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At least 1,225 records · Page 68

The effect of finite turbulence spatial scale on the amplification of turbulence by a contracting stream

The turbulence downstream of a rapid contraction is calculated for the case when the turbulence scale can have the same magnitude as the mean-flow spatial scale. The approach used is based on the formulation of Goldstein (1978) for turbulence downstream of a contraction, with the added assumptions of a parallel mean flow at downstream infinity and turbulence calculated far enough downstream so that the nonuniformity of the mean flow field has decayed, and by treating the inverse contraction ratio as a small parameter. Consideration is given to the large-contraction-ratio and classical rapid-distortion theory limits, and to results at an arbitrary contraction ratio. It is shown that the amplification effect of the contraction is reduced when the spatial scale of the turbulence increases, with the upstream turbulence actually suppressed for a contraction ratio less than five and a turbulence spatial scale greater than three times the transverse dimensions of the downstream channel.

Goldstein, M. E.↗

A year in the life of a parallel file system

I/O performance is a critical aspect of data-intensive scientific computing. We seek to advance the state of the practice in understanding and diagnosing I/O performance issues through investigation of a comprehensive I/O performance data set that captures a full year of production storage activity at two leadership-scale computing facilities. We demonstrate techniques to identify regions of interest, perform focused investigations of both long-term trends and transient anomalies, and uncover the contributing factors that lead to performance fluctuation. We find that a year in the life of a parallel file system is comprised of distinct regions of long-term performance variation in addition to short-term performance transients. We demonstrate how systematic identification of these performance regions, combined with comprehensive analysis, allows us to isolate the factors contributing to different performance maladies at different time scales. From this, we present specific lessons learned and important considerations for HPC storage practitioners.

Lockwood, GK↗

Parallel accelerated Custom Correlation Coefficient calculations for genomics applications

The massive quantities of genomic data being made available through gene sequencing techniques are enabling breakthroughs in genomic science in many areas such as medical advances in the diagnosis and treatment of diseases. Analyzing this data, however, is a computational challenge insofar as the computational costs of the relevant algorithms can grow with quadratic, cubic or higher complexity—leading to the need for leadership scale computing. In this paper we describe a new approach to calculations of the Custom Correlation Coefficient (CCC) between Single Nucleotide Polymorphisms (SNPs) across a population, suitable for parallel systems equipped with graphics processing units (GPUs) or Intel Xeon Phi processors. We describe the mapping of the algorithms to accelerated processors, techniques used for eliminating redundant calculations due to symmetries, and strategies for efficient mapping of the calculations to many-node parallel systems. Results are presented demonstrating high per-node performance and near-ideal parallel scalability with rates of more than nine quadrillion (9 × 10 15 ) elementwise comparisons achieved per second with the latest optimized code on the ORNL Titan system, this being orders of magnitude faster than rates achieved using other codes and platforms as reported in the literature. Also it is estimated that as many as 90 quadrillion (90 × 10 15 ) comparisons per second may be achievable on the upcoming ORNL Summit system, an additional 10X performance increase. Finally, in a companion paper we describe corresponding techniques applied to calculations of the Proportional Similarity metric for comparative genomics applications.

97 MATHEMATICS AND COMPUTING↗

PSelInv—A Distributed Memory Parallel Algorithm for Selected Inversion: The Symmetric Case

We describe an efficient parallel implementation of the selected inversion algorithm for distributed memory computer systems, which we call PSelInv. The PSelInv method computes selected elements of a general sparse matrix Athat can be decomposed as A= LU, where L is lower triangular and U is upper triangular. The implementation described in this article focuses on the case of sparse symmetric matrices. It contains an interface that is compatible with the distributed memory parallel sparse direct factorization SuperLU-DIST. Yet, the underlying data structure and design of PSelInv allows it to be easily combined with other factorization routines, such as PARDISO. We discuss general parallelization strategies such as data and task distribution schemes. Specifically, we describe how to exploit the concurrency exposed by the elimination tree associated with the LU factorization of A. We demonstrate the efficiency and accuracy of PSelInv by presenting several numerical experiments. In particular, we show that PSelInv can run efficiently on more than 4,000 cores for a modestly sized matrix. We also show how PSelInv can be used to accelerate large-scale electronic structure calculations.

97 MATHEMATICS AND COMPUTING↗

Micro- and meso-scale simulations of magnetospheric processes related to the aurora and substorm morphology

The primary methodology during the grant period has been the use of micro or meso-scale simulations to address specific questions concerning magnetospheric processes related to the aurora and substorm morphology. This approach, while useful in providing some answers, has its limitations. Many of the problems relating to the magnetosphere are inherently global and kinetic. Effort during the last year of the grant period has increasingly focused on development of a global-scale hybrid code to model the entire, coupled magnetosheath - magnetosphere - ionosphere system. In particular, numerical procedures for curvilinear coordinate generation and exactly conservative differencing schemes for hybrid codes in curvilinear coordinates have been developed. The new computer algorithms and the massively parallel computer architectures now make this global code a feasible proposition. Support provided by this project has played an important role in laying the groundwork for the eventual development or a global-scale code to model and forecast magnetospheric weather.

