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At least 73 records · Page 4

Modeling Sound Propagation Through Non-Axisymmetric Jets

A method for computing the far-field adjoint Green's function of the generalized acoustic analogy equations under a locally parallel mean flow approximation is presented. The method is based on expanding the mean-flow-dependent coefficients in the governing equation and the scalar Green's function in truncated Fourier series in the azimuthal direction and a finite difference approximation in the radial direction in circular cylindrical coordinates. The combined spectral/finite difference method yields a highly banded system of algebraic equations that can be efficiently solved using a standard sparse system solver. The method is applied to test cases, with mean flow specified by analytical functions, corresponding to two noise reduction concepts of current interest: the offset jet and the fluid shield. Sample results for the Green's function are given for these two test cases and recommendations made as to the use of the method as part of a RANS-based jet noise prediction code.

Leib, Stewart J.↗

Exploration with Scalable Gaussian Process Reinforcement Learning

Exploration is a challenging problem in reinforcement learning (RL), especially in environments with sparse rewards. Quantifying and utilizing the parametric uncertainty has been shown to be paramount for successful exploration [Osband et al., 2018]. Bayesian, or approximately Bayesian, methods present a principled means of estimating the parametric uncertainty in RL problems. Gaussian processes, nonparametric Bayesian models, are often impractical due to poor scalability and computational bottlenecks. We introduce a scalable Gaussian process RL (GPRL) method which directly induces sparsity in the covariance matrix to facilitate faster computation. This is a departure from previous GPRL methods which instead rely on data reduction and subsampling. We compare various covariance-based exploration techniques (Thompson sampling, upper confidence bound, and probabilistic maximum variance) which leverage our scalable GP framework in sparse reward environments. Finally, we show favorable comparison against the bootstrapped deep Q-Network.

97 MATHEMATICS AND COMPUTING↗

A General-applications Direct Global Matrix Algorithm for Rapid Seismo-acoustic Wavefield Computations

A new matrix method for rapid wave propagation modeling in generalized stratified media, which has recently been applied to numerical simulations in diverse areas of underwater acoustics, solid earth seismology, and nondestructive ultrasonic scattering is explained and illustrated. A portion of recent efforts jointly undertaken at NATOSACLANT and NORDA Numerical Modeling groups in developing, implementing, and testing a new fast general-applications wave propagation algorithm, SAFARI, formulated at SACLANT is summarized. The present general-applications SAFARI program uses a Direct Global Matrix Approach to multilayer Green's function calculation. A rapid and unconditionally stable solution is readily obtained via simple Gaussian ellimination on the resulting sparsely banded block system, precisely analogous to that arising in the Finite Element Method. The resulting gains in accuracy and computational speed allow consideration of much larger multilayered air/ocean/Earth/engineering material media models, for many more source-receiver configurations than previously possible. The validity and versatility of the SAFARI-DGM method is demonstrated by reviewing three practical examples of engineering interest, drawn from ocean acoustics, engineering seismology and ultrasonic scattering.

Schmidt, H.↗

High-performance equation solvers and their impact on finite element analysis

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number of operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

Poole, Eugene L.↗

High-performance equation solvers and their impact on finite element analysis

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number od operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

Poole, Eugene L.↗

Initial CEED API (CEED-MS10)

