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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Replicated Computational Results (RCR) Report for “Adaptive Precision Block-Jacobi for High Performance Preconditioning in the Ginkgo Linear Algebra Software”

The article by Flegar et al. titled “Adaptive Precision Block-Jacobi for High Performance Preconditioning in the Ginkgo Linear Algebra Software” presents a novel, practical implementation of an adaptive precision block-Jacobi preconditioner. Performance results using state-of-the-art GPU architectures for the block-Jacobi preconditioner generation and application demonstrate the practical usability of the method, compared to a traditional full-precision block-Jacobi preconditioner. A production-ready implementation is provided in the Ginkgo numerical linear algebra library. In this report, the Ginkgo library is reinstalled and performance results are generated to perform a comparison to the original results when using Ginkgo’s Conjugate Gradient solver with either the full or the adaptive precision block-Jacobi preconditioner for a suite of test problems on an NVIDIA GPU accelerator. After completing this process, the published results are deemed reproducible.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Parametric dependencies of resonant layer responses across linear, two-fluid, drift-MHD regimes

Non-axisymmetric magnetic fields arising in a tokamak either by external or internal perturbations can induce complex non-ideal MHD responses in their resonant surfaces while remaining ideally evolved elsewhere. This layer response can be characterized in a linear regime by a single parameter called the inner-layer Delta, which enables outer-layer matching and the prediction of torque balance to non-linear island regimes. Here, we follow strictly one of the most comprehensive analytic treatments including two-fluid and drift MHD effects and keep the fidelity of the formulation by incorporating the numerical method based on the Riccati transformation when quantifying the inner-layer Delta. The proposed scheme reproduces not only the predicted responses in essentially all asymptotic regimes but also with continuous transitions as well as improved accuracies. In particular, the Delta variations across the inertial regimes with viscous or semi-collisional effects have been further resolved, in comparison with additional analytic solutions. The results imply greater shielding of the electromagnetic torque at the layer than what would be expected by earlier work when the viscous or semi-collisional effects can compete against the inertial effects, and also due to the intermediate regulation by kinetic Alfven wave resonances as rotation slows down. These are important features that can alter the nonaxisymmetric plasma responses including the field penetration by external fields or island seeding process in rotating tokamak plasmas.

MHD instability↗
DOE OSTI2018

Small Non-Linear Solver

SNLS (small non-linear solver) is a C++ library for solving non-linear systems. The emphasis is on small systems on equations for which direct factorization of the Jacobian is appropriate. The systems of equations may be numerically ill-conditioned. Implementation is amenable to GPU usage, with the idea that class instantiate would occur within device functions.

Wayne, BrettM.↗
DOE OSTI2019

HALA: Handy Accelerated Linear Algebra

Accelerated linear algebra libraries often come with C-style of interfaces or even older Fortran77 standards, which makes it difficult to use within generic template programming environment of modern C++. For example, the BLAS and derived standards such as cuBLAS do not accept overloads and a different functions have to be called for each input type, thus it is very challenging to write a single template that handles multiple precision modes and works well with different C++ containers. HALA offers a series of templates that wrap around the BLAS/cuBLAS and other similar methods, automatically infer the relevant types and call the appropriate back-end. The templates work out-of-the-box with all C++ standard vector-like containers and can be easily extended (with template specializations) to handle user-provided containers. The HALA API is also overloaded to handle both GPU and CPU cases with a single "engine" class, thus a single high-level algorithms can utilize both CPU or GPU backends, i.e., the HALA API is unified and handles the variations between cuBLAS and BLAS. In addition to BLAS and cuBLAS, wrapper templates are provided for subset of LAPACK, cuSparse, and Cholmod methods. Work is in progress to complete as many of these standards as possible. HALA also includes a module for low-level extended register vectorization for complex number arithmetic and several simple solvers that build on the basic linear algebra capabilities. A single unified C++ API will benefit fast prototyping and easily writing code that is portable across GPU/CPU platforms as well as precision types and user containers. Note that HALA does not provide any accelerated algorithms, it simply serves as a "handy" front-end to other standards.

