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At least 811 records · Page 45

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DOE OSTI2020

Direction-optimizing Label Propagation and its Application for Community Detection

Label Propagation is a machine learning algorithm typically used for classification. It has also been found to be an effective method for detecting communities in networks. It has two attractive features as a community detection method: it has nearly linear runtime and it requires no \textit{a priori} community information. We propose a new Direction Optimizing Label Propagation Algorithm (DOLPA) that relies on the use of {\em frontiers} and alternates between label {\em push} and label {\em pull} operations to enhance the performance of LPA. Specifically, DOLPA has parameters for tuning the processing order of vertices in a graph. This reduces the number of edges visited and improves the quality of solution. We apply DOLPA to community detection and present the design and implementation of the algorithm as well as its shared-memory parallelization using OpenMP. Empirically, we evaluate our algorithm using synthetic graphs as well as real-world networks. Compared with the state-of-art \textit{Parallel Label Propagation} algorithm, we achieve at least two times the F-Score while reducing the runtime by 50\% for synthetic graphs with overlapping communities. We also compare DOLPA against the state-of-art parallel implementation of the Louvain method using the same graphs and show that DOLPA achieves about three times the F-Score at 10\% the runtime. On real-world graphs, we get a speedup of up to $10\times$ using 64 threads.

Liu, X↗

DOE OSTI2015

On the use of Abelian point group symmetry in density-fitted local MP2 using various types of virtual orbitals

Electron correlation methods based on symmetry-adapted canonical Hartree-Fock orbitals can be speeded up significantly in the well known group theoretical manner, using the fact that integrals vanish unless the integrand is totally symmetric. In contrast to this, local electron correlation methods cannot benefit from such simplifications, since the localized molecular orbitals (LMOs) generally do not transform according to irreducible representations of the underlying point group symmetry. Instead, groups of LMOs become symmetry-equivalent and this can be exploited to accelerate local calculations. We describe an implementation of such a symmetry treatment for density-fitted local Møller-Plesset perturbation theory, using various types of virtual orbitals: Projected atomic orbitals, orbital specific virtuals, and pair natural orbitals. The savings by the symmetry treatment are demonstrated by calculations for several large molecules having different point group symmetries. Benchmarks for the parallel execution efficiency of our method are also presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1977

Multiple scattering in reflection nebulae. I - A Monte Carlo approach. II - Uniform plane-parallel nebulae with foreground stars. III - Nebulae with embedded illuminating stars

A method for calculating the surface brightness distribution on a plane-parallel reflection nebula of uniform density illuminated by a star located either in front of, behind, or arbitrarily inside the scattering medium is proposed. The Monte Carlo technique is used to find solutions to the radiative transfer problem. The scattering properties of the nebular particles are parameterized by the albedo for single scattering and a three-parameter analytic phase function. Calculations are then presented for the surface brightness distribution across the face of such nebulae with (1) a foreground star and (2) immersed stars. The calculations include the full effects of multiple scattering, are independent of a particular assumed grain material or size distribution, and are applicable to any wavelength region for which observations can be obtained.

Witt, A. N.↗

DOE OSTI2023

Distributed-Memory Parallel JointNMF

Joint Nonnegative Matrix Factorization (JointNMF) is a hybrid method for mining information from datasets that contain both feature and connection information. We propose distributed-memory parallelizations of three algorithms for solving the JointNMF problem based on Alternating Nonnegative Least Squares, Projected Gradient Descent, and Projected Gauss-Newton. We extend well-known communication-avoiding algorithms using a single processor grid case to our coupled case on two processor grids. We demonstrate the scalability of the algorithms on up to 960 cores (40 nodes) with 60% parallel efficiency. The more sophisticated Alternating Nonnegative Least Squares (ANLS) and Gauss-Newton variants outperform the first-order gradient descent method in reducing the objective on large-scale problems. We perform a topic modelling task on a large corpus of academic papers that consists of over 37 million paper abstracts and nearly a billion citation relationships, demonstrating the utility and scalability of the methods.

