SEARCH · Engineering Papers

Results for “Scalable Algorithms”

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

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42

All sources NASA NTRS DOE OSTI

DOE OSTI2018

TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed-matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared-memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command-line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of TopoMS and compares it with state-of-the-art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero-de-la-Roza et al., Comput. Phys. Commun. 2014, 185, 1007). TopoMS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine-grid solution, robustness against lattice bias, and topological consistency. TopoMS is released publicly under BSD License.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Distributed Tomographic Reconstruction with Quantization

Conventional tomographic reconstruction typically depends on centralized servers for both data storage and computation, leading to concerns about memory limitations and data privacy. Distributed reconstruction algorithms mitigate these issues by partitioning data across multiple nodes, reducing server load and enhancing privacy. However, these algorithms often encounter challenges related to memory constraints and communication overhead between nodes. In this paper, we introduce a decentralized Alternating Directions Method of Multipliers (ADMM) with configurable quantization. By distributing local objectives across nodes, our approach is highly scalable and can efficiently reconstruct images while adapting to available resources. To overcome communication bottlenecks, we propose two quantization techniques based on K-means clustering and JPEG compression. Numerical experiments with benchmark images illustrate the tradeoffs between communication efficiency, memory use, and reconstruction accuracy.

Miao, Runxuan↗

DOE OSTI2023

A multiplexed bacterial two-hybrid for rapid characterization of protein–protein interactions and iterative protein design

Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Interregional Transmission Operational Coordination (IRTOC)

This report presents a modeling and evaluation framework developed through the Inter-Regional Transmission Operational Coordination (IRTOC) project to study market-to-market (M2M) congestion management across day-ahead and real-time markets. The framework extends the Sienna platform through Sienna Decomposition, a multi-stage evaluation architecture that enables flexible representation of multiple regions and systematic assessment of alternative market coordination designs. Additional modeling capabilities include reserve deliverability constraints, High-Voltage Direct Current (HVDC) optimization for Alternating Current (AC) congestion management, and several real-time distributed coordination algorithms. Case studies using the RTS-GMLC test system and a large-scale Eastern Interconnection model demonstrate that the framework can evaluate alternative coordination structures and quantify their economic and operational impacts. The proposed framework provides a scalable platform for analyzing inter-regional coordination strategies in large-scale electricity markets.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Liquid Crystal Orientation and Shape Optimization for the Active Response of Liquid Crystal Elastomers

Liquid crystal elastomers (LCEs) are responsive materials that can undergo large reversible deformations upon exposure to external stimuli, such as electrical and thermal fields. Controlling the alignment of their liquid crystals mesogens to achieve desired shape changes unlocks a new design paradigm that is unavailable when using traditional materials. While experimental measurements can provide valuable insights into their behavior, computational analysis is essential to exploit their full potential. Accurate simulation is not, however, the end goal; rather, it is the means to achieve their optimal design. Such design optimization problems are best solved with algorithms that require gradients, i.e., sensitivities, of the cost and constraint functions with respect to the design parameters, to efficiently traverse the design space. In this work, a nonlinear LCE model and adjoint sensitivity analysis are implemented in a scalable and flexible finite element-based open source framework and integrated into a gradient-based design optimization tool. To display the versatility of the computational framework, LCE design problems that optimize both the material, i.e., liquid crystal orientation, and structural shape to reach a target actuated shapes or maximize energy absorption are solved. Multiple parameterizations, customized to address fabrication limitations, are investigated in both 2D and 3D. The case studies are followed by a discussion on the simulation and design optimization hurdles, as well as potential avenues for improving the robustness of similar computational frameworks for applications of interest.

42 ENGINEERING↗

NASA NTRS1998

Charon Message-Passing Toolkit for Scientific Computations

The Charon toolkit for piecemeal development of high-efficiency parallel programs for scientific computing is described. The portable toolkit, callable from C and Fortran, provides flexible domain decompositions and high-level distributed constructs for easy translation of serial legacy code or design to distributed environments. Gradual tuning can subsequently be applied to obtain high performance, possibly by using explicit message passing. Charon also features general structured communications that support stencil-based computations with complex recurrences. Through the separation of partitioning and distribution, the toolkit can also be used for blocking of uni-processor code, and for debugging of parallel algorithms on serial machines. An elaborate review of recent parallelization aids is presented to highlight the need for a toolkit like Charon. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability.

