Publications

Abstract not provided.

Abstract not provided.

A graph is a mathematical representation of a network; we say it consists of a set of vertices, which are connected by edges. Graphs have numerous applications in various fields, as they can model all sorts of connections, processes, or relations. For example, graphs can model intricate transit systems or the human nervous system. However, graphs that are large or complicated become difficult to analyze. This is why there is an increased interest in the area of graph partitioning, reducing the size of the graph into multiple partitions. For example, partitions of a graph representing a social network might help identify clusters of friends or colleagues. Graph partitioning is also a widely used approach to load balancing in parallel computing. The partitioning of a graph is extremely useful to decompose the graph into smaller parts and allow for easier analysis. There are different ways to solve graph partitioning problems. For this work, we focus on a spectral partitioning method which forms a partition based upon the eigenvectors of the graph Laplacian (details presented in Acer, et. al.). This method uses the LOBPCG algorithm to compute these eigenvectors. LOBPCG can be accelerated by an operator called a preconditioner. For this internship, we evaluate a randomized Cholesky (rchol) preconditioner for its effectiveness on graph partitioning problems with LOBPCG. We compare it with two standard preconditioners: Jacobi and Incomplete Cholesky (ichol). This research was conducted from August to December 2021 in conjunction with Sandia National Laboratories.

We propose a novel statistical inference paradigm for zero-inflated multiway count data that dispenses with the need to distinguish between true and false zero counts. Our approach ignores all zero entries and applies zero-truncated Poisson regression on the positive counts. Inference is accomplished via tensor completion that imposes low-rank structure on the Poisson parameter space. Our main result shows that an $\textit{N}$-way rank-R parametric tensor 𝓜 ϵ (0, ∞)^{$I$Χ∙∙∙Χ$I$} generating Poisson observations can be accurately estimated from approximately $IR^2 \text{log}^2_2(I)$ non-zero counts for a nonnegative canonical polyadic decomposition. Several numerical experiments are presented demonstrating that our zero-truncated paradigm is comparable to the ideal scenario where the locations of false zero counts are known $\textit{a priori}$.

Nuclear spins were among the first physical platforms to be considered for quantum information processing1,2, because of their exceptional quantum coherence3 and atomic-scale footprint. However, their full potential for quantum computing has not yet been realized, owing to the lack of methods with which to link nuclear qubits within a scalable device combined with multi-qubit operations with sufficient fidelity to sustain fault-tolerant quantum computation. Here we demonstrate universal quantum logic operations using a pair of ion-implanted 31P donor nuclei in a silicon nanoelectronic device. A nuclear two-qubit controlled-Z gate is obtained by imparting a geometric phase to a shared electron spin4, and used to prepare entangled Bell states with fidelities up to 94.2(2.7)%. The quantum operations are precisely characterized using gate set tomography (GST)5, yielding one-qubit average gate fidelities up to 99.95(2)%, two-qubit average gate fidelity of 99.37(11)% and two-qubit preparation/measurement fidelities of 98.95(4)%. These three metrics indicate that nuclear spins in silicon are approaching the performance demanded in fault-tolerant quantum processors6. We then demonstrate entanglement between the two nuclei and the shared electron by producing a Greenberger–Horne–Zeilinger three-qubit state with 92.5(1.0)% fidelity. Because electron spin qubits in semiconductors can be further coupled to other electrons7–9 or physically shuttled across different locations10,11, these results establish a viable route for scalable quantum information processing using donor nuclear and electron spins.

Anomalous behavior is ubiquitous in subsurface solute transport due to the presence of high degrees of heterogeneity at different scales in the media. Although fractional models have been extensively used to describe the anomalous transport in various subsurface applications, their application is hindered by computational challenges. Simpler nonlocal models characterized by integrable kernels and finite interaction length represent a computationally feasible alternative to fractional models; yet, the informed choice of their kernel functions still remains an open problem. We propose a general data-driven framework for the discovery of optimal kernels on the basis of very small and sparse data sets in the context of anomalous subsurface transport. Using spatially sparse breakthrough curves recovered from fine-scale particle-density simulations, we learn the best coarse-scale nonlocal model using a nonlocal operator regression technique. Predictions of the breakthrough curves obtained using the optimal nonlocal model show good agreement with fine-scale simulation results even at locations and time intervals different from the ones used to train the kernel, confirming the excellent generalization properties of the proposed algorithm. A comparison with trained classical models and with black-box deep neural networks confirms the superiority of the predictive capability of the proposed model.

