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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.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.

Hsu, Darren J.↗
DOE OSTI2023

HipBone: A performance-portable graphics processing unit-accelerated C++ version of the NekBone benchmark

We present hipBone, an open-source performance-portable proxy application for the Nek5000 (and NekRS) computational fluid dynamics applications. HipBone is a fully GPU-accelerated C++ implementation of the original NekBone CPU proxy application with several novel algorithmic and implementation improvements which optimize its performance on modern fine-grain parallel GPU accelerators. Our optimizations include a conversion to store the degrees of freedom of the problem in assembled form in order to reduce the amount of data moved during the main iteration and a portable implementation of the main Poisson operator kernel. We demonstrate near-roofline performance of the operator kernel on three different modern GPU accelerators from two different vendors. We present a novel algorithm for splitting the application of the Poisson operator on GPUs which aggressively hides MPI communication required for both halo exchange and assembly. Our implementation of nearest-neighbor MPI communication then leverages several different routing algorithms and GPU-Direct RDMA capabilities, when available, which improves scalability of the benchmark. We demonstrate the performance of hipBone on three different clusters housed at Oak Ridge National Laboratory, namely, the Summit supercomputer and the Frontier early-access clusters, Spock and Crusher. Our tests demonstrate both portability across different clusters and very good scaling efficiency, especially on large problems.

Computer Science↗
NASA NTRS2024

EdgeCortix SAKURA-I Machine-Learning, PCIe Accelerator SEE Heavy Ion Test Report

To enable autonomy in space, machine-learning and computer vision applications become invaluable for sensor processing. However, these algorithms are computationally complex and unfeasible for many embedded central processing units (CPUs) and usually require external coprocessors, such as graphics processing units (GPUs) or accelerators specific to the application, including application specific integrated circuits (ASICs). In power-constrained systems, GPUs tend to consume more power than is acceptable (>40W), so lower-power accelerators have shown promise to provide the performance needed under spacecraft constraints. For radiation engineers, developing methodologies that can properly test CPUs, GPUs, and accelerators, and enable comparisons between them remains a necessary complication to solve as the devices become more complex. The methodology in this test aims to be a start in developing a baseline single-event effect (SEE) test for client-device machine learning accelerators. This category of devices do not host their own operating system. This testing campaign is a continuation of a previous 200 MeV proton test performed in January 2024. This report covers two heavy ion tests of the SAKURA-I card: one in April 2024, and one in June 2024. Additional data was needed after the April test due to ion-range issues experienced at higher linear-energy transfers (LETs). These range issues are described in more detail in Section 8. This experiment characterizes SEEs and data error susceptibility of the EdgeCortix SAKURA-I machine-learning accelerator under heavy ions. The device was monitored for single event upsets (SEUs) and single event functional interrupts (SEFIs) at the Lawrence Berkeley National Laboratory’s 88-inch cyclotron. The SAKURA-I board accelerates machine-learning inference applications on a host computer through a PCIex16 connection. For the purposes of devising an end to end automated analysis workflow for this experiment, the YOLO-V5 and SSD300 objection-detection models, and the ResNet-50, EfficientNet, and MobileNetV2 image classification models were used as a representative suite of analytical machine-learning models.

Seth S Roffe↗
NASA NTRS2019

"Sensor Web Evolution - Webs of Webs for NASA Science - Focus on small Uninhabited Aerial Systems (sUAS)"

