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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Accelerating Multivariate Functional Approximation Computation with Domain Decomposition Techniques⋆

Modeling large datasets through Multivariate Functional Approximations (MFA) provide an elegant way to handle many visualization and scientific analysis workflows. The process necessitates scalable data partitioning methods to compute MFA representations efficiently without compromising the accuracy or continuity of the reconstructed solution. We propose a domain -decomposed method for computing the MFA with B -spline bases, which reduces the total work per task and uses a restricted Additive Schwarz (RAS) method to converge the control point data degrees -of -freedom along subdomain boundaries. We provide an in-depth analysis of the parallel approach with domain decomposition solvers, aiming to minimize local subdomain error residuals and recover high -order continuity at subdomain interfaces with appropriate choices of knot overlaps. The communication cost, determined by the overlap regions in the RAS implementation, is optimized to recover the numerical error profile of the single subdomain case. Our proposed method stands in contrast to previous methods, which typically only recover either C 0 or at best C 1 continuity for arbitrary B -spline degree expansions, or those that require post -processing to blend discontinuities in the reconstructed data. We demonstrate the effectiveness of our approach using analytical and real -world datasets in 1D, 2D, and 3D through both strong and weak scaling studies. The performance results indicate that the overall cost of computing the approximation is directly proportional to the underlying nearest -neighbor communication implementation, and is only weakly dependent on the overlap region size that determines the size of the messages. This finding underscores the efficiency and scalability of our proposed method, making it a promising solution for handling large datasets in scientific workflows.

additive Schwarz solvers↗
DOE OSTI2022

A Framework for Error-Bounded Approximate Computing, with an Application to Dot Products

Approximate computing techniques, which trade off the computation accuracy of an algorithm for better performance and energy efficiency, have been successful in reducing computation and power costs in several domains. However, error sensitive applications in high-performance computing are unable to benefit from existing approximate computing strategies that are not developed with guaranteed error bounds. While approximate computing techniques can be developed for individual high-performance computing applications by domain specialists, this often requires additional theoretical analysis and potentially extensive software modification. Hence, the development of low-level error-bounded approximate computing strategies that can be introduced into any high-performance computing application without requiring additional analysis or significant software alterations is desirable. In this paper, we provide a contribution in this direction by proposing a general framework for designing error-bounded approximate computing strategies and apply it to the dot product kernel to develop \bf qdot---an error-bounded approximate dot product kernel. Following the introduction of qdot, here we perform a theoretical analysis that yields a deterministic bound on the relative approximation error introduced by qdot. Empirical tests are performed to illustrate the tightness of the derived error bound and to demonstrate the effectiveness of qdot on a synthetic dataset, as well as two scientific benchmarks---the conjugate gradient (CG) and power methods. In some instances, using qdot for the dot products in CG can result in many components being quantized to half precision without increasing the iteration count required for convergence to the same solution as CG using a double precision dot product.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

High Performance Approximate Computing

This code repository contains the implementation of the "High-Performance Approximate Computing" (HPAC) toolkit. The toolkit allows you to approximate your own C/C++. The developer uses "pragma's" to annotate code regions as approximate. The compiler extensions lower these pragmas to either compiletime approximate techniques or runtime approximation techniques. At execution time, the implemented runtime system decides which annotated regions it should approximate. HPAC also provides a set of script utilities. The utilities perform a grid search within approximation parameters and performance. The user can analyze the raw data to identify optimal approximation techniques for the application.

Parasyris, Konstantinos↗
DOE OSTI2021

A weighted Shifted Boundary Method for free surface flow problems

The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods and was recently introduced for the Poisson, linear advection/diffusion, Stokes, Navier-Stokes, acoustics, and shallow-water equations. By reformulating the original boundary value problem over a surrogate (approximate) computational domain, the SBM avoids integration over cut cells and the associated problematic issues regarding numerical stability and matrix conditioning. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions. Hence the name of the method, that shifts the location and values of the boundary conditions. In this article, we extend the SBM to the simulation of incompressible Navier-Stokes flows with moving free-surfaces, by appropriately weighting its variational form with the elemental volume fraction of active fluid. This approach prevents spurious pressure oscillations in time, which would otherwise be produced if the total active fluid volume were to change abruptly over a time step. In fact, the proposed weighted SBM method induces small mass (i.e., volume) conservation errors, which converge quadratically in the case of piecewise-linear finite element interpolations, as the grid is refined. Finally, we present an extensive set of two- and three-dimensional tests to demonstrate the robustness and accuracy of the method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

