Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Parallelism”

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.

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

At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Portable Parallel Algorithms and Frameworks for Exascale Graph Analytics

Graphs (or networks) are a tool used to model the interactions among various entities. Efficiently processing large graphs has recently attracted significant attention due to the applications of graphs in various domains, such as biology, chemistry, and cyber-security. Analyzing the structure and properties of these graphs is an important component of many scientific computing pipelines. With the explosion in the volume of data, graphs have become very large and can contain hundreds of billions of vertices and trillions of edges. Therefore, it is crucial to develop high-performance methods to enable graph analysis to be done quickly and energy-efficiently. Furthermore, these solutions should be highly parallel in order to take advantage of modern parallel machines. However, designing efficient solutions is not enough. With the wide variety of computing environments available, each with different programmability and performance characteristics, it is necessary to develop solutions that are portable in terms of both performance (i.e., provide theoretical guarantees) and programmability (i.e., provide high level abstractions).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A Parallel Graph Environment for Real-World Data Analytics Workflows

Economic competitiveness and national security depend increasingly on the insightful analysis of large data sets. The diversity of real-world data sources and analytic workflows impose challenging hardware and software requirements for parallel graph platforms. The irregular nature of graph methods is not supported well by the deep memory hierarchies of conventional distributed systems, requiring new processor and runtime system designs to tolerate memory and synchronization latencies. Moreover, the efficiency of relational table operations and matrix computations are not attainable when data is stored in common graph data structures. In this paper, we present HAGGLE, a high-performance, scalable data analytics platform. The platform’s hybrid data model supports a variety of distributed, thread-safe data structures, parallel programming constructs, and persistent and streaming data. An abstract runtime layer enables us to map the stack to conventional, distributed computer systems with accelerators. The runtime uses multithreading, active messages, and data aggregation to hide memory and synchronization latencies on large-scale systems.

Graph Analytics↗
DOE OSTI2021

Applying Time-Parallelization to Turbulent Flows

Parallelization of the temporal domain is explored for the solution of turbulent flows. Multigrid reduction-in-time (MGRIT) is used to advance the large-scale fluid dynamics in time sequentially on the coarsest space-time grid but propagate the information in time parallel on all other levels. The goal of this process is to accurately and efficiently resolve the coarse-scale turbulence structure and use that to drive the fine-scales of the turbulent flow. The extra forcing from nonlinear multigrid facilitates the coupling and interaction between fine and coarse scales, through which the multiscale nonlinear physics is properly captured. Adaptive mesh refinement is employed to finely resolve only the regions with strong gradients, which provides further computational efficiency. The underlying computational fluid dynamics solver is a fourth-order finite-volume scheme with the standard 4-stage Runge-Kutta method. An advanced approach is devised and implemented to enable MGRIT to solve highly turbulent flows successfully. Furthermore, the method is applied to solve a Taylor-Green vortex problem and a doubleshear-layer turbulent mixing flow. Results are promising, validating that MGRIT with the filtering approach has the potential to efficiently solve general turbulent flows.

Computational Fluid Dynamics↗
DOE OSTI2022

Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light

As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Oblique instability of quasi-parallel whistler waves in the presence of cold and warm electron populations

