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At least 991 records · Page 55

Charon Message-Passing Toolkit for Scientific Computations

The Charon toolkit for piecemeal development of high-efficiency parallel programs for scientific computing is described. The portable toolkit, callable from C and Fortran, provides flexible domain decompositions and high-level distributed constructs for easy translation of serial legacy code or design to distributed environments. Gradual tuning can subsequently be applied to obtain high performance, possibly by using explicit message passing. Charon also features general structured communications that support stencil-based computations with complex recurrences. Through the separation of partitioning and distribution, the toolkit can also be used for blocking of uni-processor code, and for debugging of parallel algorithms on serial machines. An elaborate review of recent parallelization aids is presented to highlight the need for a toolkit like Charon. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability.

VanderWijngarrt, Rob F.↗

Carbon Emissions from Deforestation in the Brazilian Amazon Region

A simulation model based on satellite observations of monthly vegetation greenness from the Moderate Resolution Imaging Spectroradiometer (MODIS) was used to estimate monthly carbon fluxes in terrestrial ecosystems of Brazilian Amazon and Cerrado regions over the period 2000-2002. The NASA-CASA (Carnegie Ames Stanford Approach) model estimates of annual forest production were used for the first time as the basis to generate a prediction for the standing pool of carbon in above-ground biomass (AGB; gC/sq m) for forested areas of the Brazilian Amazon region. Plot-level measurements of the residence time of carbon in wood in Amazon forest from Malhi et al. (2006) were interpolated by inverse distance weighting algorithms and used with CASA to generate a new regional map of AGB. Data from the Brazilian PRODES (Estimativa do Desflorestamento da Amazonia) project were used to map deforested areas. Results show that net primary production (NPP) sinks for carbon varied between 4.25 Pg C/yr (1 Pg=10(exp 15)g) and 4.34 Pg C for the region and were highest across the eastern and northern Amazon areas, whereas deforestation sources of CO2 flux from decomposition of residual woody debris were higher and less seasonal in the central Amazon than in the eastern and southern areas. Increased woody debris from past deforestation events was predicted to alter the net ecosystem carbon balance of the Amazon region to generate annual CO2 source fluxes at least two times higher than previously predicted by CASA modeling studies. Variations in climate, land cover, and forest burning were predicted to release carbon at rates of 0.5 to 1 Pg C/yr from the Brazilian Amazon. When direct deforestation emissions of CO2 from forest burning of between 0.2 and 0.6 Pg C/yr in the Legal Amazon are overlooked in regional budgets, the year-to-year variations in this net biome flux may appear to be large, whereas our model results implies net biome fluxes had actually been relatively consistent from year to year during the period 2000-2002. This is the first study to use MODIS data to model all carbon pools (wood, leaf, root) dynamically in simulations of Amazon forest deforestation from clearing and burning of all kinds.

Potter, C.↗

A dictionary learning algorithm for compression and reconstruction of streaming data in preset order

There has been an emerging interest in developing and applying dictionary learning (DL) to process massive datasets in the last decade. Many of these efforts, however, focus on employing DL to compress and extract a set of important features from data, while considering restoring the original data from this set a secondary goal. On the other hand, although several methods are able to process streaming data by updating the dictionary incrementally as new snapshots pass by, most of those algorithms are designed for the setting where the snapshots are randomly drawn from a probability distribution. In this paper, we present a new DL approach to compress and denoise massive dataset in real time, in which the data are streamed through in a preset order (instances are videos and temporal experimental data), so at any time, we can only observe a biased sample set of the whole data. Here, our approach incrementally builds up the dictionary in a relatively simple manner: if the new snapshot is adequately explained by the current dictionary, we perform a sparse coding to find its sparse representation; otherwise, we add the new snapshot to the dictionary, with a Gram-Schmidt process to maintain the orthogonality. To compress and denoise noisy datasets, we apply the denoising to the snapshot directly before sparse coding, which deviates from traditional dictionary learning approach that achieves denoising via sparse coding. Compared to full-batch matrix decomposition methods, where the whole data is kept in memory, and other mini-batch approaches, where unbiased sampling is often assumed, our approach has minimal requirement in data sampling and storage: i) each snapshot is only seen once then discarded, and ii) the snapshots are drawn in a preset order, so can be highly biased. Through experiments on climate simulations and scanning transmission electron microscopy (STEM) data, we demonstrate that the proposed approach performs competitively to those methods in data reconstruction and denoising.

