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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 1,315 records · Page 73

Toward Large-Scale Image Segmentation on Summit

Semantic segmentation of images is an important computer vision task that emerges in a variety of application domains such as medical imaging, robotic vision and autonomous vehicles to name a few. While these domain-specific image analysis tasks involve relatively small image sizes (~ 10 2 × 10 2 ), there are many applications that need to train machine learning models on image data with extents that are orders of magnitude larger (~10 4 × 10 4 ). Training deep neural network (DNN) models on large extent images is extremely memory-intensive and often exceeds the memory limitations of a single graphical processing unit, a hardware accelerator of choice for computer vision workloads. Here, an efficient, sample parallel approach to train U-Net models on large extent image data sets is presented. Its advantages and limitations are analyzed and near-linear strong-scaling speedup demonstrated on 256 nodes (1536 GPUs) of the Summit supercomputer. Using a single node of the Summit supercomputer, an early evaluation of a recently released model parallel framework called GPipe is demonstrated to deliver ~ 2X speedup in executing a U-Net model with an order of magnitude larger number of trainable parameters than reported before. Performance bottlenecks for pipelined training of U-Net models are identified and mitigation strategies to improve the speedups are discussed. Together, these results open up the possibility of combining both approaches into a unified scalable pipelined and data parallel algorithm to efficiently train U-Net models with very large receptive fields on data sets of ultra-large extent images.

Seal, Sudip↗

Elviz – exploration of metagenome assemblies with an interactive visualization tool

Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, including both the sequences themselves and metadata describing their abundance, assembly, predicted functional characteristics and environmental parameters. The ability to explore these data visually is critically important to meaningful biological interpretation. Current genomics applications cannot effectively integrate sequence data, assembly metadata, and annotation to support both genome and community-level inquiry. Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing. Compared to the current alternative of generating a succession of static figures, Elviz can greatly accelerate the speed of metagenome analysis. Elviz can be used to explore both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genome Institute (JGI). Elviz is freely available at http://genome.jgi.doe.gov/viz and runs on most current web-browsers.

59 BASIC BIOLOGICAL SCIENCES↗

GALSPEC: A Tool for Computing the Spectra of Star-Forming Galaxies of Low Metallicity

The far-ultraviolet spectral region is rich in diagnostics of star formation in galaxies; it gives information not only about the star-forming complex, but also about the dust and circumstellar gas. We have therefore developed a tool, called GALSPEC, for computing far-UV spectra of star-forming galaxies. The user controls the process through a graphical user interface (GUI) by specifying the input parameters for the stars, dust, and gas. GALSPEC computes the integrated spectrum of a star-forming complex, given the rate of star formation, metallicity (0.2 Z(sub \odot) or 0.5 Z(sub \odot)), and IMF upper mass limit. To compute the integrated spectrum, GALSPEC makes use of a library of stellar spectra composed of observed spectra from HST and model spectra calculated with the TLUSTY/SYNSPEC program (Hubeny & Lanz 1995). GALSPEC then applies wavelength-dependent extinction according to Calzetti's starburst extinction law. The mechanical luminosity from massive stars and supernovae sweeps up interstellar material thereby forming an expanding shell with a central cavity. GALSPEC computes the absorption spectrum of the shell using the CLOUDSPEC program (Hubeny 2000), a combination of Ferland's CLOUDY program and SYNSPEC.

Heap, S. R.↗

Advanced Potential Energy Surfaces for Molecular Simulation

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). Here in this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. Finally, we have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent developments of NASTRAN pre- amd post-processors: Response spectrum analysis (RESPAN) and interactive graphics (GIFTS)

Two specific NASTRAN preprocessors and postprocessors are examined. A postprocessor for dynamic analysis and a graphical interactive package for model generation and review of resuls are presented. A computer program that provides response spectrum analysis capability based on data from NASTRAN finite element model is described and the GIFTS system, a graphic processor to augment NASTRAN is introduced.