Eswar, Srinivas↗

DOE OSTI2016

Limited‐memory adaptive snapshot selection for proper orthogonal decomposition

Summary Reduced order models are useful for accelerating simulations in many‐query contexts, such as optimization, uncertainty quantification, and sensitivity analysis. However, offline training of reduced order models (ROMs) can have prohibitively expensive memory and floating‐point operation costs in high‐performance computing applications, where memory per core is limited. To overcome this limitation for proper orthogonal decomposition, we propose a novel adaptive selection method for snapshots in time that limits offline training costs by selecting snapshots according an error control mechanism similar to that found in adaptive time‐stepping ordinary differential equation solvers. The error estimator used in this work is related to theory bounding the approximation error in time of proper orthogonal decomposition‐based ROMs, and memory usage is minimized by computing the singular value decomposition using a single‐pass incremental algorithm. Results for a viscous Burgers' test problem demonstrate convergence in the limit as the algorithm error tolerances go to zero; in this limit, the full‐order model is recovered to within discretization error. A parallel version of the resulting method can be used on supercomputers to generate proper orthogonal decomposition‐based ROMs, or as a subroutine within hyperreduction algorithms that require taking snapshots in time, or within greedy algorithms for sampling parameter space. Copyright © 2016 John Wiley & Sons, Ltd.

Oxberry, Geoffrey M.↗

DOE OSTI2018

Large-eddy Simulations of Spray Variability Effects on Flow Variability in a Direct-injection Spark-ignition Engine Under Non-combusting Operating Conditions

Large-eddy Simulations (LES) have been carried out to investigate spray variability and its effect on cycle-to-cycle flow variability in a direct-injection spark-ignition (DISI) engine under non-reacting conditions. Initial simulations were performed of an injector in a constant volume spray chamber to validate the simulation spray set-up. Comparisons showed good agreement in global spray measures such as the penetration. Local mixing data and shot-to-shot variability were also compared using Rayleigh-scattering images and probability contours. The simulations were found to reasonably match the local mixing data and shot-to-shot variability using a random-seed perturbation methodology. After validation, the same spray set-up with only minor changes was used to simulate the same injector in an optically accessible DISI engine. Particle Image Velocimetry (PIV) measurements were used to quantify the flow velocity in a horizontal plane intersecting the spark plug gap. The engine was operated in a skip-fired operating mode and comparisons focused on cycles that included fuel injection, but no spark event and therefore no combustion. 105 total LES engine cycles were simulated using a parallel cycle simulation approach and 3 different perturbation methods in an attempt to isolate the effects of shot-to-shot spray variability and the initial turbulent flow field as well as their interaction effects on overall engine CCVs. The experimental mean and standard deviations were reasonably well matched by the simulations, though quantitative comparisons near the injection event during the intake stroke were difficult due to the high uncertainty in the PIV measurements at these crank angles. The 3 simulation perturbation methods resulted in very similar results, though further analysis found the current parallel cycle approach may be limiting the ability of the simulations to isolate the spray and flow effects.

Cycle-to-cycle Variability↗

NASA NTRS1990

Discrete approximations to optimal trajectories using direct transcription and nonlinear programming

A recently developed method for solving optimal trajectory problems uses a piecewise-polynomial representation of the state and control variables, enforces the equations of motion via a collocation procedure, and thus approximates the original calculus-of-variations problem with a nonlinear-programming problem, which is solved numerically. This paper identifies this method as a direct transcription method and proceeds to investigate the relationship between the original optimal-control problem and the nonlinear-programming problem. The discretized adjoint equation of the collocation method is found to have deficient accuracy, and an alternate scheme which discretizes the equations of motion using an explicit Runge-Kutta parallel-shooting approach is developed. Both methods are applied to finite-thrust spacecraft trajectory problems, including a low-thrust escape spiral, a three-burn rendezvous, and a low-thrust transfer to the moon.

Enright, Paul J.↗

NASA NTRS1989

Parallel-vector solution of large-scale structural analysis problems on supercomputers

A direct linear equation solution method based on the Choleski factorization procedure is presented which exploits both parallel and vector features of supercomputers. The new equation solver is described, and its performance is evaluated by solving structural analysis problems on three high-performance computers. The method has been implemented using Force, a generic parallel FORTRAN language.