A weighted shifted boundary method for immersed moving boundary simulations of Stokes' flow

The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods, and relies on reformulating the original boundary value problem over a surrogate (approximate) computational domain. The surrogate domain is constructed so as to avoid cut cells and the associated problematic implementation and numerical integration issues. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions: hence the name of the method, that shifts the location and values of the boundary conditions. Here, in this article, we extend the SBM to the simulation of incompressible Stokes flow, by appropriately weighting its variational form with the elemental volume fraction of active fluid. This approach allows to drastically reduce spurious pressure oscillations in time, which are produced if the total volume of active fluid were to change abruptly over a time step. The proposed Weighted SBM (W-SBM) exactly preserves states of hydrostatic equilibrium, and induces small mass and momentum conservation errors, which converge as the grid is refined. This is in analogy to cutFEMs and related unfitted approaches, which rely on an affine representation of cut boundaries. We demonstrate the robustness and accuracy of the proposed method with an extensive suite of two-dimensional tests.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Approximate Bayesian Computation applied to the Diffuse Gamma-Ray Sky

ABSTRACT Many sources contribute to the diffuse gamma-ray background (DGRB), including star forming galaxies, active galactic nuclei, and cosmic ray interactions in the Milky Way. Exotic sources, such as dark matter annihilation, may also make some contribution. The photon counts-in-pixels distribution is a powerful tool for analysing the DGRB and determining the relative contributions of different sources. However, including photon energy information in a likelihood analysis of the counts-in-pixels distribution quickly becomes computationally intractable as the number of source types and energy bins increase. Here, we apply the likelihood-free method of approximate Bayesian computation (ABC) to the problem. We consider a mock analysis that includes contributions from dark matter annihilation in Galactic subhaloes as well as astrophysical backgrounds. We show that our results using ABC are consistent with the exact likelihood when energy information is discarded, and that significantly tighter parameter constraints can be obtained with ABC when energy information is included. ABC presents a powerful tool for analysing the DGRB and understanding its varied origins.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Microsimulation model calibration using incremental mixture approximate Bayesian computation

Microsimulation models (MSMs) are used to inform policy by predicting population-level outcomes under different scenarios. MSMs simulate individual-level event histories that mark the disease process (such as the development of cancer) and the effect of policy actions (such as screening) on these events. MSMs often have many unknown parameters; calibration is the process of searching the parameter space to select parameters that result in accurate MSM prediction of a wide range of targets. We develop Incremental Mixture Approximate Bayesian Computation (IMABC) for MSM calibration which results in a simulated sample from the posterior distribution of model parameters given calibration targets. IMABC begins with a rejection-based ABC step, drawing a sample of points from the prior distribution of model parameters and accepting points that result in simulated targets that are near observed targets. Next, the sample is iteratively updated by drawing additional points from a mixture of multivariate normal distributions and accepting points that result in accurate predictions. Posterior estimates are obtained by weighting the final set of accepted points to account for the adaptive sampling scheme. We demonstrate IMABC by calibrating CRC-SPIN 2.0, an updated version of a MSM for colorectal cancer (CRC) that has been used to inform national CRC screening guidelines.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Application of the Approximate Bayesian Computation Algorithm to Gamma-Ray Spectroscopy

Radioisotope identification (RIID) algorithms for gamma-ray spectroscopy aim to infer what isotopes are present and in what amounts in test items. RIID algorithms either use all energy channels in the analysis region or only energy channels in and near identified peaks. Because many RIID algorithms rely on locating peaks and estimating each peak’s net area, peak location and peak area estimation algorithms continue to be developed for gamma-ray spectroscopy. This paper shows that approximate Bayesian computation (ABC) can be effective for peak location and area estimation. Algorithms to locate peaks can be applied to raw or smoothed data, and among several smoothing options, the iterative bias reduction algorithm (IBR) is recommended; the use of IBR with ABC is shown to potentially reduce uncertainty in peak location estimation. Extracted peak locations and areas can then be used as summary statistics in a new ABC-based RIID. ABC allows for easy experimentation with candidate summary statistics such as goodness-of-fit scores and peak areas that are extracted from relatively high dimensional gamma spectra with photopeaks (1024 or more energy channels) consisting of count rates versus energy for a large number of gamma energies.

