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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Supporting the Development of Resilient Message Passing Applications using Simulation

An emerging aspect of high-performance computing (HPC) hardware/software co-design is investigating performance under failure. The work in this paper extends the Extreme-scale Simulator (xSim), which was designed for evaluating the performance of message passing interface (MPI) applications on future HPC architectures, with fault-tolerant MPI extensions proposed by the MPI Fault Tolerance Working Group. xSim permits running MPI applications with millions of concurrent MPI ranks, while observing application performance in a simulated extreme-scale system using a lightweight parallel discrete event simulation. The newly added features offer user-level failure mitigation (ULFM) extensions at the simulated MPI layer to support algorithm-based fault tolerance (ABFT). The presented solution permits investigating performance under failure and failure handling of ABFT solutions. The newly enhanced xSim is the very first performance tool that supports ULFM and ABFT.

Engelmann, Christian↗
DOE OSTI2016

Application of an Evolutionary Algorithm for Parameter Optimization in a Gully Erosion Model

Herein we demonstrate how to use model optimization to determine a set of best-fit parameters for a landform model simulating gully incision and headcut retreat. To achieve this result we employed the Covariance Matrix Adaptation Evolution Strategy (CMA-ES), an iterative process in which samples are created based on a distribution of parameter values that evolve over time to better fit an objective function. CMA-ES efficiently finds optimal parameters, even with high-dimensional objective functions that are non-convex, multimodal, and non-separable. We ran model instances in parallel on a high-performance cluster, and from hundreds of model runs we obtained the best parameter choices. This method is far superior to brute-force search algorithms, and has great potential for many applications in earth science modeling. We found that parameters representing boundary conditions tended to converge toward an optimal single value, whereas parameters controlling geomorphic processes are defined by a range of optimal values.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

A scalable, fully implicit algorithm for the reduced two-field low-β extended MHD model

Here, we demonstrate a scalable fully implicit algorithm for the two-field low-β extended MHD model. This reduced model describes plasma behavior in the presence of strong guide fields, and is of significant practical impact both in nature and in laboratory plasmas. The model displays strong hyperbolic behavior, as manifested by the presence of fast dispersive waves, which make a fully implicit treatment very challenging. In this study, we employ a Jacobian-free Newton–Krylov nonlinear solver, for which we propose a physics-based preconditioner that renders the linearized set of equations suitable for inversion with multigrid methods. As a result, the algorithm is shown to scale both algorithmically (i.e., the iteration count is insensitive to grid refinement and timestep size) and in parallel in a weak-scaling sense, with the wall-clock time scaling weakly with the number of cores for up to 4096 cores. For a 4096 × 4096 mesh, we demonstrate a wall-clock-time speedup of ~6700 with respect to explicit algorithms. The model is validated linearly (against linear theory predictions) and nonlinearly (against fully kinetic simulations), demonstrating excellent agreement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Utilizing many-core accelerators for halo and center finding within a cosmology simulation

Efficiently finding and computing statistics about “halos” (regions of high density) are essential analysis steps for N-body cosmology simulations. However, in state-of-the-art simulation codes, these analysis operators do not currently take advantage of the shared-memory data-parallelism available on multi-core and many-core architectures. The Hybrid / Hardware Accelerated Cosmology Code (HACC) is designed as an MPI+X code, but the analysis operators are parallelized only among MPI ranks, because of the difficulty in porting different X implementations (e.g., OpenMP, CUDA) across all architectures on which it is run. In this paper, we present portable data-parallel algorithms for several variations of halo finding and halo center finding algorithms. These are implemented with the PISTON component of the VTK-m framework, which uses Nvidia's Thrust library to construct data-parallel algorithms that allow a single implementation to be compiled to multiple backends to target a variety of multi-core and many-core architectures. Finally, we compare the performance of our halo and center finding algorithms against the original HACC implementations on the Moonlight, Stampede, and Titan supercomputers. The portability of Thrust allowed the same code to run efficiently on each of these architectures. On Titan, the performance improvements using our code have enabled halo analysis to be performed on a very large data set (81923 particles across 16,384 nodes of Titan) for which analysis using only the existing CPU algorithms was not feasible.