Whistler waves propagating nearly parallel to the ambient magnetic field experience a nonlinear instability due to transverse currents when the background plasma has a population of sufficiently low energy electrons. Intriguingly, this nonlinear process may generate oblique electrostatic waves, including whistlers near the resonance cone with properties resembling oblique chorus waves in the Earth’s magnetosphere. Focusing on the generation of oblique whistlers, earlier analysis of the instability is extended here to the case where low-energy background plasma consists of both a “cold” population with energy of a few eV and a “warm” electron component with energy of the order of 100 eV. This is motivated by spacecraft observations in the Earth’s magnetosphere where oblique chorus waves were shown to interact resonantly with the warm electrons. The main new results are: 1) the instability producing oblique electrostatic waves is sensitive to the shape of the electron distribution at low energies. In the whistler range of frequencies, two distinct peaks in the growth rate are typically present for the model considered: a peak associated with the warm electron population at relatively low wavenumbers and a peak associated with the cold electron population at relatively high wavenumbers; 2) overall, the instability producing oblique whistler waves near the resonance cone persists (with a reduced growth rate) even in the cases where the temperature of the cold population is relatively high, including cases where cold population is absent and only the warm population is included; 3) particle-in-cell simulations show that the instability leads to heating of the background plasma and formation of characteristic plateau and beam features in the parallel electron distribution function in the range of energies resonant with the instability. The plateau/beam features have been previously detected in spacecraft observations of oblique chorus waves. However, they have been attributed to external sources and have been proposed to be the mechanism generating oblique chorus. In the present scenario, the causality link is reversed and the instability generating oblique whistler waves is shown to be a possible mechanism for formation of the plateau and beam features.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Enabling Parallel Performance and Portability of Solid Mechanics Simulations Across CPU and GPU Architectures

Efficiently simulating solid mechanics is vital across various engineering applications. As constitutive models grow more complex and simulations scale up in size, harnessing the capabilities of modern computer architectures has become essential for achieving timely results. This paper presents advancements in running parallel simulations of solid mechanics on multi-core CPUs and GPUs using a single-code implementation. This portability is made possible by the C++ matrix and array (MATAR) library, which interfaces with the C++ Kokkos library, enabling the selection of fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. MATAR simplifies the transition from Fortran to C++ and Kokkos, making it easier to modernize legacy solid mechanics codes. We applied this approach to modernize a suite of constitutive models and to demonstrate substantial performance improvements across different computer architectures. This paper includes comparative performance studies using multi-core CPUs along with AMD and NVIDIA GPUs. Results are presented using a hypoelastic–plastic model, a crystal plasticity model, and the viscoplastic self-consistent generalized material model (VPSC-GMM). The results underscore the potential of using the MATAR library and modern computer architectures to accelerate solid mechanics simulations.

Morgan, Nathaniel (ORCID:0000000276118449)↗
DOE OSTI2016

SUPPRESSION OF PARALLEL TRANSPORT IN TURBULENT MAGNETIZED PLASMAS AND ITS IMPACT ON THE NON-THERMAL AND THERMAL ASPECTS OF SOLAR FLARES

The transport of the energy contained in electrons, both thermal and suprathermal, in solar flares plays a key role in our understanding of many aspects of the flare phenomenon, from the spatial distribution of hard X-ray emission to global energetics. Motivated by recent RHESSI observations that point to the existence of a mechanism that confines electrons to the coronal parts of flare loops more effectively than Coulomb collisions, we here consider the impact of pitch-angle scattering off turbulent magnetic fluctuations on the parallel transport of electrons in flaring coronal loops. It is shown that the presence of such a scattering mechanism in addition to Coulomb collisional scattering can significantly reduce the parallel thermal and electrical conductivities relative to their collisional values. We provide illustrative expressions for the resulting thermoelectric coefficients that relate the thermal flux and electrical current density to the temperature gradient and the applied electric field. We then evaluate the effect of these modified transport coefficients on the flare coronal temperature that can be attained, on the post-impulsive-phase cooling of heated coronal plasma, and on the importance of the beam-neutralizing return current on both ambient heating and the energy loss rate of accelerated electrons. We also discuss the possible ways in which anomalous transport processes have an impact on the required overall energy associated with accelerated electrons in solar flares.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