Burr, Tom↗
DOE OSTI2021

Calibration of the Diffusivity Predictions of Centipede Using Approximate Bayesian Computation and Applications in Nyx (Engineering Scale) and Xolotl-MARMOT (Meso-Scale) Simulations

Fission gas evolution and release in UO 2 nuclear fuel are important fuel performance metrics and occur in several distinct stages: 1) nucleation, growth and resolution of intra-granular bubbles, 2) diffusion to grain boundaries and 3) nucleation and growth of bubbles at grain boundaries, which eventually form a connected network (percolation) enabling release of gas from grain boundaries through connections to triple junctions, grain edges or free surfaces. The NE-SciDAC project is developing several computational tools to model this problem, which are connected in a hierarchical multi-scale framework. The information transfer in the multi-scale framework is a critical step that, in addition to best-estimates, should include uncertainty quantification. Despite taking a first-principles multi-scale approach, there is a need to perform parameter calibration to ensure consistency with available experimental data. In the present study, uncertainty quantification (UQ) and parameter calibration is demonstrated for one of the lower length scale codes in the multi-scale framework (Centipede) and then the results, including instances of the propagated uncertainties, are used in other codes within the framework, specifically Nyx and Xolotl-MARMOT. We calibrated the model parameters in Centipede, a computer code used to predict diffusivities of uranium (U) and xenon (Xe) in the context of the simulation of fission gas in uranium oxide (UO 2 ) nuclear fuel. The Centipede code depends on 183 parameters, all of which are subject to uncertainty. The three data sets used in our calibration effort are taken from the literature. This data is available as a set of measurements, including measurement errors. Our goal is to calibrate a statistical model that predicts both the value of the measurement and the uncertainty associated with the measurement. We perform a Bayesian calibration of the model parameters using a dedicated approximate Bayesian computation (ABC) likelihood function. To avoid excessive computational costs, we replace the expensive Centipede simulation code by a higher-order surrogate model, constructed using only the 9 most important parameters. These important parameters are identified by a preliminary global sensitivity analysis (GSA) study. Among the important parameters are T0 (the temperature at which UO 2 is perfectly stoichiometric) and Hf_pO2 (the temperature dependence of the oxygen (O) partial pressure) that should be considered as operating conditions to be estimated along with the other parameters. We consider two different cases: one where we define one set of these operating conditions for all data sets, and one where we define distinct operating condition parameters for each data set. The Xe diffusivities predicted by the latter case show distinct features that could not be observed in the former. Next, we use the diffusivity predictions by Centipede as input to Nyx, a reduced order fuel performance code focused on gas behavior alone, in order to estimate quantities associated with inter-granular bubble formation at conditions specified by the experiments. Finally, the diffusivities obtained from the calibrated Centipede runs were used in coupled Xolotl-MARMOT simulations of intra- and inter-granular gas evolution. The results are compared to simulations using the baseline diffusivities from Turnbull et al.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

NISQ+: Boosting quantum computing power by approximating quantum error correction