Krylov subspace recycling is a powerful tool when solving a long series of large, sparse linear systems that change only slowly over time. In PDE constrained shape optimization, these series appear naturally, as typically hundreds or thousands of optimization steps are needed with only small changes in the geometry. In this setting, however, applying Krylov subspace recycling can be a difficult task. As the geometry evolves, in general, so does the finite element mesh defined on or representing this geometry, including the numbers of nodes and elements and element connectivity. This is especially the case if re-meshing techniques are used. As a result, the number of algebraic degrees of freedom in the system changes, and in general the linear system matrices resulting from the finite element discretization change size from one optimization step to the next. Changes in the mesh connectivity also lead to structural changes in the matrices. In the case of re-meshing, even if the geometry changes only a little, the corresponding mesh might differ substantially from the previous one. Obviously, this prevents any straightforward mapping of the approximate invariant subspace of the linear system matrix (the focus of recycling in this work) from one optimization step to the next; similar problems arise for other selected subspaces. In this paper, we present an algorithm to map an approximate invariant subspace of the linear system matrix for the previous optimization step to an approximate invariant subspace of the linear system matrix for the current optimization step, for general meshes. This is achieved by exploiting the map from coefficient vectors to finite element functions on the mesh, combined with interpolation or approximation of functions on the finite element mesh. We demonstrate the effectiveness of our approach numerically with several proof of concept studies for a specific meshing technique.

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.

Magnetic skyrmions are nanoscale whirls of magnetism that can be propagated with electrical currents. The repulsion between skyrmions inspires their use for reversible computing based on the elastic billiard ball collisions proposed for conservative logic in 1982. In this letter, we evaluate the logical and physical reversibility of this skyrmion logic paradigm, as well as the limitations that must be addressed before dissipation-free computation can be realized.

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.

Simple but mission-critical internet-based applications that require extremely high reliability, availability, and verifiability (e.g., auditability) could benefit from running on robust public programmable blockchain platforms such as Ethereum. Unfortunately, program code running on such blockchains is normally publicly viewable, rendering these platforms unsuitable for applications requiring strict privacy of application code, data, and results. In this work, we investigate using MPC techniques to protect the privacy of a blockchain computation. While our main goal is to hide both the data and the computed function itself, we also consider the standard MPC setting where the function is public. We describe GABLE (Garbled Autonomous Bots Leveraging Ethereum), a blockchain MPC architecture and system. The GABLE architecture specifies the roles and capabilities of the players. GABLE includes two approaches for implementing MPC over blockchain: Garbled Circuits (GC), evaluating universal circuits, and Garbled Finite State Automata (GFSA). We formally model and prove the security of GABLE implemented over garbling schemes, a popular abstraction of GC and GFSA from (Bellare et al., CCS 2012). We analyze in detail the performance (including Ethereum gas costs) of both approaches and discuss the trade-offs. We implement a simple prototype of GABLE and report on the implementation issues and experience.

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.

As transistors have been scaled over the past decade, modern systems have become increasingly susceptible to faults. Increased transistor densities and lower capacitances make a particle strike more likely to cause an upset. At the same time, complex computer systems are increasingly integrated into safety-critical systems such as autonomous vehicles. These two trends make the study of system reliability and fault tolerance essential for modern systems. To analyze and improve system reliability early in the design process, new tools are needed for RTL fault analysis.This paper proposes Eris, a novel framework to identify vulnerable components in hardware designs through fault-injection and fault propagation tracking. Eris builds on ESSENT - a fast C/C++ RTL simulation framework - to provide fault injection, fault tracking, and control-flow deviation detection capabilities for RTL designs. To demonstrate Eris' capabilities, we analyze the reliability of the open source Rocket Chip SoC by randomly injecting faults during thousands of runs on four microbenchmarks. As part of this analysis we measure the sensitivity of different hardware structures to faults based on the likelihood of a random fault causing silent data corruption, unrecoverable data errors, program crashes, and program hangs. We detect control flow deviations and determine whether or not they are benign. Additionally, using Eris' novel fault-tracking capabilities we are able to find 78% more vulnerable components in the same number of simulations compared to RTL-based fault injection techniques without these capabilities. We will release Eris as an open-source tool to aid future research into processor reliability and hardening.

We have extended the computational singular perturbation (CSP) method to differential algebraic equation (DAE) systems and demonstrated its application in a heterogeneous-catalysis problem. The extended method obtains the CSP basis vectors for DAEs from a reduced Jacobian matrix that takes the algebraic constraints into account. We use a canonical problem in heterogeneous catalysis, the transient continuous stirred tank reactor (T-CSTR), for illustration. The T-CSTR problem is modelled fundamentally as an ordinary differential equation (ODE) system, but it can be transformed to a DAE system if one approximates typically fast surface processes using algebraic constraints for the surface species. We demonstrate the application of CSP analysis for both ODE and DAE constructions of a T-CSTR problem, illustrating the dynamical response of the system in each case. We also highlight the utility of the analysis in commenting on the quality of any particular DAE approximation built using the quasi-steady state approximation (QSSA), relative to the ODE reference case.

