Given a graph, finding the distance-2 maximal independent set (MIS-2) of the vertices is a problem that is useful in several contexts such as algebraic multigrid coarsening or multilevel graph partitioning. Such multilevel methods rely on finding the independent vertices so they can be used as seeds for aggregation in a multilevel scheme. We present a parallel MIS-2 algorithm to improve performance on modern accelerator hardware. This algorithm is implemented using the Kokkos programming model to enable performance portability. We demonstrate the portability of the algorithm and the performance on a variety of architectures (x86/ARM CPUs and NVIDIA/AMD GPUs). The resulting algorithm is also deterministic, producing an identical result for a given input across all of these platforms. The new MIS-2 implementation outperforms implementations in state of the art libraries like CUSP and ViennaCL by 3-8x while producing similar quality results. We further demonstrate the benefits of this approach by developing parallel graph coarsening scheme for two different use cases. First, we develop an algebraic multigrid (AMG) aggregation scheme using parallel MIS-2 and demonstrate the benefits as opposed to previous approaches used in the MueLu multigrid package in Trilinos. We also describe an approach for implementing a parallel multicolor 'cluster' Gauss-Seidel preconditioner using this MIS-2 coarsening, and demonstrate better performance with an efficient, parallel, mul-ticolor Gauss-Seidel algorithm.
Deep operator learning has emerged as a promising tool for reduced-order modelling and PDE model discovery. Leveraging the expressive power of deep neural networks, especially in high dimensions, such methods learn the mapping between functional state variables. While proposed methods have assumed noise only in the dependent variables, experimental and numerical data for operator learning typically exhibit noise in the independent variables as well, since both variables represent signals that are subject to measurement error. In regression on scalar data, failure to account for noisy independent variables can lead to biased parameter estimates. With noisy independent variables, linear models fitted via ordinary least squares (OLS) will show attenuation bias, wherein the slope will be underestimated. In this work, we derive an analogue of attenuation bias for linear operator regression with white noise in both the independent and dependent variables, showing that the norm upper bound of the operator learned via OLS decreases with increasing noise in the independent variable. In the nonlinear setting, we computationally demonstrate underprediction of the action of the Burgers operator in the presence of noise in the independent variable. We propose error-in-variables (EiV) models for two operator regression methods, MOR-Physics and DeepONet, and demonstrate that these new models reduce bias in the presence of noisy independent variables for a variety of operator learning problems. Considering the Burgers operator in 1D and 2D, we demonstrate that EiV operator learning robustly recovers operators in high-noise regimes that defeat OLS operator learning. We also introduce an EiV model for time-evolving PDE discovery and show that OLS and EiV perform similarly in learning the Kuramoto-Sivashinsky evolution operator from corrupted data, suggesting that the effect of bias in OLS operator learning depends on the regularity of the target operator.
We develop a framework for Gaussian processes regression constrained by boundary value problems. The framework may be applied to infer the solution of a well-posed boundary value problem with a known second-order differential operator and boundary conditions, but for which only scattered observations of the source term are available. Scattered observations of the solution may also be used in the regression. The framework combines co-kriging with the linear transformation of a Gaussian process together with the use of kernels given by spectral expansions in eigenfunctions of the boundary value problem. Thus, it benefits from a reduced-rank property of covariance matrices. We demonstrate that the resulting framework yields more accurate and stable solution inference as compared to physics-informed Gaussian process regression without boundary condition constraints.
Fault tolerance is a key challenge as high performance computing systems continue to increase component counts, individual component reliability decreases, and hardware and software complexity increases. To better understand the potential impacts of failures on next-generation systems, significant effort has been devoted to collecting, characterizing and analyzing failures on current systems. These studies require large volumes of data and complex analysis in an attempt to identify statistical properties of the failure data. In this paper, we examine the lifetime of failures on the Cielo supercomputer that was located at Los Alamos National Laboratory, looking specifically at the time between faults on this system. Through this analysis, we show that the time between uncorrectable faults for this system obeys Benford’s law, This law applies to a number of naturally occurring collections of numbers and states that the leading digit is more likely to be small, for example a leading digit of 1 is more likely than 9. We also show that a number of common distributions used to model failures also follow this law. This work provides critical analysis on the distribution of times between failures for extreme-scale systems. Specifically, the analysis in this work could be used as a simple form of failure prediction or used for modeling realistic failures.