97 MATHEMATICS AND COMPUTING↗

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TH-C-18A-02: Machine Learning and STAPLE Based Simultaneous Longitudinal Segmentation of Bone and Marrow Structures From Dual Energy CT

Purpose: To develop a fully-automatic longitudinal bone and marrow segmentation method in the pelvic region from dual energy computed tomography (DECT). Methods: We developed a two-step automatic bone and marrow segmentation method for simultaneous longitudinal evaluation of patients with metastatic bone disease using dual energy CT (DECT). Our approach transforms the DECT images into a multi-material decomposition (MMD) model that represents the voxels as a mixture of multiple materials. A support vector machine (SVM) was trained using a single scan. In the first step of the longitudinal segmentation the trained SVM model detects bone and marrow structures on all available longitudinal scans. Segmentation is further refined through active contour segmentation. In the second step, the segmentations from the individual scans are merged by employing the simultaneous truth and performance level estimation (STAPLE) algorithm. The scans are registered using affine and deformable registration. We found that our approach improves the segmentation in all the scans under reliable registration performance between the same scans. Improving registration was not under the scope of this work. Results: We applied our approach to segment bone and marrow in DECT scans in the pelvic regions for multiple patients. Each patient had three to five follow up scans. All the patients in the analysis had artificial metal prostheses which introduced challenges for the registration. Our algorithm achieved reasonable accurate segmentation despite the presence of metal artifacts and high-density oral contrast in neighboring structures. Our approach obtained an overall segmentation accuracy of 80% using DICE metric. Conclusion: We developed a two-step automatic longitudinal segmentation technique for bone and marrow region structures in the pelvic areas from dual energy CT. Our approach achieves robust segmentation despite the presence of confounding structures with similar intensities as the bone and marrow regions due to uptake of oral contrast and metal artifacts.

60 APPLIED LIFE SCIENCES↗

ALESQP: An Augmented Lagrangian Equality-Constrained SQP Method for Optimization with General Constraints

Here we present a new algorithm for infinite-dimensional optimization with general constraints, called ALESQP. In short, ALESQP is an augmented Lagrangian method that penalizes inequality constraints and solves equality-constrained nonlinear optimization subproblems at every iteration. The subproblems are solved using a matrix-free trust-region sequential quadratic programming (SQP) method that takes advantage of iterative, i.e., inexact linear solvers, and is suitable for large-scale applications. A key feature of ALESQP is a constraint decomposition strategy that allows it to exploit problem-specific variable scalings and inner products. We analyze convergence of ALESQP under different assumptions. We show that strong accumulation points are stationary. Consequently, in finite dimensions ALESQP converges to a stationary point. In infinite dimensions we establish that weak accumulation points are feasible in many practical situations. Under additional assumptions we show that weak accumulation points are stationary. We present several infinite-dimensional examples where ALESQP shows remarkable discretization-independent performance in all of its iterative components, requiring a modest number of iterations to meet constraint tolerances at the level of machine precision. Also, we demonstrate a fully matrix-free solution of an infinite-dimensional problem with nonlinear inequality constraints.

97 MATHEMATICS AND COMPUTING↗

Introduction to Vector Field Visualization

Vector field visualization techniques are essential to help us understand the complex dynamics of flow fields. These can be found in a wide range of applications such as study of flows around an aircraft, the blood flow in our heart chambers, ocean circulation models, and severe weather predictions. The vector fields from these various applications can be visually depicted using a number of techniques such as particle traces and advecting textures. In this tutorial, we present several fundamental algorithms in flow visualization including particle integration, particle tracking in time-dependent flows, and seeding strategies. For flows near surfaces, a wide variety of synthetic texture-based algorithms have been developed to depict near-body flow features. The most common approach is based on the Line Integral Convolution (LIC) algorithm. There also exist extensions of LIC to support more flexible texture generations for 3D flow data. This tutorial reviews these algorithms. Tensor fields are found in several real-world applications and also require the aid of visualization to help users understand their data sets. Examples where one can find tensor fields include mechanics to see how material respond to external forces, civil engineering and geomechanics of roads and bridges, and the study of neural pathway via diffusion tensor imaging. This tutorial will provide an overview of the different tensor field visualization techniques, discuss basic tensor decompositions, and go into detail on glyph based methods, deformation based methods, and streamline based methods. Practical examples will be used when presenting the methods; and applications from some case studies will be used as part of the motivation.

