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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Improving climate model coupling through a complete mesh representation: a case study with E3SM (v1) and MOAB (v5.x)

One of the fundamental factors contributing to the spatiotemporal inaccuracy in climate modeling is the mapping of solution field data between different discretizations and numerical grids used in the coupled component models. The typical climate computational workflow involves evaluation and serialization of the remapping weights during the preprocessing step, which is then consumed by the coupled driver infrastructure during simulation to compute field projections. Tools like Earth System Modeling Framework (ESMF) and TempestRemap offer capability to generate conservative remapping weights, while the Model Coupling Toolkit (MCT) that is utilized in many production climate models exposes functionality to make use of the operators to solve the coupled problem. However, such multistep processes present several hurdles in terms of the scientific workflow and impede research productivity. In order to overcome these limitations, we present a fully integrated infrastructure based on the Mesh Oriented datABase (MOAB) library, which allows for a complete description of the numerical grids and solution data used in each submodel. Through a scalable advancing-front intersection algorithm, the supermesh of the source and target grids are computed, which is then used to assemble the high-order, conservative, and monotonicity-preserving remapping weights between discretization specifications. The Fortran-compatible interfaces in MOAB are utilized to directly link the submodels in the Energy Exascale Earth System Model (E3SM) to enable online remapping strategies in order to simplify the coupled workflow process. We demonstrate the superior computational efficiency of the remapping algorithms in comparison with other state-of-the-science tools and present strong scaling results on large-scale machines for computing remapping weights between the spectral element atmosphere and finite volume discretizations on the polygonal ocean grids.

58 GEOSCIENCES↗
DOE OSTI2025

A Linear-Complexity Tensor Butterfly Algorithm for Compressing High-Dimensional Oscillatory Integral Operators

This paper presents a multilevel tensor compression algorithm called tensor butterfly algorithm for efficiently representing large-scale and high-dimensional oscillatory integral operators, including Green's functions for wave equations and integral transforms such as Radon transforms and Fourier transforms. The proposed algorithm leverages a tensor extension of the so-called complementary low-rank property of existing matrix butterfly algorithms. The algorithm partitions the discretized integral operator tensor into subtensors of multiple levels and factorizes each subtensor at the middle level as a Tucker-type interpolative decomposition, whose factor matrices are formed in a multilevel fashion. For a d-dimensional (d > 1) integral operator discretized into a 2d-mode tensor with n2d entries, the overall CPU time and memory requirement scale as O(nd), in stark contrast to the O(nd log n) complexity of existing matrix algorithms such as matrix butterfly algorithms and fast Fourier transforms (FFTs), where n is the number of points per direction. When comparing with other tensor algorithms such as quantized tensor train (QTT), the proposed algorithm also shows superior CPU and memory performance for tensor contraction. Remarkably, the tensor butterfly algorithm can efficiently model high-frequency Green's function interactions between two unit cubes, each spanning 512 wavelengths per direction, which represents problems of scale over 512× larger than that existing butterfly algorithms can handle, with the same amount of computation resources. On the other hand, for a problem representing 64 wavelengths per direction, which is the largest size existing algebraic matrix algorithms can handle, our tensor butterfly algorithm exhibits 200x speedups and 30× memory reduction compared with existing ones. Moreover, the tensor butterfly algorithm also permits O(nd)-complexity FFTs and Radon transforms up to d = 6 dimensions.

Kielstra, P Michael↗
DOE OSTI2024

Parallel interior-point solver for block-structured nonlinear programs on SIMD/GPU architectures

Here, we investigate how to port the standard interior-point method to new exascale architectures for block-structured nonlinear programs with state equations. Computationally, we decompose the interior-point algorithm into two successive operations: the evaluation of the derivatives and the solution of the associated Karush-Kuhn-Tucker (KKT) linear system. Our method accelerates both operations using two levels of parallelism. First, we distribute the computations on multiple processes using coarse parallelism. Second, each process uses SIMD/GPU accelerators locally to accelerate the operations using fine-grained parallelism. The KKT system is reduced by eliminating the inequalities and the state variables from the corresponding equations. We demonstrate our method's capability on the supercomputer Polaris, a testbed for the future exascale Aurora system. Each node is equipped with four GPUs, a setup amenable to our two-level approach. Our experiments on the stochastic optimal power flow problem show that the reduction method is 50x faster than the sparse linear solver HSL MA57 running in serial on the CPU, and 6x faster than Pardiso running in parallel on CPU on the same number of processes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

