPU.

Computer Science↗

Fault Detection via Occupation Kernel Principal Component Analysis

Reliable operation of automatic systems is heavily dependent on the ability to detect faults in the underlying dynamics. While traditional model-based methods have been widely used for fault detection, data-driven approaches have garnered increasing attention due to their ease of deployment and minimal need for expert knowledge. In this letter, we present a novel principal component analysis (PCA) method that uses occupation kernels. Occupation kernels result in feature maps that are tailored to the measured data, have inherent noise-robustness due to the use of integration, and can utilize irregularly sampled system trajectories of variable lengths for PCA. The occupation kernel PCA method is used to develop a reconstruction error approach to fault detection and its efficacy is validated using numerical simulations.

42 ENGINEERING↗

WE-EF-303-04: An Advanced Image Processing Method to Improve the Spatial Resolution of Proton Radiographies

Purpose: We present an optimization method to improve the spatial resolution and the water equivalent thickness accuracy of proton radiographies. Methods: The method is designed for imaging systems measuring only the residual range of protons without relying on tracker detectors to determine the beam trajectory before and after the target. Specifically, the method was used for an imaging set-up consisting of a stack of 61 parallel-plate ionization chambers (PPIC) working as a range telescope. The method uses a decomposition approach of the residual range signal measured by the PPIC and constructs subimages with small size pixels geometrically rearranged and appropriately averaged to be merged into a final single radiography. The method was tested using Monte Carlo simulated and experimental proton radiographies of a PMMA step phantom and an anthropomorphic head phantom. Results: For the step phantom, the effective spatial resolution was found to be 4 and 3 times higher than the nominal resolution for the simulated and experimental radiographies, respectively. For the head phantom, a gamma index was calculated to quantify the conformity of the simulated proton radiographies with a digitally reconstructed X-ray radiography convolved with a Gaussian kernel equal to the proton beam spot-size. For DTA=2.5 mm and RD=2.5%, the passing ratio was 100%/85% for the optimized/non-optimized case, respectively. An extension of the method allows reducing the dose given to the patient during radiography acquisition. We show that despite a dose reduction of 25 times (leading to a dose of 0.016 mGy for the current imaging set-up), the image quality of the optimized radiographies remains fairly unaffected for both the simulated and experimental results. Conclusion: The optimization method leads to a significant increase of the spatial resolution allowing recovering image details that are unresolved in non-optimized radiographies. These results represent a major step towards clinical application of proton radiography.

60 APPLIED LIFE SCIENCES↗

Initial Simulations of Empty Room Collapse and Reconsolidation at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is a geologic repository for defense-related nuclear waste. If left undisturbed, the virtually impermeable rock salt surrounding the repository will isolate the nuclear waste from the biosphere. If humans accidentally intrude into the repository in the future, then the likelihood of a radionuclide release to the biosphere will depend significantly on the porosity and permeability of the repository itself. Room ceilings and walls at the WIPP tend to collapse over time, causing rubble piles to form on floors of empty rooms. The surrounding rock formation will gradually compact these rubble piles until they eventually become solid salt, but the length of time for a rubble pile to reach a certain porosity and permeability is unknown. This report details the first efforts to build models to predict the porosity and permeability evolution of an empty room as it closes. Conventional geomechanical numerical methods would struggle to model empty room collapse and rubble pile consolidation, so three different meshless methods, the Immersed Isogeometric Analysis Meshfree, Reproducing Kernel Particle Method (RKPM), and the Conformal Reproducing Kernel method, were assessed. First, the meshless methods and the finite element method each simulated gradual room closure, without ceiling or wall collapse. All three methods produced equivalent room closure predictions with comparable computational speed. Second, the Immersed Isogeometric Analysis Meshfree method and RKPM simulated two-dimensional empty room collapse and rubble pile consolidation. Both methods successfully simulated large viscoplastic deformations, fracture, and rubble pile rearrangement to produce qualitatively realistic results. In addition to geomechanical simulations, the flow channels in damaged salt and crushed salt were measured using micro-computed tomography, and input into a computational fluid dynamics simulation to predict the salt's permeability. Although room for improvement exists, the current simulation approaches appear promising.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