This paper will describe the evolution of information collection, derivation and delivery mechanisms in webs of NASA sensor webs, with a focus on recent advancements in small Uninhabited Aerial Systems (sUAS). I will discuss the movement to "Fog Computing", also known as Edge Computing. Fog Computing facilitates the distribution of common operations and networking between edge devices and cloud computing facilities, optimizing the production of actionable intelligence. Initially, sUASs utilized onboard data collection as standard, with minimal data downloaded directly. Information products were derived in conventional computational environments, generally desk top computers, and information products made available to the Science Community in weeks or months. With the increased availability, and increasingly lower costs, of beyond line of sight (BLOS) satellite based communication, transmission rates and data volumes increased, and processing migrated to Cloud based services. Contemporary sUASs are moving some of that information product derivation to on vehicle services, and are creating a distributed Cloud/Fog environment. I will describe the technological advances that have made this possible, including low power multi-core Central Processing Units (CPU), and, more recently, the availability of high end Graphical Processing Units (GPU) that consume only a few watts. Intelligent system software, leveraging these hardware advances, finally allows for information product generation on-board, rather than simple data collection. Additionally, intelligent flight control systems now support mutual vehicle to vehicle collaboration, allowing sUASs to create ad-hoc sensor webs on demand, as required. Also discussed will be the lessons learned by the Authors' development of data systems for NASA's large High Altitude Long Endurance (HALE) UASs like Predator and Global Hawk, and how those lessons are being applied to sUAS development. This paper will focus on application, rather a deep dive into the technology, and will highlight improving data management through these new technologies.

Sensor Web↗
NASA NTRS2019

AladynPi – Adaptive Neural Network Molecular Dynamics Simulation Code with Physically Informed Potential: Computational Materials Mini-Application

This report provides an overview and description of commands used in the Computational Materials mini-application, AladynPi. AladynPi is an extension of a previously released mini-application, Aladyn (https://github.com/nasa/aladyn; Yamakov, V.I., and Glaessgen, E.H., NASA/TM-2018-220104). Aladyn and AladynPi are basic molecular dynamics codes written in FORTRAN 2003, which are designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to efficiently reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of the more expensive quantum mechanics-based calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory method. An input for the ANN is a set of structure coefficients, characterizing the local atomic environment of each atom, for which the atomic energy is obtained in the ANN inference process. In Aladyn, the ANN gives directly the energy of interatomic interactions. In AladynPi, the ANN gives optimized parameters for a predefined empirical function, known as bond-order-potential (BOP). The parameterized BOP function is then used to calculate the energy. AladynPi code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing manycore architectures based on graphic processing units (GPUs). The effort is supported by the High Performance Computing incubator (HPCi) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗
NASA NTRSDate not supplied

UASs in the VOG/Edge/FOG Sensor Web Environment

This paper will describe the evolution of information collection, derivation and delivery mechanisms in sensor webs utilizing Uninhabited Aerial Systems (UAS).We will discuss the movement to "Fog Computing", also known as Edge Computing. Fog Computing facilitates the distribution of common operations and networking between edge devices and cloud computing facilities, optimizing the production of actionable intelligence. Initially, UASs utilized onboard data collection as standard, with minimal data downloaded directly. Information products were derived in conventional computational environments, generally desk top computers, and information products made available to the Science Community in weeks or months. With the increased availability, and increasingly lower costs, of beyond line of sight (BLOS) satellite based communication, transmission rates and data volumes increased, and processing migrated to Cloud based services. Contemporary UASs are moving some of that information product derivation to on vehicle services, and are creating a distributed Cloud/Fog environment. The Author will describe the technological advances that have made this possible, including low power multi-core Central Processing Units (CPU), and, more recently, the availability of high end Graphical Processing Units (GPU) that consume only a few watts. Intelligent system software, leveraging these hardware advances, finally allows for information product generation on-board, rather than simple data collection. Additionally, intelligent flight control systems now support mutual vehicle to vehicle collaboration, allowing UASs to create ad-hoc sensor webs on demand, as required. Also discussed will be the lessons learned by the Authors' development of data systems for NASA's large High Altitude Long Endurance (HALE) UASs like Predator and Global Hawk, and how those lessons are being applied to other UAS development This paper will focus on applications, rather a deep dive into the technology, and will highlight improving data management through these new technologies.