He{sup 2+} HEATING VIA PARAMETRIC INSTABILITIES OF PARALLEL PROPAGATING ALFVÉN WAVES WITH AN INCOHERENT SPECTRUM

The preferential heating of heavy ions in the solar corona and solar wind has been a long-standing hot topic. In this paper we use a one-dimensional hybrid simulation model to investigate the heating of He{sup 2+} particles during the parametric instabilities of parallel propagating Alfvén waves with an incoherent spectrum. The evolution of the parametric instabilities has two stages and involves the heavy ion heating during the entire evolution. In the first stage, the density fluctuations are generated by the modulation of the pump Alfvén waves with a spectrum, which then results in rapid coupling with the pump Alfvén waves and the cascade of the magnetic fluctuations. In the second stage, each pump Alfvén wave decays into a forward density mode and a backward daughter Alfvén mode, which is similar to that of a monochromatic pump Alfvén wave. In both stages the perpendicular heating of He{sup 2+} particles occurs. This is caused by the cyclotron resonance between He{sup 2+} particles and the high-frequency magnetic fluctuations, whereas the Landau resonance between He{sup 2+} particles and the density fluctuations leads to the parallel heating of He{sup 2+} particles. The influence of the drift velocity between the protons and the He{sup 2+} particles on the heating of He{sup 2+} particles is also discussed in this paper.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

MAGNETICALLY DOMINATED PARALLEL INTERSTELLAR FILAMENTS IN THE INFRARED DARK CLOUD G14.225-0.506

The infrared dark cloud G14.225-0.506 (IRDC G14.2) displays a remarkable complex of parallel dense molecular filaments projected on the plane of the sky. Previous studies of dust emission and molecular lines have speculated whether magnetic fields could have played an important role in the formation of such elongated structures, which are hosts to numerous young stellar sources. In this work we have conducted a vast polarimetric survey at optical and near-infrared wavelengths in order to study the morphology of magnetic field lines in IRDC G14.2 through the observation of background stars. The orientation of interstellar polarization, which traces magnetic field lines, is perpendicular to most of the filamentary features within the cloud. Additionally, the larger-scale molecular cloud as a whole exhibits an elongated shape also perpendicular to magnetic fields. Estimates of magnetic field strengths indicate values in the range 320–550 μ G, which allow sub-alfvénic conditions, but do not prevent the gravitational collapse of hub–filament structures, which in general are close to the critical state. These characteristics suggest that magnetic fields played the main role in regulating the collapse from large to small scales, leading to the formation of series of parallel elongated structures. The morphology is also consistent with numerical simulations that show how gravitational instabilities develop when subjected to strong magnetic fields. Finally, the results corroborate the hypothesis that strong support from internal magnetic fields might explain why the cloud seems to be contracting on a timescale 2–3 times longer than what is expected from a free-fall collapse.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

nbodykit: An Open-source, Massively Parallel Toolkit for Large-scale Structure

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface, we provide parallel implementations of many commonly used algorithms in LSS. nbodykit is both an interactive and scalable piece of scientific software, performing well in a supercomputing environment while still taking advantage of the interactive tools provided by the Python ecosystem. Existing functionality includes estimators of the power spectrum, two- and three-point correlation functions, a friends-of-friends grouping algorithm, mock catalog creation via the halo occupation distribution technique, and approximate N-body simulations via the FastPM scheme. The package also provides a set of distributed data containers, insulated from the algorithms themselves, that enables nbodykit to provide a unified treatment of both simulation and observational data sets. nbodykit can be easily deployed in a high-performance computing environment, overcoming some of the traditional difficulties of using Python on supercomputers. We provide performance benchmarks illustrating the scalability of the software. The modular, component-based approach of nbodykit allows researchers to easily build complex applications using its tools. The package is extensively documented at http://nbodykit.readthedocs.io, which also includes an interactive set of example recipes for new users to explore. As open-source software, we hope nbodykit provides a common framework for the community to use and develop in confronting the analysis challenges of future LSS surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Evidence for Field-parallel Electron Acceleration in Solar Flares

It is proposed that the coincidence of higher brightness and upward electric current observed by Janvier et al. during a flare indicates electron acceleration by field-parallel potential drops sustained by extremely strong field-aligned currents of the order of 10{sup 4} A m{sup −2}. A consequence of this is the concentration of the currents in sheets with widths of the order of 1 m. The high current density suggests that the field-parallel potential drops are maintained by current-driven anomalous resistivity. The origin of these currents remains a strong challenge for theorists.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Parallel Diffusion Coefficient of Energetic Charged Particles in the Inner Heliosphere from the Turbulent Magnetic Fields Measured by Parker Solar Probe