Quantum computers are growing in size, and design decisions are being made now that attempt to squeeze more computation out of these machines. In this spirit, we design a method to boost the computational power of near-term quantum computers by adapting protocols used in quantum error correction to implement "Approximate Quantum Error Correction (AQEC)." By approximating fully-fledged error correction mechanisms, we can increase the compute volume (qubits × gates, or "Simple Quantum Volume (SQV)") of near-term machines. The crux of our design is a fast hardware decoder that can approximately decode detected error syndromes rapidly. Specifically, we demonstrate a proof-of-concept that approximate error decoding can be accomplished online in near-term quantum systems by designing and implementing a novel algorithm in Single-Flux Quantum (SFQ) superconducting logic technology. This avoids a critical decoding backlog, hidden in all offline decoding schemes, that leads to idle time exponential in the number of T gates in a program. Our design utilizes one SFQ processing module per physical qubit. Employing state-of-the-art SFQ synthesis tools, we show that the circuit area, power, and latency are within the constraints of contemporary quantum system designs. Under pure dephasing error models, the proposed accelerator and AQEC solution is able to expand SQV by factors between 3,402 and 11,163 on expected near-term machines. The decoder achieves a 5% accuracy-threshold and pseudo-thresholds of ~ 5%,4.75%,4.5%, and 3.5% physical error-rates for code distances 3,5,7, and 9. Decoding solutions are achieved in a maximum of ~20 nanoseconds on the largest code distances studied. By avoiding the exponential idle time in offline decoders, we achieve a 10x reduction in required code distances to achieve the same logical performance as alternative designs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

APPRENTICE

SF-19-096 In this software, there are multiple approaches to compute approximations to multivariate functions. This includes: (a) an approach that builds on Stieltjes process to efficiently compute the coefficients of the rational approximation, (b) an approach that is based on an optimization formulation to get pole-free coefficients of the rational approximation and (c) approaches that finds the coefficients of rational and polynomial approximations by finding the linear least-squares solution using singular value decomposition.

KRISNAMOORTHY, MOHAN↗
DOE OSTI2020

The second-generation Shifted Boundary Method and its numerical analysis

Recently, the Shifted Boundary Method (SBM) was proposed within the class of unfitted (or immersed, or embedded) finite element methods. By reformulating the original boundary value problem over a surrogate (approximate) computational domain, the SBM avoids integration over cut cells and the associated problematic issues regarding numerical stability and matrix conditioning. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions. Hence the name of the method, that shifts the location and values of the boundary conditions. In this article, we present enhanced variational SBM formulations for the Poisson and Stokes problems with improved flexibility and robustness. These simplified variational forms allow to relax some of the assumptions required by the mathematical proofs of stability and convergence of earlier implementations. First, we show that these new SBM implementations can be proved asymptotically stable and convergent even without the rather restrictive assumption that the inner product between the normals to the true and surrogate boundaries is positive. Second, we show that it is not necessary to introduce a stabilization term involving the tangential derivatives of the solution at Dirichlet boundaries, therefore avoiding the calibration of an additional stabilization parameter. Finally, we prove enhanced L 2 -estimates without the cumbersome assumption – of earlier proofs – that the surrogate domain is convex. Instead we rely on a conventional assumption that the boundary of the true domain is smooth, which can also be replaced by requiring convexity of the true domain. The aforementioned improvements open the way to a more general and efficient implementation of the Shifted Boundary Method, particularly in complex three-dimensional geometries. We complement these theoretical developments with numerical experiments in two and three dimensions.

42 ENGINEERING↗
DOE OSTI2021

Randomized Sketching Algorithms for Low-Memory Dynamic Optimization

This paper develops a novel limited-memory method to solve dynamic optimization problems. The memory requirements for such problems often present a major obstacle, particularly for problems with PDE constraints such as optimal flow control, full waveform inversion, and optical tomography. In these problems, PDE constraints uniquely determine the state of a physical system for a given control; the goal is to find the value of the control that minimizes an objective. While the control is often low dimensional, the state is typically more expensive to store. This paper suggests using randomized matrix approximation to compress the state as it is generated and shows how to use the compressed state to reliably solve the original dynamic optimization problem. Concretely, the compressed state is used to compute approximate gradients and to apply the Hessian to vectors. The approximation error in these quantities is controlled by the target rank of the sketch. This approximate first- and second-order information can readily be used in any optimization algorithm. As an example, we develop a sketched trust-region method that adaptively chooses the target rank using a posteriori error information and provably converges to a stationary point of the original problem. Numerical experiments with the sketched trust-region method show promising performance on challenging problems such as the optimal control of an advection-reaction-diffusion equation and the optimal control of fluid flow past a cylinder.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise tens of billions of compounds due to advances in combinatorial chemistry. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have the major drawback that they require exceptional computing capabilities for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently-proposed learning paradigm that represents data with high-dimension binary vectors; this allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encodings of a commonly-used molecular representation, the extended connectivity fingerprint (ECFP). We show that HDC-based inference methods are as much as 91 times more efficient than traditional machine learning methods, and achieve an acceleration of nearly nine orders of magnitude compared to molecular docking. Our results show that HDC accelerated methods retain competitive accuracy on a number of well-studied tasks such as molecular property predictions using the MoleculeNet dataset, and bind/no-bind activity classification using the DUD-E and LIT-PCBA datasets. Our work thus motivates further investigation into molecular representation learning to develop ultraefficient pre-screening tools.