Sewell, Christopher↗
DOE OSTI2017

Two-Level Convergence Theory for Multigrid Reduction in Time (MGRIT)

Here we develop a two-grid convergence theory for the parallel-in-time scheme known as multigrid reduction in time (MGRIT), as it is implemented in the open-source package [XBraid: Parallel Multigrid in Time, http://llnl.gov/casc/xbraid]. MGRIT is a scalable and multilevel approach to parallel-in-time simulations that nonintrusively uses existing time-stepping schemes, and in a specific two-level setting it is equivalent to the widely known parareal algorithm. The goal of this paper is twofold. First, we present a two-level MGRIT convergence analysis for linear problems where the spatial discretization matrix can be diagonalized, and then apply this analysis to our two basic model problems, the heat equation and the advection equation. One important assumption is that the coarse and fine time-grid propagators can be diagaonalized by the same set of eigenvectors, which is often the case when the same spatial discretization operator is used on the coarse and fine time grids. In many cases, the MGRIT algorithm is guaranteed to converge, and we demonstrate numerically that the theoretically predicted convergence rates are sharp in practice for our model problems. Second, we explore how the convergence of MGRIT compares to the stability of the chosen time-stepping scheme. In particular, we demonstrate that a stable time-stepping scheme does not necessarily imply convergence of MGRIT, although MGRIT with FCF-relaxation always converges for the diffusion dominated problems considered here.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

MO-F-CAMPUS-I-04: Characterization of Fan Beam Coded Aperture Coherent Scatter Spectral Imaging Methods for Differentiation of Normal and Neoplastic Breast Structures

Purpose: This study intends to characterize the spectral and spatial resolution limits of various fan beam geometries for differentiation of normal and neoplastic breast structures via coded aperture coherent scatter spectral imaging techniques. In previous studies, pencil beam raster scanning methods using coherent scatter computed tomography and selected volume tomography have yielded excellent results for tumor discrimination. However, these methods don’t readily conform to clinical constraints; primarily prolonged scan times and excessive dose to the patient. Here, we refine a fan beam coded aperture coherent scatter imaging system to characterize the tradeoffs between dose, scan time and image quality for breast tumor discrimination. Methods: An X-ray tube (125kVp, 400mAs) illuminated the sample with collimated fan beams of varying widths (3mm to 25mm). Scatter data was collected via two linear-array energy-sensitive detectors oriented parallel and perpendicular to the beam plane. An iterative reconstruction algorithm yields images of the sample’s spatial distribution and respective spectral data for each location. To model in-vivo tumor analysis, surgically resected breast tumor samples were used in conjunction with lard, which has a form factor comparable to adipose (fat). Results: Quantitative analysis with current setup geometry indicated optimal performance for beams up to 10mm wide, with wider beams producing poorer spatial resolution. Scan time for a fixed volume was reduced by a factor of 6 when scanned with a 10mm fan beam compared to a 1.5mm pencil beam. Conclusion: The study demonstrates the utility of fan beam coherent scatter spectral imaging for differentiation of normal and neoplastic breast tissues has successfully reduced dose and scan times whilst sufficiently preserving spectral and spatial resolution. Future work to alter the coded aperture and detector geometries could potentially allow the use of even wider fans, thereby making coded aperture coherent scatter imaging a clinically viable method for breast cancer detection. United States Department of Homeland Security; Duke University Medical Center - Department of Radiology; Carl E Ravin Advanced Imaging Laboratories; Duke University Medical Physics Graduate Program.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Models of TCP in high-BDP environments and their experimental validation

In recent years, the computer networking community has seen a steady growth in bandwidth-delay products (BDPs). Several TCP variants were created to combat the shortcomings of legacy TCP when it comes to operation in high-BDP environments. These variants, among which are CUBIC, STCP, and H-TCP, have been extensively studied in some empirical contexts, and some analytical models exist for CUBIC and STCP. However, since these studies have been conducted, BDPs have risen even more, and new bulk data transfer tools have emerged that utilize multiple parallel TCP streams. In view of these new developments, it is imperative to revisit the question: Which congestion control algorithms are best adapted to current networking environments? In order to help resolve this question, we contribute the following: (i) using first principles, we develop a general throughput-prediction framework that takes into account buffer sizes and maximum window constraints; (ii) we validate the models using measurements and achieve low prediction errors; (iii) we note differences in TCP dynamics between two experimental configurations and find one of them to be significantly more deterministic than the other; we also find that CUBIC and H-TCP outperform STCP, especially when multiple streams are used; and (iv) we present preliminary results for modelling multiple TCP streams for CUBIC and STCP.