Key components of CEED software development involve fast finite element operator storage and evaluation, architecture optimizations, performant algorithms for all orders, global kernels for finite element operators, efficient use of the memory sub-system, optimal data locality and motion, enhanced scalability and parallelism, and fast tensor contractions. As ultimate goals of the project, CEED is exploring and identifying the best algorithms for the full range of discretizations and applying algorithmic and software development to support ECP applications’ needs. In this milestone, we initiated the development and implementation of a common CEED API consisting of two main components: low-level and high-level APIs. We accomplished the goal of having the low-level component ready for the release of CEED v1.0 in the next quarter, see CEED-MS13. In this report we also provide a highlight from CEED’s integration with the MARBL app and the corresponding Laghos miniapp. A main theme in this work has been the systematic transition of advanced algorithms, developed and tested in Laghos, to the large-scale multi-physics settings of the MARBL code. The low-level CEED API provides a set of FE kernels and components for writing new low-level kernels. Examples include: vector and sparse linear algebra, element matrix assembly over a batch of elements, partial assembly and action for efficient high-order operators like mass, diffusion, advection, etc. The main goal of the low-level API is to establish the basis for the high-level API. Also, identifying such low-level kernels and providing a reference implementation for them serves as the basis for collaboration with vendors and STs. Another goal for the low-level API is to make it easy for applications with their own discretization infrastructure, who do not want to switch directly to using the high-level CEED API, to still evaluate and use the core operations provided by the low-level API. One of the challenges with high-order methods is that a global sparse matrix is no longer a good representation of a high-order linear operator, both with respect to the FLOPs needed for its evaluation, as well as the memory transfer needed for a matvec. Thus, another important question we tried to address while developing the low-level API is: is it possible to abstract out in a natural and efficient way the different implementations and data structures that arise when dealing with various computational device types: CPUs, GPUs, etc. Fully answering this question is beyond the scope of this particular milestone, since that requires longer time as we develop and expand the devices we support. The future high-level API will be the frontend provided by CEED consisting of high-level abstractions such as meshes, finite element spaces and solutions, bilinear forms, solvers, etc. At this high-level, an important aspect of the API will be to provide a uniform abstraction layer for writing code in a portable manner. To achieve that, we plan to utilize the MPI programming model combined with a device abstraction layer (DAL) for finite element computations that we will develop. The DAL will serve as the bridge between the low- and the high-level APIs, allowing a variety of programming models to be used for the low-level kernel implementations. The software artifacts delivered as part of this milestone include an initial CEED API software implementation (libCEED) provided through the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q1 of FY18, including: the Nek5000 v17.0 MFEM v3.3.2 and PETSc v3.8 releases, collaborations with ECP/ST and SciDAC projects, the inaugural Nek5000 hackathon and various outreach activities.

97 MATHEMATICS AND COMPUTING↗

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗

Applications of remote sensing to stream discharge predictions

A feasibility study has been initiated on the use of remote earth observations for augmenting stream discharge prediction for the design and/or operation of major reservoir systems, pumping systems and irrigation systems. The near-term objectives are the interpolation of sparsely instrumented precipitation surveillance networks and the direct measurement of water loss by evaporation. The first steps of the study covered a survey of existing reservoir systems, stream discharge prediction methods, gage networks and the development of a self-adaptive variation of the Kentucky Watershed model, SNOPSET, that includes snowmelt. As a result of these studies, a special three channel scanner is being built for a small aircraft, which should provide snow, temperature and water vapor maps for the spatial and temporal interpolation of stream gages.

Krause, F. R.↗

Methodology for Sensitivity Analysis, Approximate Analysis, and Design Optimization in CFD for Multidisciplinary Applications

An incremental iterative formulation together with the well-known spatially split approximate-factorization algorithm, is presented for solving the large, sparse systems of linear equations that are associated with aerodynamic sensitivity analysis. This formulation is also known as the 'delta' or 'correction' form. For the smaller two dimensional problems, a direct method can be applied to solve these linear equations in either the standard or the incremental form, in which case the two are equivalent. However, iterative methods are needed for larger two-dimensional and three dimensional applications because direct methods require more computer memory than is currently available. Iterative methods for solving these equations in the standard form are generally unsatisfactory due to an ill-conditioned coefficient matrix; this problem is overcome when these equations are cast in the incremental form. The methodology is successfully implemented and tested using an upwind cell-centered finite-volume formulation applied in two dimensions to the thin-layer Navier-Stokes equations for external flow over an airfoil. In three dimensions this methodology is demonstrated with a marching-solution algorithm for the Euler equations to calculate supersonic flow over the High-Speed Civil Transport configuration (HSCT 24E). The sensitivity derivatives obtained with the incremental iterative method from a marching Euler code are used in a design-improvement study of the HSCT configuration that involves thickness. camber, and planform design variables.