Kao, David↗

Synergies from using higher order symplectic decompositions both for ordinary differential equations and quantum Monte Carlo methods

Decomposition methods of the Suzuki-Trotter type of various orders have been derived in different fields. Applying them both to classical ordinary differential equations (ODEs) and quantum systems allows to judge their effectiveness and gives new insights for many body quantum mechanics where reference data are scarce. Further, based on data for 6 × 6 system we conclude that sampling with sign (minus-sign problem) is probably detrimental to the accuracy of fermionic simulations with determinant algorithms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ExaTN

A challenging scientific problem that will benefit from exascale computing is predictive simulation of two- and three-dimensional quantum many-body Hamiltonians in condensed matter physics, together with the related strong entanglement problems in quantum chemistry and quantum computing. Efficient numerical simulations will require new insights into wavefunction compression algorithms that scale on extremely heterogeneous HPC architectures. To address this need, we propose to develop a scalable math library of parallel multi-linear algebraic numerical primitives for hierarchical tensor compression. Our library will subsequently be used for building an efficient, performance-portable HPC framework for simulating strongly correlated quantum systems. In particular, our will will be the first to deliver a massively parallel implementation of the multiscale entanglement renormalization ansatz (MERA), a hierarchical tensor decomposition quantum scheme capable of expressing local expectation values of strongly entangled higher-dimensional quantum systems efficiently. To address the extreme complexity and high computational cost of such schemes, we will automate their parallel implementation by delivering an integrated software framework, ExaTN (Exascale Tensor Networks), that will process hierarchical tensor representations on exascale HPC systems via an asymchronous task-based programming model. As a specific application, our framework will provide scientists with a capability of simulating strongly entangled quantum systems, thus positioning ORNL as a strategic leader in modeling of strongly correlated materials.

McCaskey, AlexanderJ↗

NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study

Abstract Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.

60 APPLIED LIFE SCIENCES↗

Two alternative ways for solving the coordination problem in multilevel optimization

Two techniques for formulating the coupling between levels in multilevel optimization by linear decomposition, proposed as improvements over the original formulation, now several years old, that relied on explicit equality constraints which were shown by application experience as occasionally causing numerical difficulties. The two new techniques represent the coupling without using explicit equality constraints, thus avoiding the above diffuculties and also reducing computational cost of the procedure. The old and new formulations are presented in detail and illustrated by an example of a structural optimization. A generic version of the improved algorithm is also developed for applications to multidisciplinary systems not limited to structures.