High-Performance Computing Based EMT Simulation of Large PV or Hybrid PV Plants

Faults in the transmission grid have led to reduced power generation from power electronics resources that are typically not connected to the faulted transmission line. In many of the cases, partial loss of power is observed within the power electronics resources like large photovoltaic (PV) power plants. This phenomena is not captured in existing simulation models and/or simulators. High-fidelity switched system electromagnetic transient (EMT) dynamic models of PV power plants can improve the fidelity of models available for accurate analysis of the impact on PV plants during simulation of faults. However, these models are extremely computationally expensive and take a long time to simulate. Long simulation times limit the ability to use these models as larger regions are studied in EMT simulations with more power electronics resources. In this paper, numerical simulation algorithms are combined with high-performance computing techniques and applied to the high-fidelity switched system EMT model of PV plants. Using these techniques, a speed-up of up to 58x is obtained, while preserving the accuracy of the simulation at greater than 98%.

Debnath, Suman↗
DOE OSTI2026

Tough Errors are no Match (TEAM): Optimizing the Quantum Compiler for Noise Resilience

This report summarizes our contributions to the Department of Energy’s Tough Errors are no Match (TEAM) project (DE-SC0020377) under Thrust 2: Quantum Programming and Compilation. The central outcomes of this work included a novel efficient quantum compiling algorithm which works without requiring the quantum computer to exactly invert its operations, answering a longstanding open problem in quantum compiling. Additional results include the implementation of zero-noise extrapolation error mitigation in collaboration with the Unitary Fund, as well as novel quantum algorithms for entanglement detection and pseudorandomness.

Bouland, Adam [Stanford Univ., CA (United States)]↗
DOE OSTI2023

A universal variational quantum eigensolver for non-Hermitian systems

Abstract Many quantum algorithms are developed to evaluate eigenvalues for Hermitian matrices. However, few practical approach exists for the eigenanalysis of non-Hermintian ones, such as arising from modern power systems. The main difficulty lies in the fact that, as the eigenvector matrix of a general matrix can be non-unitary, solving a general eigenvalue problem is inherently incompatible with existing unitary-gate-based quantum methods. To fill this gap, this paper introduces a Variational Quantum Universal Eigensolver (VQUE), which is deployable on noisy intermediate scale quantum computers. Our new contributions include: (1) The first universal variational quantum algorithm capable of evaluating the eigenvalues of non-Hermitian matrices—Inspired by Schur’s triangularization theory, VQUE unitarizes the eigenvalue problem to a procedure of searching unitary transformation matrices via quantum devices; (2) A Quantum Process Snapshot technique is devised to make VQUE maintain the potential quantum advantage inherited from the original variational quantum eigensolver—With additional $$O(log_{2}{N})$$ O ( l o g 2 N ) quantum gates, this method efficiently identifies whether a unitary operator is triangular with respect to a given basis; (3) Successful deployment and validation of VQUE on a real noisy quantum computer, which demonstrates the algorithm’s feasibility. We also undertake a comprehensive parametric study to validate VQUE’s scalability, generality, and performance in realistic applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Comparative Study of Variations in Quantum Approximate Optimization Algorithms for the Traveling Salesman Problem

The traveling salesman problem (TSP) is one of the most often-used NP-hard problems in computer science to study the effectiveness of computing models and hardware platforms. In this regard, it is also heavily used as a vehicle to study the feasibility of the quantum computing paradigm for this class of problems. In this paper, we tackle the TSP using the quantum approximate optimization algorithm (QAOA) approach by formulating it as an optimization problem. By adopting an improved qubit encoding strategy and a layer-wise learning optimization protocol, we present numerical results obtained from the gate-based digital quantum simulator, specifically targeting TSP instances with 3, 4, and 5 cities. We focus on the evaluations of three distinctive QAOA mixer designs, considering their performances in terms of numerical accuracy and optimization cost. Notably, we find that a well-balanced QAOA mixer design exhibits more promising potential for gate-based simulators and realistic quantum devices in the long run, an observation further supported by our noise model simulations. Furthermore, we investigate the sensitivity of the simulations to the TSP graph. Overall, our simulation results show that the digital quantum simulation of problem-inspired ansatz is a successful candidate for finding optimal TSP solutions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Computationally efficient Bayesian estimation of graphical networks for omics data