Taylor, Arthur C., III↗

Improved Oxygen-Beam Texturing of Glucose-Monitoring Optics

An improved method has been devised for using directed, hyperthermal beams of oxygen atoms and ions to impart desired textures to the tips of polymethylmethacrylate [PMMA] optical fibers to be used in monitoring the glucose content of blood. The improved method incorporates, but goes beyond, the method described in Texturing Blood-Glucose- Monitoring Optics Using Oxygen Beams (LEW-17642-1), NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 11a. The basic principle of operation of such a glucose-monitoring sensor is as follows: The textured surface of the optical fiber is coated with chemicals that interact with glucose in such a manner as to change the reflectance of the surface. Light is sent down the optical fiber and is reflected from, the textured surface. The resulting change in reflectance of the light is measured as an indication of the concentration of glucose. The required texture on the ends of the optical fibers is a landscape of microscopic cones or pillars having high aspect ratios (microscopic structures being taller than they are wide). The average distance between hills must be no more than about 5 mso that blood cells (which are wider) cannot enter the valleys between the hills, where they would interfere with optical sensing of glucose in the blood plasma. On the other hand, the plasma is required to enter the valleys, and high aspect ratio structures are needed to maximize the surface area in contact with the plasma, thereby making it possible to obtain a given level of optical glucose-measurement sensitivity with a relatively small volume of blood. There is an additional requirement that the hills be wide enough that a sufficient amount of light can propagate into them and, after reflection, can propagate out of them. The method described in the cited prior article produces a texture comprising cones and pillars that conform to the average-distance and aspect-ratio requirements. However, a significant fraction of the cones and pillars are so narrow that not enough light can propagate along them. The improved method makes it possible to form wider cones and pillars while still satisfying the average-distance and aspect-ratio requirements. In the improved method, as in the previously reported method, multiple optical fibers are first bundled together for simultaneous texturing of their distal tips. However, prior to texturing by exposure to an oxygen beam, the tips are first coated by vapor deposition of a thin, sparse layer of aluminum: The exposure to the aluminum vapor must be short enough (typically of the order of seconds) so that the aluminum nucleates into islands separated by uncoated areas. The coated tips are textured by exposure to a directed beam of hyperthermal (kinetic energy >1 eV) oxygen atoms and/or ions in a vacuum chamber, as in the previously reported method. The aluminum islands partially shield the underlying PMMA from oxidation and erosion by the beam, so that the cones or pillars remaining after texturing are wider than they would otherwise be. To some extent, the dimensions of the hills and the distances between them can be tailored through choice of the thickness of the aluminum coat and/or the oxygen-beam fluence. The figure illustrates an example of texturing of the tip of a PMMA optical fiber without and with prior aluminum coating.

Banks, Bruce A.↗

Combining Tensor Decompositions and Graph Analytics to Provide Cyber Situational Awareness at HPC Scale

This paper describes MADHAT (Multidimensional Anomaly Detection fusing HPC, Analytics, and Tensors), an integrated workflow that demonstrates the applicability of HPC resources to the problem of maintaining cyber situational awareness. MADHAT combines two high-performance packages: ENSIGN for large-scale sparse tensor decompositions and HAGGLE for graph analytics. Tensor decompositions isolate coherent patterns of network behavior in ways that common clustering methods based on distance metrics cannot. Parallelized graph analysis then uses directed queries on a representation that combines the elements of identified patterns with other available information (such as additional log fields, domain knowledge, network topology, whitelists and blacklists, prior feedback, and published alerts) to confirm or reject a threat hypothesis, collect context, and raise alerts. MADHAT was developed using the collaborative HPC Architecture for Cyber Situational Awareness (HACSAW) research environment and evaluated on structured network sensor logs collected from Defense Research and Engineering Network (DREN) sites using HPC resources at the U.S. Army Engineer Research and Development Center DoD Supercomputing Resource Center (ERDC DSRC). To date, MADHAT has analyzed logs with over 650 million entries.

Cyber security, Tensor decomposition, graph analyt↗

Indigo: A Domain-Specific Language for Fast, Portable Image Reconstruction

© 2018 IEEE. Linear operators used in iterative methods like conjugate gradient have typically been implemented either as ''matrix-driven'' subroutines backed by explicit sparse or dense matrices, or as ''matrix-free'' subroutines that implement specific linear operations directly (e.g. FFTs). The matrix-driven approach is generally more portable because it can target widely-Available BLAS libraries, but it can be inefficient in terms of time and space complexity. In contrast, the matrix-free approach is more performant because it leverages structure in operations, but it requires each operator be re-implemented on each new platform. To increase performance and portability, we propose a hybrid approach that represents linear operators as expression trees. Leaf nodes in the tree are either matrix-free or matrix-driven operators, and interior nodes represent mathematical compositions (sums, products, transposes) or structural compositions (stacks, block diagonals, etc.) of the leaf operators. This representation enables expert-guided reordering and fusion transformations that can improve performance or reduce memory pressure. We implement our approach in a domain-specific language called Indigo. We assess Indigo on image reconstruction problems arising in four application areas: magnetic resonance imaging, ptychography, magnetic particle imaging, and fluorescent microscopy. We give performance results from vendor BLAS libraries, and we introduce specializations to Sparse BLAS routines that achieve near-Roofline performance on multi-core, many-core, and GPU systems.

