SEARCH · Engineering Papers

Results for “Parallel optimization”

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 253 records · Page 14

All sources NASA NTRS DOE OSTI

DOE OSTI2022

A second-order distributed memory parallel fast sweeping method for the Eikonal equation

The Eikonal equation is used to calculate wave propagation and distance fields, and due to its complexity requires numerical treatment for its solution. In this work, we present a second-order distributed memory parallel fast sweeping method. The second-order solution switches on a two-point stencil when two upwind points are available, and reverts to first-order otherwise. In all examples, the second-order method improves the solution over the first-order, allowing for significant savings in memory while achieving the same accuracy. Parallelization over distributed memory saw good weak scaling with optimal convergence. The computational time for second-order was approximately 2.5 times slower than first-order, where the largest amount of mesh points ran on 144 cores (512 GB) was ≈20 billion. The savings in memory from the second-order method combined with the distributed memory algorithm result in the ability to solve problems much larger than are possible with the serial first-order method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Vertex Reordering for Real-world Graphs and Applications: An Empirical Evaluation

Vertex reordering is a way to improve locality in graph computations. Given an input (or ``natural'') order, reordering aims to compute an alternate permutation of the vertices that is aimed at maximizing a locality-based objective. Given decades of research on this topic, there are tens of graph reordering schemes, and there are also several linear arrangement ``gap'' measures for treatment as objectives. However, a comprehensive empirical analysis of the efficacy of the ordering schemes against the different gap measures, and against real-world applications is currently lacking. In this study, we present an extensive empirical evaluation of up to 11 ordering schemes, taken from different classes of approaches, on a set of 34 real-world graphs emerging from different application domains. Our study is presented in two parts: a) a thorough comparative evaluation of the different ordering schemes on their effectiveness to optimize different linear arrangement gap measures, relevant to preserving locality; and b) extensive evaluation of the impact of the ordering schemes on two real-world, parallel graph applications, namely, community detection and influence maximization. Our studies show a significant divergence among the ordering schemes (up to $40\times$ between the best and the poor) in their effectiveness to reduce the gap measures; and a wide ranging impact of the ordering schemes on various aspects including application runtime (up to $4\times$), memory and cache use, load balancing, and parallel work and efficiency. The comparative study also help reveal the nuances of a parallel environment (compared to serial) on the ordering schemes and their role in optimizing applications.

Barik, Reet↗

DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Reductive Analysis with Compiler-Guided Large Language Models for Input-Centric Code Optimizations

Input-centric program optimization aims to optimize code by considering the relations between program inputs and program behaviors. Despite its promise, a long-standing barrier for its adoption is the difficulty of automatically identifying critical features of complex inputs. This paper introduces a novel technique, reductive analysis through compiler-guided Large Language Models (LLMs), to solve the problem through a synergy between compilers and LLMs. It uses a reductive approach to overcome the scalability and other limitations of LLMs in program code analysis. The solution, for the first time, automates the identification of critical input features without heavy instrumentation or profiling, cutting the time needed for input identification by 44× (or 450× for local LLMs), reduced from 9.6 hours to 13 minutes (with remote LLMs) or 77 seconds (with local LLMs) on average, making input characterization possible to be integrated into the workflow of program compilations. Optimizations on those identified input features show similar or even better results than those identified by previous profiling-based methods, leading to optimizations that yield 92.6% accuracy in selecting the appropriate adaptive OpenMP parallelization decisions, and 20-30% performance improvement of serverless computing while reducing resource usage by 50-60%.