Graphical networks are useful, widely-used modeling approaches to represent complex biological processes with biological measurements generated by platforms such as mass spectrometry. Bayesian analyses of graphical networks for omics data have several advantages over their frequentist counterparts, such as the inclusion of prior knowledge in the estimation of models. However, Bayesian approaches to date have only been feasible for data with a couple hundred biomolecules due to prohibitive computational time, but omics data often contains tens of thousands of biomolecules. Here, we present and illustrate a more computationally efficient approach named BPlane (Bayesian PseudoLikelihood-based Algorithm for Network Estimation) to extend Bayesian modeling capabilities for larger-sized datasets, such as most untargeted proteomics data. Via simulation, we demonstrate that BPlane produces substantial computational savings over a current state-of-the-art Bayesian algorithm while maintaining competitive edge detection accuracy. On a SARS-CoV2 proteomics data with 7000 proteins, the competing algorithm takes three times as long to complete the first iteration as BPlane takes to converge after over 100 iterations.

EM algorithm↗
DOE OSTI2020

Pairing Directional Solar Inputs From Ray Tracing to Solar Receiver/Reactor Heat Transfer Models on Unstructured Meshes: Development and Case Studies

A novel method for pairing surface irradiation and volumetric absorption from Monte Carlo ray tracing to computational heat transfer models is presented. The method is well-suited to directionally and spatially complex concentrated radiative inputs (e.g., solar receivers and reactors). The method employs a generalized algorithm for directly mapping absorbed rays from a Monte Carlo ray tracing model to boundary or volumetric source terms in the computational mesh. The algorithm is compatible with unstructured, two and three-dimensional meshes with varying element shapes. Four case studies were performed on a directly irradiated, windowed solar thermochemical reactor model to validate the method. The method was shown to conserve energy and preserve spatial variation when mapping rays from a Monte Carlo ray tracing model to a computational heat transfer model in ansys fluent.

14 SOLAR ENERGY↗
DOE OSTI2023

Direct implicit and explicit energy-conserving particle-in-cell methods for modeling of capacitively coupled plasma devices

Achieving large-scale kinetic modeling is a crucial task for the development and optimization of modern plasma devices. With the trend of decreasing pressure in applications, such as plasma etching, kinetic simulations are necessary to self-consistently capture the particle dynamics. The standard, explicit, electrostatic, momentum-conserving particle-in-cell method suffers from restrictive stability constraints on spatial cell size and temporal time step, requiring resolution of the electron Debye length and electron plasma period, respectively. This results in a very high computational cost, making the technique prohibitive for large volume device modeling. We investigate the direct implicit algorithm and the explicit energy conserving algorithm as alternatives to the standard approach, both of which can reduce computational cost with a minimal (or controllable) impact on results. These algorithms are implemented into the well-tested EDIPIC-2D and LTP-PIC codes, and their performance is evaluated via 2D capacitively coupled plasma discharge simulations. The investigation reveals that both approaches enable the utilization of cell sizes larger than the Debye length, resulting in a reduced runtime, while incurring only minor inaccuracies in plasma parameters. The direct implicit method also allows for time steps larger than the electron plasma period; however, care must be taken to avoid numerical heating or cooling. It is demonstrated that by appropriately adjusting the ratio of cell size to time step, it is possible to mitigate this effect to an acceptable level.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Provable bounds for noise-free expectation values computed from noisy samples

Quantum computing has emerged as a powerful computational paradigm capable of solving problems beyond the reach of classical computers. However, today’s quantum computers are noisy, posing challenges to obtaining accurate results. Here, we explore the impact of noise on quantum computing, focusing on the challenges in sampling bit strings from noisy quantum computers and the implications for optimization and machine learning. We formally quantify the sampling overhead to extract good samples from noisy quantum computers and relate it to the layer fidelity, a metric to determine the performance of noisy quantum processors. Further, we show how this allows us to use the conditional value at risk of noisy samples to determine provable bounds on noise-free expectation values. We discuss how to leverage these bounds for different algorithms and demonstrate our findings through experiments on real quantum computers involving up to 127 qubits. The results show strong alignment with theoretical predictions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗
DOE OSTI2024