Swift, Daniel W.↗

Automated Scalability Analysis Tools for Message Passing Parallel Programs

In order to develop scalable parallel applications, a number of programming decisions have to be made during the development of the program. Performance tools that help in making these decisions are few, if existent. Traditionally, performance tools have focused on exposing performance bottlenecks of small-scale executions of the program. However, it is common knowledge that programs that perform exceptionally well on small processor configurations, more often than not, perform poorly when executed on larger processor configurations. Hence, new tools that predict the execution characteristics of scaled-up programs are an essential part of an application developers toolkit. In this paper we discuss important issues that need to be considered in order to build useful scalability analysis tools for parallel programs. We introduce a simple tool that automatically extracts scalability characteristics of a class of deterministic parallel programs. We show with the help of a number of results on the Intel iPSC/860, that predictions are within reasonable bounds.

Sarukkai, Sekhar R.↗

Coronal heating by the resonant absorption of Alfven waves: Wavenumber scaling laws.

The importance of global modes in coronal loop heating is well established. In the present work the scaling of the global-mode resonant heating rate with the perturbation wavenumbers is studied with the numerical solution of the linearized time-dependent MHD equations for a full compressible, low-beta, resistive plasma using an implicit integration scheme. The numerical simulations demonstrate that the dissipation on inhomogeneties in the background Alfven speed occurs in narrow resonant layer with the highest heating rate at the global-mode frequency. The global-mode heating rate H (sub r) was found to scale as H (Sub r) approximately k (sub y) (exp 1.03) when k (sub z) = 0.1, and as H (sub r) approximately k (sub y) (exp -1.93) when k (sub z) = 0.75, where k (sub y) and k (sub z) are the wavenumbers in the perpendicular and parallel to the magnetic field directions, respectively, while the dependence of H (sub r) on k (sub z) is more complex. The quality factor Q of the MHD resonance cavity scales as Q approximately k (sub y) (exp -1.8) for k (sub z) = 0.75 and as Q approximately k (sub y) (exp -1.46) for k (sub z) = 0.1. The numerically determined heating rate scaling, the global-mode fequency, and the quality factor are in good agreement with the analytical linear theory. The magnitude of the perturbed velocities was found to decrease with k (sub y). Assuming typical coronal loop parameters (B (sub 0) = 100-200 G, upsilon (sub A) = 2000-4000 km/s), the Alfven waves can supply the required heating to a low-Q loops.

Ofman, L.↗

Additive Manufacturing Model-Based Process Metrics: Reduced Order Modeling of the Laser Powder Bed Fusion Process

The multi-scale and complex process of printing additively manufactured (AM) parts can have unexpected, but predictable, build conditions that result in material microstructure variability. In this work, we describe a fully parallel reduced order modeling approach that has been developed to evaluate the evolution of AM processes, termed the AM moment measure method. This method couples the known sequence of the AM process with a physically informed nearest neighbors’ calculation to map the conditions of a part-scale build. The result is a map of the build that is derived directly from build files or in-situ process monitoring sensors. The methodology and terminology of the approach will be described, and computed build maps will be calculated and compared for various laser powder bed fusion (LPBF) builds of Ti-6Al-4V. Such comparative results develop understanding of how the sequential process actions can affect the LPBF-AM build quality and microstructure variability.

Laser Powder Bed Fusion↗

Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models

Single neuron models are fundamental for computational modeling of the brain's neuronal networks, and understanding how ion channel dynamics mediate neural function. A challenge in defining such models is determining biophysically realistic channel distributions. Here, we present an efficient, highly parallel evolutionary algorithm for developing such models, named NeuroGPU-EA. NeuroGPU-EA uses CPUs and GPUs concurrently to simulate and evaluate neuron membrane potentials with respect to multiple stimuli. We demonstrate a logarithmic cost for scaling the stimuli used in the fitting procedure. NeuroGPU-EA outperforms the typically used CPU based evolutionary algorithm by a factor of 10 on a series of scaling benchmarks. We report observed performance bottlenecks and propose mitigation strategies. Finally, we also discuss the potential of this method for efficient simulation and evaluation of electrophysiological waveforms.