Hirt, E. F.↗

A Simple GPU-Accelerated Two-Dimensional MUSCL-Hancock Solver for Ideal Magnetohydrodynamics

We describe our experience using NVIDIA's CUDA (Compute Unified Device Architecture) C programming environment to implement a two-dimensional second-order MUSCL-Hancock ideal magnetohydrodynamics (MHD) solver on a GTX 480 Graphics Processing Unit (GPU). Taking a simple approach in which the MHD variables are stored exclusively in the global memory of the GTX 480 and accessed in a cache-friendly manner (without further optimizing memory access by, for example, staging data in the GPU's faster shared memory), we achieved a maximum speed-up of approx. = 126 for a sq 1024 grid relative to the sequential C code running on a single Intel Nehalem (2.8 GHz) core. This speedup is consistent with simple estimates based on the known floating point performance, memory throughput and parallel processing capacity of the GTX 480.

graphics processing units↗

Computational Investigation of the Effect of Chemistry on Mars Retropropulsion Environments using a Massively Parallel GPU Approach

In this work, we investigate the effects of chemistry on a human-scale Mars lander concept using scale-resolving computational fluid dynamics (CFD) with finite-rate chemistry and a graphics processing unit (GPU)-enabled implementation of the NASA FUN3D flow solver, enabling run-times of a few days for the simulations presented. Simulations are carried out on Summit at Oak Ridge Leadership Computing Facility using thousands of GPUs. Retropropulsion ground tests require significant compromises on physical scale, instrumentation, configuration, and environments. Ground tests of retropropulsion configurations thus far have neglected effects of chemistry due to physical constraints of wind tunnel models and facilities; most experiments use inert simulant gases at low temperatures. As such, a strong reliance on high-fidelity computational analyses such as those presented in this work is required to expand the knowledge of retropropulsion aerodynamics. An overview of the GPU approach will be presented. Results are compared to a previous scaled perfect gas (air) campaign.

retropropulsion↗

Integrating aerodynamic surface modeling for computational fluid dynamics with computer aided structural analysis, design, and manufacturing

This presentation will discuss the development of a NASA Geometry Exchange Specification for transferring aerodynamic surface geometry between LeRC systems and grid generation software used for computational fluid dynamics research. The proposed specification is based on a subset of the Initial Graphics Exchange Specification (IGES). The presentation will include discussion of how the NASA-IGES standard will accommodate improved computer aided design inspection methods and reverse engineering techniques currently being developed. The presentation is in viewgraph format.

Thorp, Scott A.↗

GPU-resident sparse direct linear solvers for alternating current optimal power flow analysis

Integrating renewable resources within the transmission grid at a wide scale poses significant challenges for economic dispatch as it requires analysis with more optimization parameters, constraints, and sources of uncertainty. This motivates the investigation of more efficient computational methods, especially those for solving the underlying linear systems, which typically take more than half of the overall computation time. In this paper, we present our work on sparse linear solvers that take advantage of hardware accelerators, such as graphical processing units (GPUs), and improve the overall performance when used within economic dispatch computations. We treat the problems as sparse, which allows for faster execution but also makes the implementation of numerical methods more challenging. We present the first GPU-native sparse direct solver that can execute on both AMD and NVIDIA GPUs. We demonstrate significant performance improvements when using high-performance linear solvers within alternating current optimal power flow (ACOPF) analysis. Furthermore, we demonstrate the feasibility of getting significant performance improvements by executing the entire computation on GPU-based hardware. Finally, we identify outstanding research issues and opportunities for even better utilization of heterogeneous systems, including those equipped with GPUs.

24 POWER TRANSMISSION AND DISTRIBUTION↗

TRL Computer System User’s Guide

We have developed a wiki-based graphical user-interface system that implements our technology readiness level (TRL) uncertainty models. This document contains the instructions for using this wiki-based system.

Engel, David W.↗

1989 Computational Fluid Dynamics Highlights

This video presents highlights of 1989's CFD graphics, which show shuttle flight problems, F-18 flows, artificial heart, and rotorstrator with more complex blades.

Source record↗

Graphical Displays Assist In Analysis Of Failures

Failure Environment Analysis Tool (FEAT) computer program enables people to see and better understand effects of failures in system. Uses digraph models to determine what will happen to system if set of failure events occurs and to identify possible causes of selected set of failures. Digraphs or engineering schematics used. Also used in operations to help identify causes of failures after they occur. Written in C language.