Input-Centric Optimization↗

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 OSTI2023

Progress and R/D challenges for FCC-ee SRF

The FCC-ee machines present a huge challenge for the RF systems, which need to be adapted to very diverse beam conditions going from moderate energy and high current for the Z machine to high energy and low beam current for the ttbar. This inverse scaling results naturally from a fixed budget for the synchrotron radiation, which the SRF cavities need to compensate. A global solution was elaborated for the FCC Conceptual Design Report (Abada in Eur Phys J Spec Top 228):261–623, 2019), and is referred here as the baseline. Recently, further studies have led to a new optimized baseline, still based on traditional elliptical cavities. In parallel, a novel concept, named the Slotted Waveguide ELLiptical (SWELL), was proposed with the potential of greatly simplified logistics and reduced costs. Under several aspects, all these changes call for enhanced performance of the RF systems. A vigorous R&D program has therefore continued since the publication of the CDR, with the aim of pushing the performance and demonstrating the feasibility of a more advanced baseline and, more recently, of the SWELL option. The progress and challenges of this ambitious program were presented in the dedicated SRF sessions at FCC week 2022 and are summarized in this paper.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Separate Effects Validation for Subcooled Boiling in CTF

In 2010, the U.S. Department of Energy created its first Energy Innovation Hub, which is focused on developing high-fidelity and high-resolution modeling and simulation (M&S) tools for modeling of light water reactors (LWRs). This hub, the Consortium for Advanced Simulation of LWRs (CASL), has developed an LWR simulation tool called the Virtual Environment for Reactor Applications (VERA). The multi-physics capability of VERA is achieved through the coupling of single-physics codes, including CTF (the CASL version of Coolant Boiling in Rod Arrays— Three Field (COBRA-TF)), Michigan Parallel Characteristics Transport (MPACT), BISON, and Materials Performance and Optimization (MPO) Advanced Model for Boron Analysis (MAMBA). As part of its M&S efforts, CASL has identified various challenge problems, including Crud Induced Power Shift (CIPS), Crud-Induced Localized Corrosion (CILC), Pellet-Cladding Interaction (PCI), and Departure from Nucleate Boiling (DNB). This work addresses CASL milestone L2:VVI.P19.03, which focuses on uncertainty quantification of crud, which is relevant to both CIPS and CILC. This is achieved through an analysis and separate effects validation of the thermal hydraulic phenomenon known as subcooled boiling. As part of this work, various sources of experimental data are examined and compared to different options for empirical modeling of subcooled boiling. Through this analysis, a complete understanding of the underlying models and their implementation details are understood. A subset of these data are incorporated into a separate effects validation study of CTF. The Westinghouse Advanced Loop Tester (WALT) and Rohsenow experiments are modeled, and it is shown that the newly-implemented Gorenflo correlation is more accurate than the existing Chen and Thom correlations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Useability and Optimization Improvements in MOOSE

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to this broad use, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work transcribed in this report was conducted in direct support of the simulation tools and has already been deployed or will be deployed in the coming months. The capabilities were implemented in the same order as they are covered in this report: increased support of face variables, arbitrary spatial and temporal evaluation of material properties, and the addition of a triangular meshing library in libMesh.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

NEAMS Technical Area Support in MOOSE

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to this ubiquity, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work transcribed in this report was conducted in direct support of the simulation tools and has already been deployed. The capabilities outlined in this report include a factor of 10^4 improvement in dependency resolution speed, sorting of user objects, ability to compute residuals and Jacobians together, transfer fixes, support for the mortar method in finite volume discretizations, addition of generalized advection schemes for fluid simulations, 10^2 speedup in some Griffin simulations due to a new matrix-only solve type, and much more.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

User-oriented Improvements in the MOOSE Framework in Support of Multiphysics Simulation

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to this ubiquity, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work transcribed in this report was conducted in direct support of the simulation tools and has already been deployed or will be deployed in the coming months. The capabilities were implemented in the same order as they are covered in this report: chainable execution objects or executors, support for transfers between same-level applications in a coupling scheme, support for boundary/subdomain restricted transfers, support for transfers between applications with different coordinate or unit systems, support for MOOSE applications in the NEAMS Workbench, deployment of the MOOSE application of the Idaho National Laboratory (INL) high-performance computing (HPC) OnDemand platform, the addition of a triangular meshing library in libMesh, and increased support of face variables.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