UAS↗
NASA NTRS2018

Aladyn - Adaptive Neural Network Molecular Dynamics Simulation Code: Computational Materials Mini-Application

This report provides an overview and commands description of the Computational Materials mini-application, Aladyn. Aladyn is a simple molecular dynamics code written in FORTRAN 2008, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of quantum mechanics-based energy calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. The Aladyn code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing many core architectures based on graphic processing units (GPUs). The effort is related to the High Performance Computing Incubator (HPCI) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗
DOE OSTI2023

DeePMD-kit v2: A software package for deep potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Toward active disruption avoidance via real-time estimation of the safe operating region and disruption proximity in tokamaks

This paper describes a real-time capable algorithm for identifying the safe operating region around a tokamak operating point. The region is defined by a convex set of linear constraints, from which the distance of a point from a disruptive boundary can be calculated. The disruptivity of points is calculated from an empirical machine learning predictor that generates the likelihood of disruption. While the likelihood generated by such empirical models can be compared to a threshold to trigger a disruption mitigation system, the safe operating region calculation enables active optimization of the operating point to maintain a safe margin from disruptive boundaries. The proposed algorithm is tested using a random forest disruption predictor fit on data from DIII-D. The safe operating region identification algorithm is applied to historical data from DIII-D showing the evolution of disruptive boundaries and the potential impact of optimization of the operating point. Real-time relevant execution times are made possible by parallelizing many of the calculation steps and implementing the algorithm on a graphics processing unit. Lastly, a real-time capable algorithm for optimizing the target operating point within the identified constraints is also proposed and simulated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Vidyut3d: A GPU accelerated fluid solver for non-equilibrium plasmas on adaptive grids

We present the numerical methods, programming methodology, verification, and performance assessment of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit (CPU+GPU) architectures, in this work. Our plasma fluid model solves the coupled conservation equations for species transport, electrostatic Poisson and electron temperature on adaptive Cartesian grids. Our solver is written using performance portable adaptive-grid/particle management library, AMReX, and is portable over widely available vendor specific GPU architectures. We present verification of our solver using method of manufactured solutions that indicate formal second order accuracy with central diffusion and fifth-order weighted-essentially-non-oscillatory (WENO) advection scheme. We also verify our solver with published literature on capacitive discharges and atmospheric pressure streamer propagation. We demonstrate the use of our solver on two 3D simulation cases: an atmospheric streamer propagation in Ar-H2 mixtures and a low pressure three-electrode radio frequency reactor. Our performance studies on three different CPU+GPU architectures indicate ~ 150-400X speed-up using AMD and NVIDIA GPUs per time step compared to a single CPU core for a 4 million cell simulation with 15 species.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

GPU acceleration of hybrid functional calculations in the SPARC electronic structure code

We present a Graphics Processing Unit (GPU)-accelerated version of the real-space SPARC electronic structure code for performing hybrid functional calculations in generalized Kohn–Sham density functional theory. In particular, we develop a batch variant of the recently formulated Kronecker product-based linear solver for the simultaneous solution of multiple linear systems. We then develop a modular, math kernel based implementation for hybrid functionals on NVIDIA architectures, where computationally intensive operations are offloaded to the GPUs, while the remaining workload is handled by the central processing units (CPUs). Considering bulk and slab examples, we demonstrate that GPUs enable up to 8× speedup in node-hours and 80× in core-hours compared to CPU-only execution, reducing the time to solution on V100 GPUs to around 300 s for a metallic system with over 6000 electrons, and significantly reducing the computational resources required for a given wall time.

Kohn-Sham density functional theory↗
DOE OSTI2020

High-performance computing in water resources hydrodynamics

In this work, we present a vision of future water resources hydrodynamics codes that can fully utilize the strengths of modern high-performance computing. The advances to computing power, formerly driven by the improvement of central processing unit processors, now focus on parallel computing and, in particular, the use of graphics processing units (GPUs). However, this shift to a parallel framework requires refactoring the code to make efficient use of the data as well as changing even the nature of the algorithm that solves the system of equations. These concepts along with other features such as the precision for the computations, dry regions management, and input/output data are analyzed in this paper. A 2D multi-GPU flood code applied to a large-scale test case is used to corroborate our statements and ascertain the new challenges for the next-generation parallel water resources codes.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2018

A Single Thread to Fortran Coarray Transition Process for the Control Algorithm in the Space Radiation Code HZETRN