Error mitigation, optimization, and extrapolation on a trapped-ion testbed

Current noisy intermediate-scale quantum (NISQ) trapped-ion devices are subject to errors which can significantly impact the accuracy of calculations if left unchecked. A form of error mitigation called zero noise extrapolation (ZNE) can decrease an algorithm’s sensitivity to these errors without increasing the number of required qubits. Here we explore different methods for integrating this error mitigation technique into the Variational Quantum Eigensolver (VQE) algorithm for calculating the ground state of the HeH + molecule at 0.8 Å in the presence of experimental noise. Using the Quantum Scientific Computing Open User Testbed (QSCOUT) trapped-ion device, we test three methods of scaling noise for extrapolation: time stretching the two-qubit gates, scaling the sideband detuning parameter, and inserting two-qubit gate identity operations into the ansatz circuit. We find that time stretching and sideband detuning scaling fail to scale the noise on our particular hardware in a way that can be extrapolated to zero noise. Scaling our noise with global gate identity insertions and extrapolating after variational optimization, we achieve error suppression of 96.8%, resulting in an energy estimate within –0.004 ± 0.04 hartree of the ground state energy. This is an improvement, but still outside the chemical accuracy threshold of 0.0016 hartree. Furthermore, our results show that the efficacy of this error mitigation technique depends on choosing the correct implementation for a given device architecture.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Fast b -tagging at the high-level trigger of the ATLAS experiment in LHC Run 3

The ATLAS experiment relies on real-time hadronic jet reconstruction and b-tagging to record fully hadronic events containing b-jets. These algorithms require track reconstruction, which is computationally expensive and could overwhelm the high-level-trigger farm, even at the reduced event rate that passes the ATLAS first stage hardware-based trigger. In LHC Run 3, ATLAS has mitigated these computational demands by introducing a fast neural-network-based b-tagger, which acts as a low-precision filter using input from hadronic jets and tracks. It runs after a hardware trigger and before the remaining high-level-trigger reconstruction. This design relies on the negligible cost of neural-network inference as compared to track reconstruction, and the cost reduction from limiting tracking to specific regions of the detector. In the case of Standard Model HH → bb̅bb̅, a key signature relying on b-jet triggers, the filter lowers the input rate to the remaining high-level trigger by a factor of five at the small cost of reducing the overall signal efficiency by roughly 2%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Neuromorphic Computing for Scientific Applications

Neuromorphic computing technology continues to make strides in the development of new algorithms, devices, and materials. In addition, applications have begun to emerge where neuromorphic computing shows promising results. However, numerous barriers to further development and application remain. In this work, we identify several science areas where neuromorphic computing can either make an immediate impact (within 1 to 3 years) or the societal impact would be extremely high if the technological barriers can be addressed. We identify both opportunities and hurdles to the development of neuromorphic computing technology for these areas. Finally, we discuss future directions that need to be addressed to expand both the development and application of neuromorphic computing.

Patton, Robert↗
DOE OSTI2023

AMG Preconditioners based on parallel hybrid coarsening and multi-objective graph matching

We describe preliminary results from a multi-objective graph matching algorithm, in the coarsening step of an aggregation-based Algebraic MultiGrid (AMG) preconditioner, for solving large and sparse linear systems of equations on high-end parallel computers. We have two objectives. First, we wish to improve the convergence behavior of the AMG method when applied to highly anisotropic problems. Second, we wish to extend the parallel package \texttt{PSCToolkit} to exploit multi-threaded parallelism at the node level on multi-core processors. Our matching proposal balances the need to simultaneously compute high weights and large cardinalities by a new formulation of the weighted matching problem combining both these objectives using a parameter $\lambda$. We compute the matching by a parallel $2/3-\varepsilon$-approximation algorithm for maximum weight matchings. Results with the new matching algorithm show that for a suitable choice of the parameter $\lambda$ we compute effective preconditioners in the presence of anisotropy, i.e., smaller solve times, setup times, iterations counts, and operator complexity.

D'Ambra, Pasqua↗
DOE OSTI2021

Scalable Pattern Matching in Metadata Graphs via Constraint Checking

Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.

97 MATHEMATICS AND COMPUTING↗