NEAMS Technical Area Support in MOOSE

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

NEAMS Technical Area Support in MOOSE

The MOOSE framework is a foundational capability used by the NEAMS program to create over 15 different simulation tools for advanced nuclear reactors. Due to this ubiquity, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and other new capabilities. The work transcribed in this report was conducted in direct support of the simulation tools and has already been deployed. The capabilities outlined in this report include enabling selective polynomial basis refinement, implementing a custom convergence system, building a scalable preconditioner for saddle-point problems, and much more.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Increased accuracy of multiphysics simulations through flexible execution, transient algorithms, and modular physics

The MOOSE framework is a foundational capability used by the NEAMS program to create over 15 different simulation tools for advanced nuclear reactors. Due to MOOSE’s broad use, improvements to the framework in support of modeling and simulation goals are critical to the program. Such improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work described in this report was conducted in direct support of the simulation tools and has already been deployed. The capabilities were implemented in the same order as they are covered in this report: multiple time integrators in the same input file, initial design of framework Components, an input file Application block, extension of NetGen to 3D geometries in MOOSE, and deployment of executors in the multi-system paradigm. These five additions are fundamental capabilities that will be leveraged by many NEAMS applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Usability and Optimization Improvements in MOOSE

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to MOOSE’s broad use, improvements to the framework in support of modeling and simulation goals are critical to the program. Such improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work described in this report was conducted in direct support of the simulation tools and has already been deployed. The capabilities were implemented in the same order as they are covered in this report: multiple nonlinear systems in the same input file, implementation of generic field transfers and other transfer system enhancements, support for stateful material property redistribution for adaptivity and distributed meshes, and dynamic linking and loading of individually compiled applications. These four additions are fundamental capabilities that will be leveraged by many NEAMS applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Improvements to MOOSE user workflow through polyhedral elements, automation, and concise physics syntax

The MOOSE framework is a foundational capability used by the NEAMS program to create over 15 different simulation tools for advanced nuclear reactors. Due to MOOSE's broad use, improvements to the framework in support of modeling and simulation goals are critical to the program. Such improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and new capabilities. The work described in this report was conducted in direct support of NEAMS tools and includes: addition of support for polyhedral elements, incorporation of mesh smoothers for mesh repair, integration of the Physics and ActionComponents systems, expansion of the Convergence system, and exploration of automated input file generation. These five areas of development are fundamental capabilities that will be leveraged by many NEAMS applications.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2025

NEAMS Technical Area Support in MOOSE

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to this ubiquity, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and other new capabilities. The work described in this report was conducted in direct support of the simulation tools and has already been deployed. The capabilities outlined in this report include implementing hash table matrix assembly for efficient sparsity pattern construction for contact in BISON, developing re-step testing infrastructure for ensuring the viability of overlapping domain coupling between SAM and Pronghorn, allowing unique preconditioners for single-input multi-system solves, supporting multi-system in MOOSE’s workhorse executioners, and many more smaller feature enhancements and bug fixes.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2025

ARM-IRL: Adaptive Resilience Metric Quantification Using Inverse Reinforcement Learning

The resilience of safety-critical systems is gaining importance due to the rise in cyber and physical threats, especially within critical infrastructure. Traditional static resilience metrics may not capture dynamic system states, leading to inaccurate assessments and ineffective responses to cyber threats. This work aims to develop a data-driven, adaptive method for resilience metric learning. We propose a data-driven approach using inverse reinforcement learning (IRL) to learn a single, adaptive resilience metric. The method infers a reward function from expert control actions. Unlike previous approaches using static weights or fuzzy logic, this work applies adversarial inverse reinforcement learning (AIRL), training a generator and discriminator in parallel to learn the reward structure and derive an optimal policy. The proposed approach is evaluated on multiple scenarios: optimal communication network rerouting, power distribution network reconfiguration, and cyber–physical restoration of critical loads using the IEEE 123-bus system. The adaptive, learned resilience metric enables faster critical load restoration in comparison to conventional RL approaches.

97 MATHEMATICS AND COMPUTING↗