Vardoyan, G.↗
DOE OSTI2017

Multigroup Monte Carlo on GPUs: Comparison of history- and event-based algorithms

This article presents an investigation of the performance of different multigroup Monte Carlo transport algorithms on GPUs with a discussion of both history-based and event-based approaches. Several algorithmic improvements are introduced for both approaches. By modifying the history-based algorithm that is traditionally favored in CPU-based MC codes to occasionally filter out dead particles to reduce thread divergence, performance exceeds that of either the pure history-based or event-based approaches. The impacts of several algorithmic choices are discussed, including performance studies on Kepler and Pascal generation NVIDIA GPUs for fixed source and eigenvalue calculations. Single-device performance equivalent to 20–40 CPU cores on the K40 GPU and 60–80 CPU cores on the P100 GPU is achieved. Last, in addition, nearly perfect multi-device parallel weak scaling is demonstrated on more than 16,000 nodes of the Titan supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

molgw 1: Many-body perturbation theory software for atoms, molecules, and clusters

Here, we summarize the MOLGW code that implements density-functional theory and many-body perturbation theory in a Gaussian basis set. The code is dedicated to the calculation of the many-body self-energy within the GW approximation and the solution of the Bethe–Salpeter equation. These two types of calculations allow the user to evaluate physical quantities that can be compared to spectroscopic experiments. Quasiparticle energies, obtained through the calculation of the GW self-energy, can be compared to photoemission or transport experiments, and neutral excitation energies and oscillator strengths, obtained via solution of the Bethe–Salpeter equation, are measurable by optical absorption. The implementation choices outlined here have aimed at the accuracy and robustness of calculated quantities with respect to measurements. Furthermore, the algorithms implemented in MOLGW allow users to consider molecules or clusters containing up to 100 atoms with rather accurate basis sets, and to choose whether or not to apply the resolution-of-the-identity approximation. Finally, we demonstrate the parallelization efficacy of the MOLGW code over several hundreds of processors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

A Large Deviations Analysis of Certain Qualitative Properties of Parallel Tempering and Infinite Swapping Algorithms

Parallel tempering, or replica exchange, is a popular method for simulating complex systems. The idea is to run parallel simulations at different temperatures, and at a given swap rate exchange configurations between the parallel simulations. From the perspective of large deviations it is optimal to let the swap rate tend to infinity and it is possible to construct a corresponding simulation scheme, known as infinite swapping. In this paper we propose a novel use of large deviations for empirical measures for a more detailed analysis of the infinite swapping limit in the setting of continuous time jump Markov processes. Using the large deviations rate function and associated stochastic control problems we consider a diagnostic based on temperature assignments, which can be easily computed during a simulation. Here we show that the convergence of this diagnostic to its a priori known limit is a necessary condition for the convergence of infinite swapping. Finally, the rate function is also used to investigate the impact of asymmetries in the underlying potential landscape, and where in the state space poor sampling is most likely to occur.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

SU-E-T-160: Characterization and Monitoring of Linear Accelerator Gantry Radiation Isocenter Motion

Purpose: To characterize the motion of the radiation isocenter, over time, as a function of gantry rotation for multiple linear accelerators (linacs). Two semi-automated image-based quality control (QC) test workflows were designed to achieve this goal. Methods: The full QC-test workflow for motion characterization consisted of acquiring 16 megavoltage images at 8 gantry angles of a ball-bearing suspended off the end of the couch. Performance constancy was assessed using a shortened QC-test workflow which consisted of imaging a cube phantom placed on the couch (5 images at 4 gantry angles). Both workflows use an image processing algorithm to determine the field center and phantom position on each image and computed radiation isocenter motion as a function of gantry angle. Motion was characterized for 9 linacs of same model and performance monitored for 2 months on 3 linacs. Results: The maximum isocenter motion determined with the full-workflow for 9 linacs was within 0.38–0.79 mm. The shortened-workflow usually agreed within 0.1 mm with the full-workflow and the time required for these methods was about 4 and 15 min, respectively. For all linacs, the isocenter motion perpendicular to the gantry rotation plane followed a consistent pattern with maximum amplitude of 0.36–0.59 mm. In the gantry rotation plane, the variation among linacs was higher and the beam axis described a circle of up to 0.6 mm radius around the gantry axis of rotation (2 linacs). The radiation isocenter motion was stable as a function of time for the monitored linacs and was within ±0.1 mm of the average. Conclusion: Radiation isocenter motion parallel and perpendicular to the gantry rotation plane was characterized. In the gantry rotation plane, beam spot positioning adjustment might be used to reduce the observed radiation isocenter motion. A shortened-workflow was designed and enables performance monitoring over time.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

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 addition of Times and Positions systems, redesign of mechanical contact constraints to enable the augmented Lagrange algorithm, overhaul of the restart system, and incorporation of p-refinement in MOOSE.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A semi-automated algorithm for designing stellarator divertor and limiter plates and application to HSX

We present a semi-automated algorithm for designing three-dimensional divertor or limiter plates targeting low heat loads. The algorithm designs the plates in two stages: firstly, the parallel heat flux distribution is caught on vertically-inclined plates at one or several toroidal locations. Secondly, the power per unit area is reduced by stretching, tilting and bending the plates toroidally. Heat transport is modelled using the EMC3-Lite code, which uses an anisotropic diffusion model. We apply this scheme to HSX, a medium-sized stellarator located at the University of Wisconsin–Madison. Starting from the current machine with an extended vessel wall, we construct plates which are able to effectively catch and spread the heat for three different magnetic configurations. The scheme has a computational cost in the order of tens of CPU-minutes, making it a powerful tool for semi-automated plasma-facing component design in three-dimensional environments.