Jones, William↗
DOE OSTI2024

HDBind: encoding of molecular structure with hyperdimensional binary representations

Traditional methods for identifying “hit” molecules from a large collection of potential drug-like candidates rely on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have a significant limitation in that they require exceptional computing capabilities for even relatively small collections of molecules. Increasingly large and complex state-of-the-art deep learning approaches have gained popularity with the promise to improve the productivity of drug design, notorious for its numerous failures. However, as deep learning models increase in their size and complexity, their acceleration at the hardware level becomes more challenging. Hyperdimensional Computing (HDC) has recently gained attention in the computer hardware community due to its algorithmic simplicity relative to deep learning approaches. The HDC learning paradigm, which represents data with high-dimension binary vectors, allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas (computer vision, bioinformatics, mass spectrometery, remote sensing, edge devices, etc.). To the best of our knowledge, our work is the first to consider HDC for the task of fast and efficient screening of modern drug-like compound libraries. We also propose the first HDC graph-based encoding methods for molecular data, demonstrating consistent and substantial improvement over previous work. We compare our approaches to alternative approaches on the well-studied MoleculeNet dataset and the recently proposed LIT-PCBA dataset derived from high quality PubChem assays. We demonstrate our methods on multiple target hardware platforms, including Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs), showing at least an order of magnitude improvement in energy efficiency versus even our smallest neural network baseline model with a single hidden layer. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools. We make our code publicly available at https://github.com/LLNL/hdbind.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Scalable implementation of polynomial filtering for density functional theory calculation in PARSEC

In this work, we present an efficient implementation of polynomial filtering methods in PARSEC, a real-space pseudopotential based Kohn–Sham density functional theory solver. The implementation described here improves upon a Chebyshev-filtered subspace iteration algorithm used in the previous version of PARSEC. We present a hybrid polynomial filtering scheme that combines Chebyshev-filtered subspace iteration and a spectrum slicing method that partitions the spectrum into several spectral slices and uses bandpass-filtered subspace iteration to compute approximate eigenpairs within each interior slice simultaneously. We describe a procedure to partition a spectrum and construct polynomial filters. We also discuss a number of practical issues such as the use of appropriate data layouts for carrying out the computation on a two-dimensional process grid and how to achieve good load balance by allocating an appropriate number of process groups to each spectral slice. Numerical examples are presented to demonstrate the effectiveness of the hybrid polynomial filtering method as well as the superior parallel scalability of spectrum slicing in comparison to that of Chebyshev-filtered subspace iteration.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Estimates of Quantum Tunneling Effects for Hydrogen Diffusion in PuO 2

We detail the estimation of activation energies and quantum nuclear vibrational tunneling effects for hydrogen diffusion in PuO 2 based on Density Functional Theory calculations and a quantum double well approximation. We find that results are relatively insensitive to choice of exchange correlation functional. In addition, the representation of spin in the system and use of an extended Hubbard U correction has only a small effect on hydrogen point defect formation energies when the PuO 2 lattice is held fixed at the experimental density. We then compute approximate activation energies for transitions between hydrogen interstitial sites seeded by a semi-empirical quantum model and determine the quantum tunneling enhancement relative to classical kinetic rates. Our model indicates that diffusion rates in H/PuO 2 systems could be enhanced by more than one order of magnitude at ambient conditions and that these effects persist at high temperature. The method we propose here can be used as a fast screening tool for assessing possible quantum nuclear vibrational effects in any number of condensed phase materials and surfaces, where hydrogen hopping tends to follow well defined minimum energy pathways.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