VanderWijngaart, Rob F.↗

NASA NTRS1998

Charon Message-Passing Toolkit for Scientific Computations

VanderWijngarrt, Rob F.↗

NASA NTRS2022

A Survey of Mathematical Structures for Lunar Networks

To sustain the current and increasing accessibility of space, a scalable communications infrastructure (i.e. the Solar System Internet, SSI) is necessary. The goal of this paper is to begin the discovery of the fundamental underlying mathematical structure of space networks to help the research community harness these structures for algorithm development and optimization. To ensure the applicability of the research, the approaches are considered through the lens of simulated scenarios inspired by the Artemis Back-to-the-Moon mission set for 2024. We note that any approach to an SSI must fit under the umbrella of Delay Tolerant Networking (DTN), due to celestial mobility, high link latencies, high variance in link latencies, disconnections, lack of end-to-end paths, and so on. These difficulties are exacerbated by the fact that the underlying structure of a space network is a time-evolving network and may experience multiple discontinuities in its topology. In this paper we propose several novel approaches to a mathematical foundation for Delay Tolerant Networking Theory that fall outside the traditional scope of temporal network theory. These techniques include methods from Topological Data Analysis, Dynamic Graph Analysis, Applied Algebraic Geometry, Probability Theory, and Game Theory. Some of these methods include tools adapted to the study of dynamic metric spaces, such as zigzag persistent homology and their higher parameter analogs. We find that several of these methods target desired engineering outcomes such as discovery and automatic sub-netting. While each approach is theoretical, they are also algorithmic in nature and offer immediate practical applications. The paper concludes with comparisons of the various methods along with suggestions for future work.

Delay tolerant networking↗

DOE OSTI2024

Scalable Full-Stack Benchmarks for Quantum Computers

Not Available

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

A Parametric, Data-Driven, Non-Intrusive Reduced-Order Model Framework for Crystal Plasticity Simulations of Voids

The influence of the internal structure at micrometer length scales on the deformation of polycrystalline materials can be effectively captured using crystal plasticity finite element methods (CPFEM). However, the complexity and nonlinearity of the deformation equations CPFEM solves demand significant computational power and resources to achieve accurate predictions, limiting its broader application. To address this challenge, we have identified a reduced-order representation of the complex data in order to establish a computationally efficient reduced-order models (ROM) and drastically reduce the computational expense of CPFEM. Specifically, in this work, we developed a parametric, data-driven, and non-intrusive ROM framework for CPFEM using proper orthogonal decomposition (POD) and sparse variational Gaussian process (SVGP) regression for single-crystal microstructures under tensile loading conditions. The developed protocol enables one to compress field into a latent/low-dimensional space described by principal component analysis (PCA) via the singular value decomposition (SVD) algorithm. As a result, the high-dimensional data are reduced to a significantly smaller amount of dimensions with POD bases and POD coefficients. Furthermore, we deployed an ensemble of SVGPs—extended from the classical Gaussian process (GP) regression for scalability and handling big data—in a massively parallel manner to train and predict latent POD coefficients using known POD bases from a set of previously obtained simulations results. Lastly, using the predicted POD coefficients, we reconstructed the full-field results and showed reasonable agreement compared with the true values obtained from running CPFEM. The developed framework is validated with a set of CPFEM simulations of a single embedded void in single-crystal aluminum alloy. While the framework is broadly applicable, this work specifically focuses on single-crystal microstructures, a single load case (e.g., tensile), and a specific void geometry (spherical).