Storaasli, Olaf O.↗

DOE OSTI2018

Method of Determining the Reliability of Real-Time In-reactor Monitoring of VVER

A methodological approach and the basic tenets for evaluating the reliability of in-reactor monitoring of VVER are presented. The method is based on the statistical analysis of indications in real time and includes methods for evaluating the admissible maximum error of the measurement channels used for monitoring as well as the average value and admissible deviation of indications in groups of parallel monitoring channels, as well as a method of evaluating reliability by comparing the values of a parameter with the regime values. In comparing the indications of a monitoring channel with the indications of other parallel channels, the median value is proposed as the baseline value. The developed method is implemented in the Diagnostika SVRK special software, which has been successfully tested during the commissioning of the No. 1 unit at the Novovoronezh NPP-2.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Parallel interior-point solver for block-structured nonlinear programs on SIMD/GPU architectures

Here, we investigate how to port the standard interior-point method to new exascale architectures for block-structured nonlinear programs with state equations. Computationally, we decompose the interior-point algorithm into two successive operations: the evaluation of the derivatives and the solution of the associated Karush-Kuhn-Tucker (KKT) linear system. Our method accelerates both operations using two levels of parallelism. First, we distribute the computations on multiple processes using coarse parallelism. Second, each process uses SIMD/GPU accelerators locally to accelerate the operations using fine-grained parallelism. The KKT system is reduced by eliminating the inequalities and the state variables from the corresponding equations. We demonstrate our method's capability on the supercomputer Polaris, a testbed for the future exascale Aurora system. Each node is equipped with four GPUs, a setup amenable to our two-level approach. Our experiments on the stochastic optimal power flow problem show that the reduction method is 50x faster than the sparse linear solver HSL MA57 running in serial on the CPU, and 6x faster than Pardiso running in parallel on CPU on the same number of processes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Parallelized Screening of Characterized and DFT-Modeled Bimetallic Colloidal Cocatalysts for Photocatalytic Hydrogen Evolution

Using a newly designed and developed parallelized photoreactor and colorimetric detection method, a large sampling of bimetallic co-catalysts (Pd/Sn, Pd/Mo, Pd/Ru, Pd/Pb, Pd/Ni, Ni/Sn, Mo/Sn and Pt/Sn) for photocatalytic water reduction have been tested in this work. Of these co-catalysts, the combination of palladium and tin showed the highest synergistic behavior and peak hydrogen gas production at a low relative fraction of palladium. The resulting Pd/Sn bimetallic co-catalysts were characterized using high-angle annular dark-field (HAADF) and scanning transmission electron microscopy energy dispersive X-ray spectroscopy (STEM-EDS), and specifically, investigation of the palladium/tin mixture indicated that palladium and tin elements reside within the same particle. The experimental catalytic activity for the palladium/tin mixture was compared to density functional theory-derived energy values associated with the adsorption of hydrogen onto a surface. This comparison demonstrated that the typical peak found in electrochemical Sabatier volcano plots at ΔG H* = ~0 eV was replicated in the experimental photocatalytic system with a peak activity observed at ΔG H* = -0.036 eV. Computational confirmation of the results expressed here demonstrates the efficacy of colorimetric detection of hydrogen in parallel and presents a model for increasingly rapid catalyst screening.

08 HYDROGEN↗

NASA NTRS1986

Higher-order structure of rRNA

A comparative search for phylogenetically covarying basepair replacements within potential helices has been the only reliable method to determine the correct secondary structure of the 3 rRNAs, 5S, 16S, and 23S. The analysis of 16S from a wide phylogenetic spectrum, that includes various branches of the eubacteria, archaebacteria, eucaryotes, in addition to the mitochondria and chloroplast, is beginning to reveal the constraints on the secondary structures of these rRNAs. Based on the success of this analysis, and the assumption that higher order structure will also be phylogenetically conserved, a comparative search was initiated for positions that show co-variation not involved in secondary structure helices. From a list of potential higher order interactions within 16S rRNA, two higher-order interactions are presented. The first of these interactions involves positions 570 and 866. Based on the extent of phylogenetic covariation between these positions while maintaining Watson-Crick pairing, this higher-order interaction is considered proven. The other interaction involves a minimum of six positions between the 1400 and 1500 regions of the 16S rRNA. Although these patterns of covariation are not as striking as the 570/866 interaction, the fact that they all exist in an anti-parallel fashion and that experimental methods previously implicated these two regions of the molecule in tRNA function suggests that these interactions be given serious consideration.