Exa-scale computing is the direction by industry and government are going to generate solutions to problems they deem necessary. Computing hardware is being developed to achieve the transition from Peta-scale to Exa-scale with more CPUs (Central Processing Units) that have more cores per CPU and more accelerators (GPGPUs (General Purpose Graphics Processing Units) and MICs (Many Integrated Cores)) per node. To fully utilize the hardware available now and in the future, algorithms must become multi-threaded. There are a few methods to generate multi-threaded software such as MPI (Message Passing Interface) and OpenMP (Multi-Processing) / OpenACC (ACCelerator). This paper concentrates on using Coarray Fortran to convert the Fortran 95 based HZETRN (High Z and Energy TRaNsport) code's control algorithm from a single threaded code to a multithreaded code. The resultant Coarray code was 32.5 times faster (with a theoretical speed-up of 74.5 times) than the single threaded version on the hardware tested, as reliable as the Fortran 95 version, and, as it uses native Fortran, was as maintainable as the Fortran 95 version. The Coarray code can be maintained by the same project engineers and scientists who created the original single threaded code. This transition process can be utilized on a C language based code with a compiler that has the UPC (Universal Parallel C) extensions to C.

Singleterry, Robert C., Jr.↗
DOE OSTI2023

Thermo4PFM: Facilitating Phase-field simulations of alloys with thermodynamic driving forces

Phase-field modeling is a popular front-tracking approach used to model solidification. Its time-evolution equations are often coupled to alloy composition and/or thermal diffusion in high-resolution multiphysics approaches. Materials thermodynamic properties tabulated in CALPHAD databases can be used for phase-field modeling to parameterize bulk energies of alloys. In addition, they can be naturally integrated into models such as the Kim-Kim-Suzuki (KKS) model where driving forces depend on the differences between chemical potentials of co-existing phases. In that case, a small system of coupled nonlinear equations needs to be solved at every point in space where the phase-field order parameter is to be updated and evolved in time. Here we present Thermo4PFM, a solver for the KKS equations for binary and ternary alloys, with two or three phases, and parameterized with CALPHAD models. Thermo4PFM is open source, written in C++, and can take advantage of Graphics Processing Units (GPU) accelerators. Using OpenMP offload capabilities for C++ classes, an excellent performance is demonstrated on GPU using the LLVM compiler. CALPHAD data is read from simple JSON files using an open source parser from the boost library.

36 MATERIALS SCIENCE↗
NASA NTRS2018

Standardizing GPU Radiation Test Approaches

While some Graphical Processing Units (GPUs) are discrete components (i.e.GTX1050), others take the form of an IP block or embedded engine within a System on Chip (SoC) device such as the Qualcomm Snapdragon"TM" 820 which contains a Qualcomm Adreno"TM" 530 GPU. Within this device are various functional blocks which can be exercised with software payloads. NVidia's Jetson"TM" TX1 SoC is provided on a System on Module (SOM). Within it are Central Processing Unit (CPU) cores and an nVidia GPU which can be accessed similarly to a discrete GPU coprocessor. While the packaging is different, each one of these GPUs needs to be tested using the same standardized code.

Single Event Effects (SEE)↗
DOE OSTI2021

A survey of software implementations used by application codes in the Exascale Computing Project

The US Department of Energy Office of Science and the National Nuclear Security Administration initiated the Exascale Computing Project (ECP) in 2016 to prepare mission-relevant applications and scientific software for the delivery of the exascale computers starting in 2023. The ECP currently supports 24 efforts directed at specific applications and six supporting co-design projects. These 24 application projects contain 62 application codes that are implemented in three high-level languages—C, C++, and Fortran—and use 22 combinations of graphical processing unit programming models. The most common implementation language is C++, which is used in 53 different application codes. The most common programming models across ECP applications are CUDA and Kokkos, which are employed in 15 and 14 applications, respectively. This article provides a survey of the programming languages and models used in the ECP applications codebase that will be used to achieve performance on the future exascale hardware platforms.

97 MATHEMATICS AND COMPUTING↗