Stoyanov, MiroslavK.↗
DOE OSTI2021

Linear Grains

LIGR (Linear Grains) implements a linear (Fourier mode) analysis of a shock propagating through density perturbations. It has two primary capabilities. First, it calculates the shock front distortion and post-shock flow variables (density, velocity, pressure) for single Fourier mode pairs in two dimensions (a pair of x and y modes). Second, it calculates these same quantities for a grains-like pre-shock density perturbation, which consists of a sum of many Fourier modes. This grains-like perturbation is a periodic grid of rectangles at a specifiable density and size (the grains), separated by regions of a different specifiable size and density (interstitial spaces between the grains). The single-mode analysis is based on the work of Velikovich et al., Phys. Plasmas 14 072706 (2007).

Li, GraceJ↗
DOE OSTI2025

Ipopt Interface to Re::Solve Linear Solver

The software provides Ipopt optimization package an interface to the Re::Solve linear solver library. Re::Solve features GPU-resident direct and iterative linear solvers that could be used to accelerate optimization computations.

Alam, Maksudul [Oak Ridge National Laboratory (ORN↗
DOE OSTI2024

LAPIS: Linear Algebra Performance for Intermediate Subprograms

SAND2025-11594O LAPIS (Linear Algebra Performance for Intermediate Subprograms) is a compiler infrastructure for linear algebra that targets both high productivity and performance portability. It is based on the open-source MLIR package from the LLVM project. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Kelley, Brian↗
DOE OSTI2025

Bayesian Linear Regression for Hugoniot Data

This repository provides the code and datasets used in the paper Bayesian Analysis of Linear Shock Compression Data. This paper analyzes publicly available shock compression datasets on copper, argon, and nickel from Marsh (1980) using Bayesian linear regression, and compares the results with those obtained using bootstrapping methods. References: - Marsh, S. P. (1980). LASL shock Hugoniot data (Vol. 5). Univ of California Press.

Bernstein, JasonA [Lawrence Livermore National Lab↗
DOE OSTI2019

Theoretical Understanding of the Linear Relationship between Convective Updrafts and Cloud-Base Height for Shallow Cumulus Clouds. Part I: Maritime Conditions

Zheng and Rosenfeld found linear relationships between the convective updrafts and cloud-base height z b using ground-based observations over both land and ocean. The empirical relationships allow for a novel satellite remote sensing technique of inferring the cloud-base updrafts and cloud condensation nuclei concentration, both of which are important for understanding aerosol–cloud–climate interactions but have been notoriously difficult to retrieve from space. In Part I of a two-part study, a theoretical framework is established for understanding this empirical relationship over the ocean. Part II deals with continental cumulus clouds. Using the bulk concept of mixed-layer (ML) model for shallow cumulus, I found that this relationship arises from the conservation law of energetics that requires the radiative flux divergence of an ML to balance surface buoyancy flux. Given a certain ML radiative cooling rate per unit mass Q, a deeper ML (higher z b ) undergoes more radiative cooling and requires stronger surface buoyancy flux to balance it, leading to stronger updrafts. The rate with which the updrafts vary with z b is modulated by Q. The cooling rate Q manifests strong resilience to external large-scale forcing that spans a wide range of climatology, allowing the slope of the updrafts– z b relationship to remain nearly invariant. This causes the relationship to manifest linearity. The physical mechanism underlying the resilience of Q to large-scale forcing, such as free-tropospheric moisture and sea surface temperature, is investigated through the lens of the radiative transfer theory (two-stream Schwarzschild equations) and an ML model for shallow cumulus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Theoretical Understanding of the Linear Relationship between Convective Updrafts and Cloud-Base Height for Shallow Cumulus Clouds. Part II: Continental Conditions