Centered on modern C++ and the SYCL standard for heterogeneous programming, Data Parallel C++ (dpc++) and Intel's oneAPI software ecosystem aim to lower the barrier to entry for the use of accelerators like FPGAs in diverse applications. In this work, we consider the usage of FPGAs for scientific computing, in particular with a multigrid solver, MueLu. We report on early experiences implementing kernels of the solver in DPC++ for execution on Stratix 10 FPGAs, and we evaluate several algorithmic design and implementation choices. These choices not only impact performance, but also shed light on the capabilities and limitations of DPC++ and oneAPI.

Quantum computers can now run interesting programs, but each processor’s capability—the set of programs that it can run successfully—is limited by hardware errors. These errors can be complicated, making it difficult to accurately predict a processor’s capability. Benchmarks can be used to measure capability directly, but current benchmarks have limited flexibility and scale poorly to many-qubit processors. We show how to construct scalable, efficiently verifiable benchmarks based on any program by using a technique that we call circuit mirroring. With it, we construct two flexible, scalable volumetric benchmarks based on randomized and periodically ordered programs. We use these benchmarks to map out the capabilities of twelve publicly available processors, and to measure the impact of program structure on each one. We find that standard error metrics are poor predictors of whether a program will run successfully on today’s hardware, and that current processors vary widely in their sensitivity to program structure.

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.

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.

Stochasticity is ubiquitous in the world around us. However, our predominant computing paradigm is deterministic. Random number generation (RNG) can be a computationally inefficient operation in this system especially for larger workloads. Our work leverages the underlying physics of emerging devices to develop probabilistic neural circuits for RNGs from a given distribution. However, codesign for novel circuits and systems that leverage inherent device stochasticity is a hard problem. This is mostly due to the large design space and complexity of doing so. It requires concurrent input from multiple areas in the design stack from algorithms, architectures, circuits, to devices. In this paper, we present examples of optimal circuits developed leveraging AI-enhanced codesign techniques using constraints from emerging devices and algorithms. Our AI-enhanced codesign approach accelerated design and enabled interactions between experts from different areas of the micro-electronics design stack including theory, algorithms, circuits, and devices. We demonstrate optimal probabilistic neural circuits using magnetic tunnel junction and tunnel diode devices that generate an RNG from a given distribution.

Multi-model Monte Carlo methods have been illustrated to be an efficient and accurate alternative to standard Monte Carlo (MC) in the model-based propagation of uncertainty in entry, descent, and landing (EDL) applications. These multi-model MC methods fuse predictions from low-fidelity models with the high-fidelity EDL model of interest to produce unbiased statistics with a fraction of the computational cost. The accuracy and efficiency of the multi-model MC methods are dependent upon the magnitude of correlations of the low-fidelity models with the high-fidelity model, but also upon the correlation amongst the low-fidelity models, and their relative computational cost. Because of this layer of complexity, the question of how to optimally select the set of low-fidelity models has remained open. In this work, methods for optimal model construction and tuning are investigated as a means to increase the speed and precision of trajectory simulation for EDL. Specifically, the focus is on the inclusion of low-fidelity model tuning within the sample allocation optimization that accompanies multi-model MC methods. Results indicate that low-fidelity model tuning can significantly improve efficiency and precision of trajectory simulations and provide an increased edge to multi-model MC methods when compared to standard MC.

Software sustainability is critical for Computational Science and Engineering (CSE) software. Measuring sustainability is challenging because sustainability consists of many attributes. One factor that impacts software sustainability is the complexity of the source code. This paper introduces an approach for utilizing complexity data, with a focus on hotspots of and changes in complexity, to assist developers in performing code reviews and inform project teams about longer-term changes in sustainability and maintainability from the perspective of cyclomatic complexity. We present an analysis of data associated with four real-world pull requests to demonstrate how the metrics may help guide and inform the code review process and how the data can be used to measure changes in complexity over time.

Abstract not provided.

Neural networks (NN)s have been increasingly proposed as surrogates for approximation of systems with computationally expensive physics for rapid online evaluation or exploration. As these surrogate models are integrated into larger optimization problems used for decision making, there is a need to verify their behavior to ensure adequate performance over the desired parameter space. We extend the ideas of optimization-based neural network verification to provide guarantees of surrogate performance over the feasible optimization space. In doing so, we present formulations to represent neural networks within decision-making problems, and we develop verification approaches that use model constraints to provide increasingly tight error estimates. We demonstrate the capabilities on a simple steady-state reactor design problem.

This paper reports on Catalyst usability and initial adoption by SPARC analysts. The use case approach highlights the analysts' perspective. Impediments to adoption can be due to deficiencies in software capabilities, or analysts may identify mundane inconveniences and barriers that prevent them from fully leveraging Catalyst. With that said, for many analyst tasks Catalyst provides enough relative advantage that they have begun applying it in their production work, and they recognize the potential for it to solve problems they currently struggle with. The findings in this report include specific issues and minor bugs in ParaView Python scripting, which are viewed as having straightforward solutions, as well as a broader adoption analysis.