Sobieszczanski-Sobieski, Jaroslaw↗

Efficient Implementation of an Optimal Interpolator for Large Spatial Data Sets

Scattered data interpolation is a problem of interest in numerous areas such as electronic imaging, smooth surface modeling, and computational geometry. Our motivation arises from applications in geology and mining, which often involve large scattered data sets and a demand for high accuracy. The method of choice is ordinary kriging. This is because it is a best unbiased estimator. Unfortunately, this interpolant is computationally very expensive to compute exactly. For n scattered data points, computing the value of a single interpolant involves solving a dense linear system of size roughly n x n. This is infeasible for large n. In practice, kriging is solved approximately by local approaches that are based on considering only a relatively small'number of points that lie close to the query point. There are many problems with this local approach, however. The first is that determining the proper neighborhood size is tricky, and is usually solved by ad hoc methods such as selecting a fixed number of nearest neighbors or all the points lying within a fixed radius. Such fixed neighborhood sizes may not work well for all query points, depending on local density of the point distribution. Local methods also suffer from the problem that the resulting interpolant is not continuous. Meyer showed that while kriging produces smooth continues surfaces, it has zero order continuity along its borders. Thus, at interface boundaries where the neighborhood changes, the interpolant behaves discontinuously. Therefore, it is important to consider and solve the global system for each interpolant. However, solving such large dense systems for each query point is impractical. Recently a more principled approach to approximating kriging has been proposed based on a technique called covariance tapering. The problems arise from the fact that the covariance functions that are used in kriging have global support. Our implementations combine, utilize, and enhance a number of different approaches that have been introduced in literature for solving large linear systems for interpolation of scattered data points. For very large systems, exact methods such as Gaussian elimination are impractical since they require 0(n(exp 3)) time and 0(n(exp 2)) storage. As Billings et al. suggested, we use an iterative approach. In particular, we use the SYMMLQ method, for solving the large but sparse ordinary kriging systems that result from tapering. The main technical issue that need to be overcome in our algorithmic solution is that the points' covariance matrix for kriging should be symmetric positive definite. The goal of tapering is to obtain a sparse approximate representation of the covariance matrix while maintaining its positive definiteness. Furrer et al. used tapering to obtain a sparse linear system of the form Ax = b, where A is the tapered symmetric positive definite covariance matrix. Thus, Cholesky factorization could be used to solve their linear systems. They implemented an efficient sparse Cholesky decomposition method. They also showed if these tapers are used for a limited class of covariance models, the solution of the system converges to the solution of the original system. Matrix A in the ordinary kriging system, while symmetric, is not positive definite. Thus, their approach is not applicable to the ordinary kriging system. Therefore, we use tapering only to obtain a sparse linear system. Then, we use SYMMLQ to solve the ordinary kriging system. We show that solving large kriging systems becomes practical via tapering and iterative methods, and results in lower estimation errors compared to traditional local approaches, and significant memory savings compared to the original global system. We also developed a more efficient variant of the sparse SYMMLQ method for large ordinary kriging systems. This approach adaptively finds the correct local neighborhood for each query point in the interpolation process.

Memarsadeghi, Nargess↗

Efficient computation of N -point correlation functions in D dimensions

We present efficient algorithms for computing the N-point correlation functions (NPCFs) of random fields in arbitrary D-dimensional homogeneous and isotropic spaces. Such statistics appear throughout the physical sciences and provide a natural tool to describe stochastic processes. Typically, algorithms for computing the NPCF components have $\mathscr O$(n N ) complexity (for a dataset containing n particles); their application is thus computationally infeasible unless N is small. By projecting the statistic onto a suitably defined angular basis, we show that the estimators can be written in a separable form, with complexity $\mathscr O$(n 2 ) or $\mathscr O$(n g log n g ) if evaluated using a Fast Fourier Transform on a grid of size n g . Our decomposition is built upon the D-dimensional hyperspherical harmonics; these form a complete basis on the (D – 1) sphere and are intrinsically related to angular momentum operators. Concatenation of (N – 1) such harmonics gives states of definite combined angular momentum, forming a natural separable basis for the NPCF. As N and D grow, the number of basis components quickly becomes large, providing a practical limitation to this (and all other) approaches: However, the dimensionality is greatly reduced in the presence of symmetries; for example, isotropic correlation functions require only states of zero combined angular momentum. We provide a Julia package implementing our estimators and show how they can be applied to a variety of scenarios within cosmology and fluid dynamics. The efficiency of such estimators will allow higher-order correlators to become a standard tool in the analysis of random fields.

97 MATHEMATICS AND COMPUTING↗

Optimal mapping of irregular finite element domains to parallel processors

Mapping the solution domain of n-finite elements into N-subdomains that may be processed in parallel by N-processors is an optimal one if the subdomain decomposition results in a well-balanced workload distribution among the processors. The problem is discussed in the context of irregular finite element domains as an important aspect of the efficient utilization of the capabilities of emerging multiprocessor computers. Finding the optimal mapping is an intractable combinatorial optimization problem, for which a satisfactory approximate solution is obtained here by analogy to a method used in statistical mechanics for simulating the annealing process in solids. The simulated annealing analogy and algorithm are described, and numerical results are given for mapping an irregular two-dimensional finite element domain containing a singularity onto the Hypercube computer.