Anisotropy↗

DOE OSTI2025

Accelerating high-order continuum kinetic plasma simulations using multiple GPUs

Kinetic plasma simulations solve the Vlasov-Poisson or Vlasov-Maxwell equations to evolve scalar-variable distribution functions in position-velocity phase space and vector-variable electromagnetic fields in configuration space. The immense computational cost of evolving high-dimensional variables, and their large number of degrees of freedom, often limits the utility of continuum kinetic simulations and presents a challenge when it comes to accurately simulating real-world physical phenomena. To address this challenge, we present techniques that accelerate and minimize the computational work required for a scalable Vlasov-Poisson solver. We show theoretical hardware compute and communication bounds for solving a fourth-order finite-volume Vlasov-Poisson system. These bounds are then used to inform and evaluate the design of performance portable algorithms for a multiple graphics processing unit (GPU) accelerated version of the Vlasov-Poisson solver VCK-CPU [1]. We demonstrate that the multi-GPU Vlasov solver implementation, VCK-GPU, simultaneously minimizes required inter-process data transfer while also being bounded by the machine network performance limits. This results in an overall strong scaling speedup per timestep of up to 40x in three-dimensional phase space (one position, two velocity coordinates) and 54x in four dimensional phase space (two position, two velocity coordinates) and a 341x increase in simulation throughput of the GPU accelerated code over the existing CPU code. The GPU code is also able to weak scale up to 256 compute nodes and 1024 GPUs. In conclusion, we demonstrate that the improved compute performance enables exploring configurations which were previously computationally infeasible, including resolving fine-scale distribution function filamentation and multi-species dynamics with realistic electron-proton mass ratios.

Continuum kinetics↗

DOE OSTI2020

Quantum computation of silicon electronic band structure

Development of quantum architectures during the last decade has inspired hybrid classical–quantum algorithms in physics and quantum chemistry that promise simulations of fermionic systems beyond the capability of modern classical computers, even before the era of quantum computing fully arrives. Strong research efforts have been recently made to obtain minimal depth quantum circuits which could accurately represent chemical systems. Here, we show that unprecedented methods used in quantum chemistry, designed to simulate molecules on quantum processors, can be extended to calculate properties of periodic solids. In particular, we present minimal depth circuits implementing the variational quantum eigensolver algorithm and successfully use it to compute the band structure of silicon on a quantum machine for the first time. We are convinced that the presented quantum experiments performed on cloud-based platforms will stimulate more intense studies towards scalable electronic structure computation of advanced quantum materials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Model-based interface design for smart field-device integration

Operational complexity is ever-increasing for electric utilities that face challenges including integration of DERs, customer expectation of energy choices, the proliferation of non-utility-owned resources, new business models with energy service providers, and new technology with IT/OT convergence. To maintain and improve the quality of operations, planning, and decision-making in general, utilities need to manage and navigate the complexity. Managing complexity requires a modular, scalable, and flexible solution. Connecting large amounts of DERs and introducing new services requires increased grid control and evolving applications. In this paper, we show an approach utilizing model-based standardized interfaces that simplifies integration and deployment of new algorithms and smart field devices for interoperability across legacy or new systems. A modular design is presented for a reference implementation of widely used DNP3 and IEEE 2030.5 interfaces within an open-source, standards-based data integration platform for integration of smart field devices with independently developed, best-of-breed applications.

Model-driven development, system integration, smar↗

DOE OSTI2019

mystic - a brief introduction

The mystic framework enables the solving of difficult optimization problems through three major innovations: (1) plug-and-play component-based optimization algorithms, (2) the ability to dynamically construct and apply generalzed trnasforms, K , where x' = K(x) , and (3) workflows providing asynchronous execution and statefulness. These features, in conjunction with supporting packages pathos , pyina , and klepto , can provide massively-parallel scalable workflows for quickly solving optimization problems in complex nonlinear spaces. mystic can be used to simplify non-convex optimization problems by transforming away nonlinearities through user-built kernel transforms. This tutorial demonstrates using mystic for machine learning with automated dimensional-reduction, using embarrasingly parallel solver ensembles to find an accurate interpolated surrogate for a nonlinear surface, and the determination of worst-case bounds on expectation value of an objective function under uncertainty.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Machine Learning Classical Interatomic Potentials for Molecular Dynamics from First-Principles Training Data