Diffusion coefficients of energetic charged particles in turbulent magnetic fields are a fundamental aspect of diffusive transport theory but remain incompletely understood. In this work, we use quasi-linear theory to evaluate the spatial variation of the parallel diffusion coefficient κ ∥ from the measured magnetic turbulence power spectra in the inner heliosphere. We consider the magnetic field and plasma velocity measurements from Parker Solar Probe made during Orbits 5–13. The parallel diffusion coefficient is calculated as a function of radial distance from 0.062 to 0.8 au, and the particle energy from 100 keV to 1 GeV. We find that κ ∥ increases exponentially with both heliocentric distance and energy of particles. The fluctuations in κ ∥ are related to the episodes of large-scale magnetic structures in the solar wind. By fitting the results, we also provide an empirical formula of κ ∥ = (5.16 ± 1.22) × 10 18 r 1.17 ± 0.08 E 0.71 ± 0.02 (cm 2 s -1 ) in the inner heliosphere, which can be used as a reference in studying the transport and acceleration of solar energetic particles as well as the modulation of cosmic rays.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Electron Influence on the Parallel Proton Firehose Instability in 10-moment, Multifluid Simulations

Instabilities driven by pressure anisotropy play a critical role in modulating the energy transfer in space and astrophysical plasmas. For the first time, we simulate the evolution and saturation of the parallel proton firehose instability using a multifluid model without adding artificial viscosity. These simulations are performed using a 10-moment, multifluid model with local and gradient relaxation heat-flux closures in high-β proton–electron plasmas. When these higher-order moments are included and pressure anisotropy is permitted to develop in all species, we find that the electrons have a significant impact on the saturation of the parallel proton firehose instability, modulating the proton pressure anisotropy as the instability saturates. Even for lower β's more relevant to heliospheric plasmas, we observe a pronounced electron energization in simulations using the gradient relaxation closure. Our results indicate that resolving the electron pressure anisotropy is important to correctly describe the behavior of multispecies plasma systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Simulating coupled surface–subsurface flows with ParFlow v3.5.0: capabilities, applications, and ongoing development of an open-source, massively parallel, integrated hydrologic model

Surface flow and subsurface flow constitute a naturally linked hydrologic continuum that has not traditionally been simulated in an integrated fashion. Recognizing the interactions between these systems has encouraged the development of integrated hydrologic models (IHMs) capable of treating surface and subsurface systems as a single integrated resource. IHMs are dynamically evolving with improvements in technology, and the extent of their current capabilities are often only known to the developers and not general users. This article provides an overview of the core functionality, capability, applications, and ongoing development of one open-source IHM, ParFlow. ParFlow is a parallel, integrated, hydrologic model that simulates surface and subsurface flows. ParFlow solves the Richards equation for three-dimensional variably saturated groundwater flow and the two-dimensional kinematic wave approximation of the shallow water equations for overland flow. The model employs a conservative centered finite-difference scheme and a conservative finite-volume method for subsurface flow and transport, respectively. ParFlow uses multigrid-preconditioned Krylov and Newton–Krylov methods to solve the linear and nonlinear systems within each time step of the flow simulations. The code has demonstrated very efficient parallel solution capabilities. ParFlow has been coupled to geochemical reaction, land surface (e.g., the Common Land Model), and atmospheric models to study the interactions among the subsurface, land surface, and atmosphere systems across different spatial scales. This overview focuses on the current capabilities of the code, the core simulation engine, and the primary couplings of the subsurface model to other codes, taking a high-level perspective.