Powders under compression form mesostructures of particle agglomerations in response to both inter- and intra-particle forces. The ability to computationally predict the resulting mesostructures with reasonable accuracy requires models that capture the distributions associated with particle size and shape, contact forces, and mechanical response during deformation and fracture. The following report presents experimental data obtained for the purpose of validating emerging mesostructures simulated by discrete element method and peridynamic approaches. A custom compression apparatus, suitable for integration with our micro-computed tomography (micro-CT) system, was used to collect 3-D scans of a bulk powder at discrete steps of increasing compression. Details of the apparatus and the microcrystalline cellulose particles, with a nearly spherical shape and mean particle size, are presented. Comparative simulations were performed with an initial arrangement of particles and particle shapes directly extracted from the validation experiment. The experimental volumetric reconstruction was segmented to extract the relative positions and shapes of individual particles in the ensemble, including internal voids in the case of the microcrystalline cellulose particles. These computationally determined particles were then compressed within the computational domain and the evolving mesostructures compared directly to those in the validation experiment. The ability of the computational models to simulate the experimental mesostructures and particle behavior at increasing compression is discussed.
Numerical simulations of Greenland and Antarctic ice sheets involve the solution of large-scale highly nonlinear systems of equations on complex shallow geometries. This work is concerned with the construction of Schwarz preconditioners for the solution of the associated tangent problems, which are challenging for solvers mainly because of the strong anisotropy of the meshes and wildly changing boundary conditions that can lead to poorly constrained problems on large portions of the domain. Here, two-level generalized Dryja-Smith-Widlund (GDSW)-type Schwarz preconditioners are applied to different land ice problems, i.e., a velocity problem, a temperature problem, as well as the coupling of the former two problems. We employ the message passing interface (MPI)- parallel implementation of multilevel Schwarz preconditioners provided by the package FROSch (fast and robust Schwarz) from the Trilinos library. The strength of the proposed preconditioner is that it yields out-of-the-box scalable and robust preconditioners for the single physics problems. To the best of our knowledge, this is the first time two-level Schwarz preconditioners have been applied to the ice sheet problem and a scalable preconditioner has been used for the coupled problem. The preconditioner for the coupled problem differs from previous monolithic GDSW preconditioners in the sense that decoupled extension operators are used to compute the values in the interior of the subdomains. Several approaches for improving the performance, such as reuse strategies and shared memory OpenMP parallelization, are explored as well. In our numerical study we target both uniform meshes of varying resolution for the Antarctic ice sheet as well as nonuniform meshes for the Greenland ice sheet. We present several weak and strong scaling studies confirming the robustness of the approach and the parallel scalability of the FROSch implementation. Among the highlights of the numerical results are a weak scaling study for up to 32 K processor cores (8 K MPI ranks and 4 OpenMP threads) and 566 M degrees of freedom for the velocity problem as well as a strong scaling study for up to 4 K processor cores (and MPI ranks) and 68 M degrees of freedom for the coupled problem.
U.S. national research laboratories and agencies play an integral role in advancing science and technology for the public good. The authors of this article, as research software engineers (RSEs) and allies from eight unique national R&D organizations, came together to explore RSE needs from the perspective of national institutions. We identified three key areas of improvement for future RSEs to pursue science in the national interest: community establishment, hiring and retention, and recognition. To retain and cultivate this essential talent, U.S. national institutions must evolve to support appropriate career pathways for RSEs, and to recognize and reward RSEs’ work.
Magann, Alicia B.; Mccaul, Gerard; Rabitz, Herschel A.; Bondar, Denys I.
The characterization of mixtures of non-interacting, spectroscopically similar quantum components has important applications in chemistry, biology, and materials science. We introduce an approach based on quantum tracking control that allows for determining the relative concentrations of constituents in a quantum mixture, using a single pulse which enhances the distinguishability of components of the mixture and has a length that scales linearly with the number of mixture constituents. To illustrate the method, we consider two very distinct model systems: mixtures of diatomic molecules in the gas phase, as well as solid-state materials composed of a mixture of components. A set of numerical analyses are presented, showing strong performance in both settings.