Driscoll, Michael↗

Discrete range clustering using Monte Carlo methods

For automatic obstacle avoidance guidance during rotorcraft low altitude flight, a reliable model of the nearby environment is needed. Such a model may be constructed by applying surface fitting techniques to the dense range map obtained by active sensing using radars. However, for covertness, passive sensing techniques using electro-optic sensors are desirable. As opposed to the dense range map obtained via active sensing, passive sensing algorithms produce reliable range at sparse locations, and therefore, surface fitting techniques to fill the gaps in the range measurement are not directly applicable. Both for automatic guidance and as a display for aiding the pilot, these discrete ranges need to be grouped into sets which correspond to objects in the nearby environment. The focus of this paper is on using Monte Carlo methods for clustering range points into meaningful groups. One of the aims of the paper is to explore whether simulated annealing methods offer significant advantage over the basic Monte Carlo method for this class of problems. We compare three different approaches and present application results of these algorithms to a laboratory image sequence and a helicopter flight sequence.

Chatterji, G. B.↗

Preconditioned domain decomposition scheme for three-dimensional aerodynamic sensitivity analysis

A discrete sensitivity analysis algorithm had previously been developed and applied to two-dimensional aerodynamic optimization problems, where the computational domains were discretized by using single grids. The sparse, unsymmetric systems of linear equations resulting from this algorithm were solved by a direct matrix inversion matrix. However, for large two-dimensional problems and, practically, all three-dimensional problems, direct inversion methods become inapplicable, primarily due to the prohibitive computer storage needed. In an attempt to alleviate such hindrances, the sensitivity analysis with domain decomposition (SADD) scheme was developed. This scheme divides the computational domain into smaller and nonoverlapping subdomains (multiblock grids) that are solved separately. Then, the final solution is constructed from the subdomain solutions. As the number of grid points in the interface boundaries of the subdomains becomes large, the computer memory required to store the effective coefficient matrix of these interface points starts to increase. Presented in this Technical Note is a preconditioned iterative procedure to overcome this particular problem.

Eleshaky, Mohamed E.↗

A graphics processing unit accelerated sparse direct solver and preconditioner with block low rank compression

We present the GPU implementation efforts and challenges of the sparse solver package STRUMPACK. The code is made publicly available on github with a permissive BSD license. STRUMPACK implements an approximate multifrontal solver, a sparse LU factorization which makes use of compression methods to accelerate time to solution and reduce memory usage. Multiple compression schemes based on rank-structured and hierarchical matrix approximations are supported, including hierarchically semi-separable, hierarchically off-diagonal butterfly, and block low rank. Here, in this paper, we present the GPU implementation of the block low rank (BLR) compression method within a multifrontal solver. Our GPU implementation relies on highly optimized vendor libraries such as cuBLAS and cuSOLVER for NVIDIA GPUs, rocBLAS and rocSOLVER for AMD GPUs and the Intel oneAPI Math Kernel Library (oneMKL) for Intel GPUs. Additionally, we rely on external open source libraries such as SLATE (Software for Linear Algebra Targeting Exascale), MAGMA (Matrix Algebra on GPU and Multi-core Architectures), and KBLAS (KAUST BLAS). SLATE is used as a GPU-capable ScaLAPACK replacement. From MAGMA we use variable sized batched dense linear algebra operations such as GEMM, TRSM and LU with partial pivoting. KBLAS provides efficient (batched) low rank matrix compression for NVIDIA GPUs using an adaptive randomized sampling scheme. The resulting sparse solver and preconditioner runs on NVIDIA, AMD and Intel GPUs. Interfaces are available from PETSc, Trilinos and MFEM, or the solver can be used directly in user code. We report results for a range of benchmark applications, using the Perlmutter system from NERSC, Frontier from ORNL, and Aurora from ALCF. For a high frequency wave equation on a regular mesh, using 32 Perlmutter compute nodes, the factorization phase of the exact GPU solver is about 6.5× faster compared to the CPU-only solver. The BLR-enabled GPU solver is about 13.8× faster than the CPU exact solver. For a collection of SuiteSparse matrices, the STRUMPACK exact factorization on a single GPU is on average 1.9× faster than NVIDIA’s cuDSS solver.