This is the Part II of a two-part study that seeks a theoretical understanding of an empirical relationship for shallow cumulus clouds: subcloud updraft velocity covaries linearly with the cloud-base height. This work focuses on continental cumulus clouds that are more strongly forced by surface fluxes and more deviated from equilibrium than those over oceans (Part I). We use a simple analytical model for shallow cumulus that is well tested against a high-resolution (25 m in the horizontal) large-eddy simulation model. Consistent with a conventional idea, we find that surface Bowen ratio is the key variable that regulates the covariability of both parameters: under the same solar insolation, a drier surface allows for stronger buoyancy flux, triggering stronger convection that deepens the subcloud layer. We find that the slope of the Bowen-ratio-regulated relationship between the two parameters (defined as λ) is dependent on both the local time and the stability of the lower free atmosphere. The value of λ decreases with time exponentially from sunrise to early afternoon and linearly from early afternoon to sunset. The value of λ is larger in a more stable atmosphere. In addition, continental λ in the early afternoon more than doubles the oceanic λ. Validation of the theoretical results against ground observations over the Southern Great Plains shows a reasonable agreement. Physical mechanisms underlying the findings are explained from the perspective of different time scales at which updrafts and cloud-base height respond to a surface flux forcing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A Computationally Efficient Linear Semi-Lagrangian Scheme for the Advection of Microphysical Variables in Cloud-Resolving Models

An efficient semi-Lagrangian (SL) numerical scheme for the advection of positive-definite microphysical variables in cloud-resolving models is proposed. The scheme is a linear combination of SL schemes of the first and second order. The proposed scheme is compared with two high-order, monotonic, nonlinear Eulerian schemes, in two 2D tests. In the first test, advection of a positive scalar field with large gradients is performed within complicated idealized steering flows. In the second test, a hail storm is simulated using the 2D Hebrew University Cloud Model, describing the interactions between 15 size distributions of different microphysical quantities (each distribution is described by 43 mass bins). The proposed scheme is computationally efficient, has a low numerical diffusion and a high level of mass conservation accuracy, and preserves the sum of multiple advected variables as well as the linear relationships between the advected scalar variables. Although the proposed SL scheme is not exactly positive definite, the negative values and their number, which may appear only in the case of very strong gradients, are negligible. The scheme produces results similar to those of nonlinear Eulerian advection schemes while reducing computation time by approximately a factor of 10.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Consistent linearization of micromorphic continuum theories

We outline the procedure of consistent linearization and apply it to the micromorphic, microstretch, and micropolar theories of continua. This yields tractable linear theories for nonlinearly elastic microstructured materials undergoing finite deformations. The results may be readily utilized in computational mechanics, stability and bifurcation analyses, and small-deformation problems in the context of these types of continua. Our results generalize those existing in current literature and facilitate their recovery upon incorporating appropriate kinematic and constitutive assumptions.

McAvoy, Ryan C.↗
DOE OSTI2024

Evolution of the SLATE linear algebra library

SLATE (Software for Linear Algebra Targeting Exascale) is a distributed, dense linear algebra library targeting both CPU-only and GPU-accelerated systems, developed over the course of the Exascale Computing Project (ECP). While it began with several documents setting out its initial design, significant design changes occurred throughout its development. In some cases, these were anticipated: an early version used a simple consistency flag that was later replaced with a full-featured consistency protocol. In other cases, performance limitations and software and hardware changes prompted a redesign. Sequential communication tasks were parallelized; host-to-host MPI calls were replaced with GPU device-to-device MPI calls; more advanced algorithms such as Communication Avoiding LU and the Random Butterfly Transform (RBT) were introduced. Early choices that turned out to be cumbersome, error prone, or inflexible have been replaced with simpler, more intuitive, or more flexible designs. Applications have been a driving force, prompting a lighter weight queue class, nonuniform tile sizes, and more flexible MPI process grids. Of paramount importance has been building a portable library that works across several different GPU architectures – AMD, Intel, and NVIDIA – while keeping a clean and maintainable codebase. Here we explore the evolving design choices and their effects, both in terms of performance and software sustainability.

Gates, Mark↗
DOE OSTI2021

Exactly unitary discrete representations of the metaplectic transform for linear-time algorithms

The metaplectic transform (MT), a generalization of the Fourier transform sometimes called the linear canonical transform, is a tool used ubiquitously in modern optics, for example, when calculating the transformations of light beams in paraxial optical systems. The MT is also an essential ingredient of the geometrical-optics modeling of caustics that we recently proposed. In particular, this application relies on the near-identity MT (NIMT); however, the NIMT approximation used so far is not exactly unitary and leads to numerical instability. Here, we develop a discrete MT that is exactly unitary, and approximate it to obtain a discrete NIMT that is also unitary and can be computed in linear time. We prove that the discrete NIMT converges to the discrete MT when iterated, thereby allowing the NIMT to compute MTs that are not necessarily near-identity. Finally, we then demonstrate the new algorithms with a series of examples.