Flower, J.↗

Flow simulations about steady-complex and unsteady moving configurations using structured-overlapped and unstructured grids

The limiting factor in simulating flows past realistic configurations of interest has been the discretization of the physical domain on which the governing equations of fluid flow may be solved. In an attempt to circumvent this problem, many Computational Fluid Dynamic (CFD) methodologies that are based on different grid generation and domain decomposition techniques have been developed. However, due to the costs involved and expertise required, very few comparative studies between these methods have been performed. In the present work, the two CFD methodologies which show the most promise for treating complex three-dimensional configurations as well as unsteady moving boundary problems are evaluated. These are namely the structured-overlapped and the unstructured grid schemes. Both methods use a cell centered, finite volume, upwind approach. The structured-overlapped algorithm uses an approximately factored, alternating direction implicit scheme to perform the time integration, whereas, the unstructured algorithm uses an explicit Runge-Kutta method. To examine the accuracy, efficiency, and limitations of each scheme, they are applied to the same steady complex multicomponent configurations and unsteady moving boundary problems. The steady complex cases consist of computing the subsonic flow about a two-dimensional high-lift multielement airfoil and the transonic flow about a three-dimensional wing/pylon/finned store assembly. The unsteady moving boundary problems are a forced pitching oscillation of an airfoil in a transonic freestream and a two-dimensional, subsonic airfoil/store separation sequence. Accuracy was accessed through the comparison of computed and experimentally measured pressure coefficient data on several of the wing/pylon/finned store assembly's components and at numerous angles-of-attack for the pitching airfoil. From this study, it was found that both the structured-overlapped and the unstructured grid schemes yielded flow solutions of comparable accuracy for these simulations. This study also indicated that, overall, the structured-overlapped scheme was slightly more CPU efficient than the unstructured approach.

Newman, James C., III↗

An interactive adaptive remeshing algorithm for the two-dimensional Euler equations

An interactive adaptive remeshing algorithm utilizing a frontal grid generator and a variety of time integration schemes for the two-dimensional Euler equations on unstructured meshes is presented. Several device dependent interactive graphics interfaces have been developed along with a device independent DI-3000 interface which can be employed on any computer that has the supporting software including the Cray-2 supercomputers Voyager and Navier. The time integration methods available include: an explicit four stage Runge-Kutta and a fully implicit LU decomposition. A cell-centered finite volume upwind scheme utilizing Roe's approximate Riemann solver is developed. To obtain higher order accurate results a monotone linear reconstruction procedure proposed by Barth is utilized. Results for flow over a transonic circular arc and flow through a supersonic nozzle are examined.

Slack, David C.↗

A Pebble Tracking Transport Algorithm for Pebble Bed Reactor Analysis

Pebble bed reactor (PBR) designs pose unique challenges to modeling and simulation. The challenges originate from the multiple levels of heterogeneity partly due to random packing in and flow through the core of fuel pebbles. This paper proposes a novel pebble tracking transport (PTT) algorithm to address some of the challenges facing PBR analysis. Each individual pebble is tracked and modeled on an unstructured mesh of which the nodes are aligned with the pebble centroids. The neutron transport equation is solved on this pebble tracking mesh with pre-assembled elemental matrices. These elemental matrices are independent of the cross sections and the streaming directions, thus can be assembled before the calculation without introducing too much memory overhead especially when combined with spatial domain decomposition. Numerical results show that these matrices can be assembled efficiently. PTT is implemented in Rattlesnake, the INL MOOSE-based multigroup radiation transport application. Both the angular and spatial convergence are investigated and the results indicate that low order angular and spatial resolution is typically sufficient for analysis. A complete work flow for PBR analysis with PTT including, pebble packing, meshing, cross section generation, solution of the transport equation, postprocessing, etc. is demonstrated with a simplified reactor with 41,048 pebbles.

97 MATHEMATICS AND COMPUTING↗

Eigenfunction Decomposition of Reactor Perturbations and Transitions Using MCNP Monte Carlo

Monte Carlo criticality calculations for nuclear reactors have typically only been able to find the primary eigenvalue and eigenmode. With the new fission matrix capability in MCNP6, it becomes possible to solve for higher modes, which are useful in wide variety of analyses. As a test case of this new capability, two reactor models in both a base configuration and a perturbed configuration were simulated in MCNP to generate fission matrices. Tools were written to find a relatively small number of eigenpairs of the resulting matrices, whereupon it was found that the implicitly restarted Arnoldi method outperformed the previously used power iteration as an eigenvalue algorithm by a factor of 1500 for a 3600 × 3600 sparse matrix.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