To keep pace with the demand for innovation through scientific computing, modern scientific software development is increasingly reliant upon a rich and diverse ecosystem of software libraries and toolchains. Research software engineers (RSEs) responsible for that infrastructure perform highly integrative work, acting as a bridge between the hardware, the needs of researchers, and the software layers situated between them; relatively little, however, has been written about the role played by RSEs in that work and what support they need to thrive. To that end, we present a two-part report on the development of half-precision floating point support in the Kokkos Ecosystem. Half-precision computation is a promising strategy for increasing performance in numerical computing and is particularly attractive for emerging application areas (e.g., machine learning), but developing practicable, portable, and user-friendly abstractions is a nontrivial task. In the first half of the paper, we conduct an engineering study on the technical implementation of the Kokkos half-precision scalar feature and showcase experimental results; in the second half, we offer an experience report on the challenges and lessons learned during feature development by the first author. We hope our study provides a holistic view on scientific library development and surfaces opportunities for future studies into effective strategies for RSEs engaged in such work.
Many teams struggle to adapt and right-size software engineering best practices for quality assurance to fit their context. Introducing software quality is not usually framed in a way that motivates teams to take action, thus resulting in it becoming a "check the box for compliance"activity instead of a cultural practice that values software quality and the effort to achieve it. When and how can we provide effective incentives for software teams to adopt and integrate meaningful and enduring software quality practices? We explored this question through a persona-based ideation exercise at the 2021 Collegeville Workshop on Scientific Software in which we created three unique personas that represent different scientific software developer perspectives.
This manuscript presents the recent advances in Mixed-Integer Nonlinear Programming (MINLP) and Generalized Disjunctive Programming (GDP) with a particular scope for superstructure optimization within Process Systems Engineering (PSE). We present an environment of open-source software packages written in Python and based on the algebraic modeling language Pyomo. These packages include MindtPy, a solver for MINLP that implements decomposition algorithms for such problems, CORAMIN, a toolset for MINLP algorithms providing relaxation generators for nonlinear constraints, Pyomo.GDP, a modeling extension for Generalized Disjunctive Programming that allows users to represent their problem as a GDP natively, and GDPOpt, a collection of algorithms explicitly tailored for GDP problems. Combining these tools has allowed us to solve several problems relevant to PSE, which we have gathered in an easily installable and accessible library, GDPLib. We show two examples of these models and how the flexibility of modeling given by Pyomo.GDP allows for efficient solutions to these complex optimization problems. Finally, we show an example of integrating these tools with the framework IDAES PSE, leading to optimal process synthesis and conceptual design with advanced multi-scale PSE modeling systems.
Zhang, Chen; Jacobson, Clas; Zhang, Qi; Biegler, Lorenz T.; Eslick, John C.; Zamarripa, Miguel A.; Stinchfield, Georgia; Siirola, John D.; Laird, Carl D.
This document presents tests from the Sierra Structural Mechanics verification test suite. Each of these tests is run nightly with the Sierra/SD code suite and the results of the test checked versus the correct analytic result. For each of the tests presented in this document the test setup, derivation of the analytic solution, and comparison of the Sierra/SD code results to the analytic solution is provided. This document can be used to confirm that a given code capability is verified or referenced as a compilation of example problems.
Neural operators have recently become popular tools for designing solution maps between function spaces in the form of neural networks. Differently from classical scientific machine learning approaches that learn parameters of a known partial differential equation (PDE) for a single instance of the input parameters at a fixed resolution, neural operators approximate the solution map of a family of PDEs [6, 7]. Despite their success, the uses of neural operators are so far restricted to relatively shallow neural networks and confined to learning hidden governing laws. In this work, we propose a novel nonlocal neural operator, which we refer to as nonlocal kernel network (NKN), that is resolution independent, characterized by deep neural networks, and capable of handling a variety of tasks such as learning governing equations and classifying images. Our NKN stems from the interpretation of the neural network as a discrete nonlocal diffusion reaction equation that, in the limit of infinite layers, is equivalent to a parabolic nonlocal equation, whose stability is analyzed via nonlocal vector calculus. The resemblance with integral forms of neural operators allows NKNs to capture long-range dependencies in the feature space, while the continuous treatment of node-to-node interactions makes NKNs resolution independent. The resemblance with neural ODEs, reinterpreted in a nonlocal sense, and the stable network dynamics between layers allow for generalization of NKN’s optimal parameters from shallow to deep networks. This fact enables the use of shallow-to-deep initialization techniques [8]. Our tests show that NKNs outperform baseline methods in both learning governing equations and image classification tasks and generalize well to different resolutions and depths.