97 MATHEMATICS AND COMPUTING↗

Gamma-Ray Point-Source Localization and Sparse Image Reconstruction using Poisson Likelihood

Gamma-ray imaging trys to reconstruct the spatial and intensity distribution of gamma-emitting radionuclides from a set of measurements. Wholly, this problem is solved by discretizing the spatial dimensions and employing the maximum likelihood expectation maximization (ML-EM) algorithm, with or without some form of regularization. While the generality of this formulation enables use in a wide variety of scenarios, it is susceptible to overfitting, limited by the discretization of spatial coordinates, and can be computationally expensive. We present a novel approach to 3D gamma-ray image reconstruction for scenarios where sparsity may be assumed, for example radiological source search. In this work we first formulate a point-source localization (PSL) approach as an optimization problem where both position and source intensity are continuous variables. We then extend and generalize this formulation to an iterative algorithm called additive point-source localization (APSL) for sparse parametric image reconstruction. A set of simulated source search scenarios using a single non-directional detector are considered, finding improved image accuracy and computational efficiency with APSL over traditional grid-based methods.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Control of multi-agent systems: Results, open problems, and applications

The purpose of this review article is to present some recent results on the modeling and control of large systems of agents. We focus on particular applications where the agents are capable of independent actions instead of simply reacting to external forces. In the literature, such agents were referred to as autonomous, intelligent, self-propelled, greedy, and others. The main applications we have in mind are social systems (as opinion dynamics), pedestrians’ movements (also called crowd dynamics), animal groups, and vehicular traffic. We note that the last three examples include physical constraints; however, the agents are able to inject energy into the system, thus preventing the typical conservation of momentum and energy. In addition, the control problems posed by such systems are new and require innovative methods. We illustrate some ideas developed recently, including the use of sparse controls, limiting the total variation of controls, and defining new control problems for measures. After reviewing various approaches, we discuss some future research directions of potential interest. The latter encompasses both new types of equations and new types of limiting procedures to connect several scales at which a system can be represented. We conclude by illustrating a recent real-life experiment using autonomous vehicles on an open highway to smooth traffic waves. This opens the door to a new era of interventions to control real-time multi-agent systems and to increase the societal impact of such interventions guided by control research.

97 MATHEMATICS AND COMPUTING↗

Source scaling comparison and validation in Central Italy: data intensive direct S waves versus the sparse data coda envelope methodology

SUMMARY Robustness of source parameter estimates is a fundamental issue in understanding the relationships between small and large events; however, it is difficult to assess how much of the variability of the source parameters can be attributed to the physical source characteristics or to the uncertainties of the methods and data used to estimate the values. In this study, we apply the coda method by Mayeda et al. using the coda calibration tool (CCT), a freely available Java-based code (https://github.com/LLNL/coda-calibration-tool) to obtain a regional calibration for Central Italy for estimating stable source parameters. We demonstrate the power of the coda technique in this region and show that it provides the same robustness in source parameter estimation as a data-driven methodology [generalized inversion technique (GIT)], but with much fewer calibration events and stations. The Central Italy region is ideal for both GIT and coda approaches as it is characterized by high-quality data, including recent well-recorded seismic sequences such as L'Aquila (2009) and Amatrice–Norcia–Visso (2016–2017). This allows us to apply data-driven methods such as GIT and coda-based methods that require few, but high-quality data. The data set for GIT analysis includes ∼5000 earthquakes and more than 600 stations, while for coda analysis we used a small subset of 39 events spanning 3.5 < Mw < 6.33 and 14 well-distributed broad-band stations. For the common calibration events, as well as an additional 247 events (∼1.7 < Mw < ∼5.0) not used in either calibration, we find excellent agreement between GIT-derived and CCT-derived source spectra. This confirms the ability of the coda approach to obtain stable source parameters even with few calibration events and stations. Even reducing the coda calibration data set by 75 per cent, we found no appreciable degradation in performance. This validation of the coda calibration approach over a broad range of event size demonstrates that this procedure, once extended to other regions, represents a powerful tool for future routine applications to homogeneously evaluate robust source parameters on a national scale. Furthermore, the coda calibration procedure can homogenize the Mw estimates for small and large events without the necessity of introducing any conversion scale between narrow-band measures such as local magnitude (ML) and Mw, which has been shown to introduce significant bias.

Morasca, Paola (ORCID:0000000265254867)↗