anisotropic diffusion↗
DOE OSTI2022

Development of a Single-Phase, Transient, Subchannel Code, within the MOOSE Multi-Physics Computational Framework

Subchannel codes have been widely used for thermal-hydraulics analyses in nuclear reactors. This paper details the development of a novel subchannel code within the Idaho National Laboratory’s (INL) Multi-physics Object Oriented Simulation Environment (MOOSE). MOOSE is a parallel computational framework targeted at the solution of systems of coupled, nonlinear partial differential equations, that often arise in the simulation of nuclear processes. As such, it includes codes/modules able to solve the multiple linear and nonlinear physics that describe a nuclear reactor, under normal operation conditions or accidents. This includes thermal-hydraulics, fuel performance, and neutronics codes, between others. A MOOSE-based subchannel code is a new addition to the fleet of INL-developed codes, based on the MOOSE framework. In this work, we present the derivation of the subchannel equations for a single-phase fluid, we proceed with the description of the algorithm that is used to solve these equations and describe how this algorithm was implemented within MOOSE. We also present how this code can be coupled to the BISON fuel performance code. Next, we verify the friction model and the turbulent mixing model. We calibrate the turbulent modeling parameters for momentum mixing and enthalpy mixing, C T , β. We validate the code using experimental results and last demonstrate the coupling capabilities using a simple example.

42 ENGINEERING↗
DOE OSTI2016

PetIGA: A framework for high-performance isogeometric analysis

We present PetIGA, a code framework to approximate the solution of partial differential equations using isogeometric analysis. PetIGA can be used to assemble matrices and vectors which come from a Galerkin weak form, discretized with Non-Uniform Rational B-spline basis functions. We base our framework on PETSc, a high-performance library for the scalable solution of partial differential equations, which simplifies the development of large-scale scientific codes, provides a rich environment for prototyping, and separates parallelism from algorithm choice. We describe the implementation of PetIGA, and exemplify its use by solving a model nonlinear problem. To illustrate the robustness and flexibility of PetIGA, we solve some challenging nonlinear partial differential equations that include problems in both solid and fluid mechanics. Lastly, we show strong scaling results on up to 4096 cores, which confirm the suitability of PetIGA for large scale simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Scaling Up Data-Parallel Analytics Platforms: Linear Algebraic Operation Cases

Linear algebraic operations such as matrix manipulations form the kernel of many machine learning and other crucial algorithms. Scaling up as well as scaling out such algorithms are key to supporting large scale data analysis that require efficient processing over millions of data samples. To this end, we present, ARION, a hardware acceleration based approach for scaling-up individual tasks of Spark, a popular data-parallel analytics platform. We support both linear algebraic operations of between two dense matrices, and between sparse and dense matrices in distributed environments. ARION provides a flexible control of acceleration according to matrix density, along with efficient scheduling based on runtime resource utilization. We demonstrate the benefit of our approach for general matrix multiplication operations over large matrices with up to four billion elements by using Gramian matrix computation that is commonly used in machine learning. Experiments show that our approach achieves more than 2× and 1.5× end-to-end performance speedups for dense and sparse matrices, respectively, and up to 57.04× faster computation compared to MLlib, a state of the art Spark-based implementation. This work is sponsored in part by the NSF under the grants: CNS-1565314, CNS-1405697, and CNS-1615411. The manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Xu, Luna↗
DOE OSTI2020

Localized Exponential Time Differencing Method for Shallow Water Equations: Algorithms and Numerical Study

Here, we explore the performance of the exponential time differencing (ETD) method applied to the rotating shallow water equations. Comparing with explicit time stepping of the same order accuracy in time, the ETD algorithms could reduce the computational time in many cases by allowing the use of large time step sizes while still maintaining numerical stability. To accelerate the ETD simulations, we propose a localized approach that synthesizes the ETD method and overlapping domain decomposition. By dividing the original problem into many subdomain problems of smaller sizes and solving them locally, the proposed approach could speed up the calculation of matrix exponential vector products. Several standard test cases for shallow water equations of one or multiple layers are considered. The results show great potential of the localized ETD method for high-performance computing because each subdomain problem can be naturally solved in parallel at every time step.

58 GEOSCIENCES↗
DOE OSTI2021

Dakota A Multilevel Parallel Object-Oriented Framework for Design Optimization Parameter Estimation Uncertainty Quantification and Sensitivity Analysis (V.6.14) (Theory Manual)

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