Pack, Ginger↗

Kernel fusion in atomistic spin dynamics simulations on Nvidia GPUs using tensor core

In atomistic spin dynamics simulations, the time cost of constructing the space- and time-displaced pair correlation function in real space increases quadratically as the number of spins N, leading to significant computational effort. The GEMM subroutine can be adopted to accelerate the calculation of the dynamical spin-spin correlation function, but the computational cost of simulating large spin systems (>40000 spins) on CPUs remains expensive. In this work, we perform the simulation on the graphics processing unit (GPU), a hardware solution widely used as an accelerator for scientific computing and deep learning. Here we show that GPUs can accelerate the simulation up to 25-fold compared to multi-core CPUs when using the GEMM subroutine on both. To hide memory latency, we fuse the element-wise operation into the GEMM kernel using CUTLASS that can improve the performance by 26% ~ 33% compared to implementation based on cuBLAS. Furthermore, we perform the on-the-fly calculation in the epilogue of the GEMM subroutine to avoid saving intermediate results on global memory, which makes the large-scale atomistic spin dynamics simulation feasible and affordable.

97 MATHEMATICS AND COMPUTING↗

Design of teleoperation system with a force-reflecting real-time simulator

We developed a force-reflecting teleoperation system that uses a real-time graphic simulator. This system eliminates the effects of communication time delays in remote robot manipulation. The simulator provides the operator with predictive display and feedback of computed contact forces through a six-degree of freedom (6-DOF) master arm on a real-time basis. With this system, peg-in-hole tasks involving round-trip communication time delays of up to a few seconds were performed at three support levels: a real image alone, a predictive display with a real image, and a real-time graphic simulator with computed-contact-force reflection and a predictive display. The experimental results indicate the best teleoperation efficiency was achieved by using the force-reflecting simulator with two images. The shortest work time, lowest sensor maximum, and a 100 percent success rate were obtained. These results demonstrate the effectiveness of simulated-force-reflecting teleoperation efficiency.

Hirata, Mitsunori↗

Stabilized bases for high-order, interpolation semi-Lagrangian, element-based tracer transport

In a computational fluid model of the atmosphere, the advective transport of trace species, or tracers, can be computationally expensive. For efficiency, models often use semi-Lagrangian advection methods. High-order interpolation semi-Lagrangian (ISL) methods, in particular, can be extremely efficient, if the problem of property preservation specific to them can be addressed. Atmosphere models often use geometrically and logically nonuniform grids for efficiency and, as a result, element-based discretizations. Such grids and discretizations make stability a particular problem for ISL methods. Generally, high-order, element-based ISL methods that use the natural polynomial interpolant associated with a nodal finite-element discretization are unstable. Here, we derive new bases having order of accuracy up to nine, with positive nodal weights, that stabilize the element-based ISL method. We use these bases to construct the linear advection operator in the property-preserving Interpolation Semi-Lagrangian Element-based Transport (Islet) method. Then we discuss key software implementation details. Finally, we show performance results for the Energy Exascale Earth System Model's atmosphere dynamical core, comparing the original and new transport methods. These simulations used up to 27,600 Graphical Processing Units (GPU) on the Oak Ridge Leadership Computing Facility's Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SU-D-206-02: Evaluation of Partial Storage of the System Matrix for Cone Beam Computed Tomography Using a GPU Platform

Purpose: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons’ trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. Methods: We propose an optimized implementation of the Siddon’s algorithm using graphics processing units (GPUs) with a novel data storage scheme. The algorithm computes a part of the system matrix on demand, typically, for one projection angle. The proposed method was enhanced with accelerating options: storage of larger subsets of the system matrix, systematic reuse of data via geometric symmetries, an arithmetic-rich parallel code and code configuration via machine learning. It was tested on geometries mimicking a cone beam CT acquisition of a human head. To realistically assess the execution time, the ray-tracing routines were integrated into a regularized Poisson-based reconstruction algorithm. The proposed scheme was also compared to a different approach, where the system matrix is fully pre-computed and loaded at reconstruction time. Results: Fast ray-tracing of realistic acquisition geometries, which often lack spatial symmetry properties, was enabled via the proposed method. Ray-tracing interleaved with projection and backprojection operations required significant additional time. In most cases, ray-tracing was shown to use about 66 % of the total reconstruction time. In absolute terms, tracing times varied from 3.6 s to 7.5 min, depending on the problem size. The presence of geometrical symmetries allowed for non-negligible ray-tracing and reconstruction time reduction. Arithmetic-rich parallel code and machine learning permitted a modest reconstruction time reduction, in the order of 1 %. Conclusion: Partial system matrix storage permitted the reconstruction of higher 3D image grid sizes and larger projection datasets at the cost of additional time, when compared to the fully pre-computed approach. This work was supported in part by the Fonds de recherche du Quebec - Nature et technologies (FRQ-NT). The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council of Canada (Grant No. 432290).

60 APPLIED LIFE SCIENCES↗