The ever-increasing power of modern super-computers, along with the availability of highly scalable atomistic simulation codes, has begun to revolutionize predictive modeling of materials. In particular, molecular dynamics (MD) has led to breakthrough advances in diverse fields, including tribology, catalysis, sensing, and nanoparticle self-assembly. Furthermore, recent integration of MD simulations with X-ray characterization has demonstrated promise in real-time 3-D characterization of materials on the atomic scale. The popularity of MD is driven by its applicability at disparate length/time scales, ranging from ab initio MD (hundreds of atoms and tens of picoseconds) to all-atom classical MD (millions of atoms over microseconds), and coarse-grained (CG) models (micrometers and tens of microseconds). Nevertheless, a substantial gap persists between AIMD, which is highly accurate but restricted to extremely small sizes, and those based on classical force fields (atomistic and CG) with limited accuracy but access to larger length/time scales. The accuracy and predictive power of classical MD simulations is dictated by the empirical force fields, and their capability to capture the relevant physics. Here, we discuss some of our recent work on the use of machine learning (ML) to combine the accuracy and flexibility of electronic structure calculations with the speed of classical potentials. Our ML framework attempts to bridge the significant gulf that exists between the handful of research groups that develop new interatomic potential models (often requiring several years of effort), and the increasingly large user community from academia and industry that applies these models. Our data-driven approach represents significant departure from the status quo and involves several steps including generation and manipulation of extensive training data sets through electronic structure calculations, defining novel potential functional forms, employing state-of-the-art ML algorithms to formulate highly optimized training procedures, and subsequently developing user-friendly workflow tools integrating these algorithms on high-performance computers (HPCs). Our ML approach shows marked success in developing force fields for a wide range of materials from metals, oxides, nitrides, and heterointerfaces to two-dimensional (2D) materials.

Chan, Henry↗

DOE OSTI2023

Distributed memory, GPU accelerated Fock construction for hybrid, Gaussian basis density functional theory

With the growing reliance of modern supercomputers on accelerator-based architecture such a graphics processing units (GPUs), the development and optimization of electronic structure methods to exploit these massively parallel resources has become a recent priority. While significant strides have been made in the development GPU accelerated, distributed memory algorithms for many modern electronic structure methods, the primary focus of GPU development for Gaussian basis atomic orbital methods has been for shared memory systems with only a handful of examples pursing massive parallelism. Here in this work, we present a set of distributed memory algorithms for the evaluation of the Coulomb and exact exchange matrices for hybrid Kohn–Sham DFT with Gaussian basis sets via direct density-fitted (DF-J-Engine) and seminumerical (sn-K) methods, respectively. The absolute performance and strong scalability of the developed methods are demonstrated on systems ranging from a few hundred to over one thousand atoms using up to 128 NVIDIA A100 GPUs on the Perlmutter supercomputer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Axom

The Axom library consists of n collection of software components that provide core computer science infrastructure capabilities that can be shared by diverse high performance computing (HPC) applications. The current set of capabilities that Axom provides includes: Customizable support for error/warning and diagnostic message reporting and coordination among components of integrated applications (e.g., physics packages, libraries, etc.); Scalable parallel aggregation and filtering of message logging; In memory datastore for hierarchical, mesh-aware simulation data. The datastore supports data description, allocation, deallocation. parallel l/0, etc; Mesh data model abstractions that enable the development of mesh-based computational algorithms that work with many diverse, application· specific mesh types; and Computational geometry primitives for developing high performance parallel algorithms based on spatial geometry and meshes, e.g., spatial acceleration data structures, sets, maps, relations, etc.

Hornung, RichardD.↗

DOE OSTI2019

MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver

@e present MAESTROeX, a massively parallel solver for low Mach number astrophysical flows. The underlying low Mach number equation set allows for efficient, long-time integration for highly subsonic flows compared to compressible approaches. MAESTROeX is suitable for modeling full spherical stars as well as well as planar simulations of dynamics within localized regions of a star, and can robustly handle several orders of magnitude of density and pressure stratification. Previously, we have described the development of the predecessor of MAESTROeX, called MAESTRO, in a series of papers. Here, we present a new, greatly simplified temporal integration scheme that retains the same order of accuracy as our previous approaches. We also explore the use of alternative spatial mapping of the one-dimensional base state onto the full Cartesian grid. The code leverages the new AMReX software framework for block-structured adaptive mesh refinement (AMR) applications, allowing for scalability to large fractions of leadership-class machines. Finally, using our previous studies on the convective phase of single-degenerate progenitor models of SNe Ia as a guide, we characterize the performance of the code and validate the new algorithmic features. Like MAESTRO, MAESTROeX is fully open source.

79 ASTRONOMY AND ASTROPHYSICS↗