Gutell, R. R.↗

DOE OSTI2015

A Petascale Non-Hydrostatic Atmospheric Dynamical Core in the HOMME Framework

The High-Order Method Modeling Environment (HOMME) is a framework for building scalable, conserva- tive atmospheric models for climate simulation and general atmospheric-modeling applications. Its spatial discretizations are based on Spectral-Element (SE) and Discontinuous Galerkin (DG) methods. These are local methods employing high-order accurate spectral basis-functions that have been shown to perform well on massively parallel supercomputers at any resolution and scale particularly well at high resolutions. HOMME provides the framework upon which the CAM-SE community atmosphere model dynamical-core is constructed. In its current incarnation, CAM-SE employs the hydrostatic primitive-equations (PE) of motion, which limits its resolution to simulations coarser than 0.1 per grid cell. The primary objective of this project is to remove this resolution limitation by providing HOMME with the capabilities needed to build nonhydrostatic models that solve the compressible Euler/Navier-Stokes equations.

58 GEOSCIENCES↗

DOE OSTI2014

Simulation of dilute polymeric fluids in a three-dimensional contraction using a multiscale FENE model

The multiscale FENE model is applied to a 3D square-square contraction flow problem. For this purpose, the stochastic Brownian configuration field method (BCF) has been coupled with our fully parallelized three-dimensional Navier-Stokes solver NaSt3DGPF. The robustness of the BCF method enables the numerical simulation of high Deborah number flows for which most macroscopic methods suffer from stability issues. The results of our simulations are compared with that of experimental measurements from literature and show a very good agreement. In particular, flow phenomena such as a strong vortex enhancement, streamline divergence and a flow inversion for highly elastic flows are reproduced. Due to their computational complexity, our simulations require massively parallel computations. Using a domain decomposition approach with MPI, the implementation achieves excellent scale-up results for up to 128 processors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1987

Galerkin/Runge-Kutta discretizations for semilinear parabolic equations

A new class of fully discrete Galerkin/Runge-Kutta methods is constructed and analyzed for semilinear parabolic initial boundary value problems. Unlike any classical counterpart, this class offers arbitrarily high, optimal order convergence. In support of this claim, error estimates are proved, and computational results are presented. Furthermore, it is noted that special Runge-Kutta methods allow computations to be performed in parallel so that the final execution time can be reduced to that of a low order method.

Keeling, Stephen L.↗

NASA NTRS1987

Galerkin/Runge-Kutta discretizations for parabolic equations with time dependent coefficients

A new class of fully discrete Galerkin/Runge-Kutta methods is constructed and analyzed for linear parabolic initial boundary value problems with time dependent coefficients. Unlike any classical counterpart, this class offers arbitrarily high order convergence while significantly avoiding what has been called order reduction. In support of this claim, error estimates are proved, and computational results are presented. Additionally, since the time stepping equations involve coefficient matrices changing at each time step, a preconditioned iterative technique is used to solve the linear systems only approximately. Nevertheless, the resulting algorithm is shown to preserve the original convergence rate while using only the order of work required by the base scheme applied to a linear parabolic problem with time independent coefficients. Furthermore, it is noted that special Runge-Kutta methods allow computations to be performed in parallel so that the final execution time can be reduced to that of a low order method.

Keeling, Stephen L.↗

NASA NTRS1989

Galerkin/Runge-Kutta discretizations for parabolic equations with time-dependent coefficients

Keeling, Stephen L.↗

DOE OSTI2013

Resonance self-shielding methodology in MPACT

The resonance self-shielding methods of the neutron transport code Michigan Parallel Characteristics based Transport (MPACT) are described in this paper. Two resonance-integral table based methods are utilized to resolve the resonance self-shielding effect. The subgroup method is a mature approach used in MPACT as the basic functionality for the resonance calculation. Another new iterative method, named the embedded self-shielding method is also implemented in MPACT. Comparisons of the two methods as well as their numerical verifications are presented. The results show that MPACT is capable of modeling the resonance self-shielding in a variety of PWR benchmarking cases, including difficult fuel lattice cases with poison, control rods or mixed gadolinia fuel rods. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