47 OTHER INSTRUMENTATION↗
DOE OSTI2015

Evolution of circular and linear polarization in scattering environments

This study quantifies the polarization persistence and memory of circularly polarized light in forward-scattering and isotropic (Rayleigh regime) environments; and for the first time, details the evolution of both circularly and linearly polarized states through scattering environments. Circularly polarized light persists through a larger number of scattering events longer than linearly polarized light for all forward-scattering environments; but not for scattering in the Rayleigh regime. Circular polarization’s increased persistence occurs for both forward and backscattered light. The simulated environments model polystyrene microspheres in water with particle diameters of 0.1 μm, 2.0 μm, and 3.0 μm. The evolution of the polarization states as they scatter throughout the various environments are illustrated on the Poincaré sphere after one, two, and ten scattering events.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Penalized ensemble Kalman filters for high dimensional non-linear systems

The ensemble Kalman filter (EnKF) is a data assimilation technique that uses an ensemble of models, updated with data, to track the time evolution of a usually non-linear system. It does so by using an empirical approximation to the well-known Kalman filter. However, its performance can suffer when the ensemble size is smaller than the state space, as is often necessary for computationally burdensome models. This scenario means that the empirical estimate of the state covariance is not full rank and possibly quite noisy. To solve this problem in this high dimensional regime, we propose a computationally fast and easy to implement algorithm called the penalized ensemble Kalman filter (PEnKF). Under certain conditions, it can be theoretically proven that the PEnKF will be accurate (the estimation error will converge to zero) despite having fewer ensemble members than state dimensions. Further, as contrasted to localization methods, the proposed approach learns the covariance structure associated with the dynamical system. These theoretical results are supported with simulations of several non-linear and high dimensional systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Background Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgene’s repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. Objectives The original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. Conclusions SEGUID v2 produces orientation and rotation invariant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. Availability SEGUID v2 is readily available for major programming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator , can be found at https://www.seguid.org .

Pereira, Humberto↗
DOE OSTI2018

The Relative Importance of Assumed Infrasound Source Terms and Effects of Atmospheric Models on the Linear Inversion of Infrasound Time Series at the Source Physics Experiment

We invert far-field infrasound data for the equivalent seismoacoustic time-domain moment tensor to assess the effects of variable atmospheric models and source phenomena. The infrasound data were produced by a series of underground chemical explosions that were conducted during the Source Physics Experiment (SPE), which was originally designed to study seismoacoustic signal phenomena. The first goal is to investigate the sensitivity of the inversion to the variability of the estimated atmospheric model. The second goal is to determine the relative contribution of two presumed source mechanisms to the observed infrasonic wavefield. Rather than using actual atmospheric observations to estimate the necessary atmospheric Green’s functions, we build a series of atmospheric models that rely on publicly available, regional-scale atmospheric observations. The atmospheric observations are summarized and interpolated onto a 3D grid to produce a model of sound speed at the time of the experiment. For each of four SPE acoustic datasets that we invert, we produced a suite of three atmospheric models for each chemical explosion event, based on 10 yrs of meteorological data: an average model, which averages the atmospheric conditions for 10 yrs prior to each SPE event, as well as two extrema models. To parameterize the inversion, we assume that the source of infrasonic energy results from the linear combination of explosion-induced surface spall and linear seismic-to-elastic mode conversion at the Earth’s free surface. We find that the inversion yields relatively repeatable results for the estimated spall source. Conversely, the estimated isotropic explosion source is highly variable. This suggests that 1) the majority of the observed acoustic energy is produced by the spall and/or 2) our modeling of the elastic energy, and the subsequent conversion to acoustic energy, is too simplistic.

58 GEOSCIENCES↗