58 GEOSCIENCES↗
DOE OSTI2012

Reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application

Methods, apparatus, and products are disclosed for reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application that include: beginning, by each compute node, performance of a blocking operation specified by the parallel application, each compute node beginning the blocking operation asynchronously with respect to the other compute nodes; reducing, for each compute node, power to one or more hardware components of that compute node in response to that compute node beginning the performance of the blocking operation; and restoring, for each compute node, the power to the hardware components having power reduced in response to all of the compute nodes beginning the performance of the blocking operation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Performing an allreduce operation on a plurality of compute nodes of a parallel computer

Methods, apparatus, and products are disclosed for performing an allreduce operation on a plurality of compute nodes of a parallel computer. Each compute node includes at least two processing cores. Each processing core has contribution data for the allreduce operation. Performing an allreduce operation on a plurality of compute nodes of a parallel computer includes: establishing one or more logical rings among the compute nodes, each logical ring including at least one processing core from each compute node; performing, for each logical ring, a global allreduce operation using the contribution data for the processing cores included in that logical ring, yielding a global allreduce result for each processing core included in that logical ring; and performing, for each compute node, a local allreduce operation using the global allreduce results for each processing core on that compute node.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

A Fast Parallel Simulation Code for Interaction between Proto-Planetary Disk and Embedded Proto-Planets: Implementation for 3D Code

We develop a 3D simulation code for interaction between the proto-planetary disk and embedded proto-planets. The protoplanetary disk is treated as a three-dimensional (3D), self-gravitating gas whose motion is described by the locally isothermal Navier-Stokes equations in a spherical coordinate centered on the star. The differential equations for the disk are similar to those given in Kley et al. (2009) with a different gravitational potential that is defined in Nelson et al. (2000). The equations are solved by directional split Godunov method for the inviscid Euler equations plus operator-split method for the viscous source terms. We use a sub-cycling technique for the azimuthal sweep to alleviate the time step restriction. We also extend the FARGO scheme of Masset (2000) and modified in Li et al. (2001) to our 3D code to accelerate the transport in the azimuthal direction. Furthermore, we have implemented a reduced 2D (r, {theta}) and a fully 3D self-gravity solver on our uniform disk grid, which extends our 2D method (Li, Buoni, & Li 2008) to 3D. This solver uses a mode cut-off strategy and combines FFT in the azimuthal direction and direct summation in the radial and meridional direction. An initial axis-symmetric equilibrium disk is generated via iteration between the disk density profile and the 2D disk-self-gravity. We do not need any softening in the disk self-gravity calculation as we have used a shifted grid method (Li et al. 2008) to calculate the potential. The motion of the planet is limited on the mid-plane and the equations are the same as given in D'Angelo et al. (2005), which we adapted to the polar coordinates with a fourth-order Runge-Kutta solver. The disk gravitational force on the planet is assumed to evolve linearly with time between two hydrodynamics time steps. The Planetary potential acting on the disk is calculated accurately with a small softening given by a cubic-spline form (Kley et al. 2009). Since the torque is extremely sensitive to the position of the planet, we adopt the corotating frame that allows the planet moving only in radial direction if only one planet is present. This code has been extensively tested on a number of problems. For the earthmass planet with constant aspect ratio h = 0.05, the torque calculated using our code matches quite well with the the 3D linear theory results by Tanaka et al. (2002). The code is fully parallelized via message-passing interface (MPI) and has very high parallel efficiency. Several numerical examples for both fixed planet and moving planet are provided to demonstrate the efficacy of the numerical method and code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2012

A Self Consistent Multiprocessor Space Charge Algorithm that is Almost Embarrassingly Parallel

We present a space charge code that is self consistent, massively parallelizeable, and requires very little communication between computer nodes; making the calculation almost embarrassingly parallel. This method is implemented in the code COSY Infinity where the differential algebras used in this code are important to the algorithm's proper functioning. The method works by calculating the self consistent space charge distribution using the statistical moments of the test particles, and converting them into polynomial series coefficients. These coefficients are combined with differential algebraic integrals to form the potential, and electric fields. The result is a map which contains the effects of space charge. This method allows for massive parallelization since its statistics based solver doesn't require any binning of particles, and only requires a vector containing the partial sums of the statistical moments for the different nodes to be passed. All other calculations are done independently. The resulting maps can be used to analyze the system using normal form analysis, as well as advance particles in numbers and at speeds that were previously impossible.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