59 BASIC BIOLOGICAL SCIENCES↗

FAST Observations of Acceleration Processes in the Cusp--Evidence for Parallel Electric Fields

The existence of precipitating keV ions in the Earth's cusp originating at the magnetosheath provide unique means to test our understanding of particle acceleration and parallel electric fields in the lower altitude acceleration region. On numerous occasions, the FAST (The Fast Auroral Snapshot) spacecraft has encountered the Earth's cusp regions near its apogee of 4175 km which are characterized by their signatures of dispersed keV ion injections. The FAST instruments also reveal a complex microphysics inherent to many, but not all, of the cusp regions encountered by the spacecraft, that include upgoing ion beams and conics, inverted-V electrons, upgoing electron beams, and spikey DC-coupled electric fields and plasma waves. Detailed inspection of the FAST data often show clear modulation of the precipitating magnetosheath ions that indicate that they are affected by local electric potentials. For example, the magnetosheath ion precipitation is sometimes abruptly shut off precisely in regions where downgoing localized inverted-V electrons are observed. Such observations support the existence of a localized process, such as parallel electric fields, above the spacecraft which accelerate the electrons downward and consequently impede the precipitating ion precipitation. Other acceleration events in the cusp are sometimes organized with an apparent cellular structure that suggests Alfven waves or other large-scale phenomena are controlling the localized potentials. We examine several cusp encounters by the FAST satellite where the modulation of energetic session on acceleration particle populations reveals evidence of localized acceleration, most likely by parallel electric fields.

Pfaff, R. F.. Jr.↗

ELSI — An open infrastructure for electronic structure solvers

Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries (finite non-periodic vs. infinite periodic boundary conditions) yield matrices with different structures. The ELectronic Structure Infrastructure (ELSI) project provides an open-source software interface to facilitate the implementation and optimal use of high-performance solver libraries covering cubic scaling eigensolvers, linear scaling density-matrix-based algorithms, and other reduced scaling methods in between. In this paper, we present recent improvements and developments inside ELSI, mainly covering (1) new solvers connected to the interface, (2) matrix layout and communication adapted for parallel calculations of periodic and/or spin-polarized systems, (3) routines for density matrix extrapolation in geometry optimization and molecular dynamics calculations, and (4) general utilities such as parallel matrix I/O and JSON output. The ELSI interface has been integrated into four electronic structure code projects (DFTB+, DGDFT, FHI-aims, SIESTA), allowing us to rigorously benchmark the performance of the solvers on an equal footing. Based on results of a systematic set of large-scale benchmarks performed with Kohn–Sham density-functional theory and density-functional tight-binding theory, we identify factors that strongly affect the efficiency of the solvers, and propose a decision layer that assists with the solver selection process. As a result, we describe a reverse communication interface encoding matrix-free iterative solver strategies that are amenable, e.g., for use with planewave basis sets.

97 MATHEMATICS AND COMPUTING↗

Jupiter's magnetopause, bow shock, and 10-hour modulated magnetosheath: Voyagers 1 and 2

Fine scale magnetic field data from the Voyager 1 and 2 magnetopause and bow shock crossings at Jupiter were analyzed. Explicit models of the dawnside magnetopause and bow shock in Jupiter's orbital plane employ an axisymmetric parabola and hyperbola, respectively, and are determined separately for the encounters. A new phenomenon was discovered in the magnetosheath. It is manifested as (5 or) 10 hour quasi-periodic modulation of the direction of the magnetic field in the outbound magnetosheath, predominantly in the northward (N) and southward (S) directions. It was seen to occur during both encounters and appears most evident in Voyager 2 outbound observations, probably due to the extreme tailward extent of the Voyager 2 trajectory through the magnetosheath. The durations of the N to and from S transitions range from tens of minutes to approximately 3 hours. The directional variation of the field during these transitions is fairly well restricted to a plane parallel to the local model magnetopause location. These signatures may be due to magnetosheath field line draping modulated by the large scale motion of the magnetospheric plasma disk.

Lepping, R. P.↗

Performance characteristics of a variable-area vane nozzle for vectoring an ASTOVL exhaust jet up to 45 deg

Many conceptual designs for advanced short-takeoff, vertical landing (ASTOVL) aircraft need exhaust nozzles that can vector the jet to provide forces and moments for controlling the aircraft's movement or attitude in flight near the ground. A type of nozzle that can both vector the jet and vary the jet flow area is called a vane nozzle. Basically, the nozzle consists of parallel, spaced-apart flow passages formed by pairs of vanes (vanesets) that can be rotated on axes perpendicular to the flow. Two important features of this type of nozzle are the abilities to vector the jet rearward up to 45 degrees and to produce less harsh pressure and velocity footprints during vertical landing than does an equivalent single jet. A one-third-scale model of a generic vane nozzle was tested with unheated air at the NASA Lewis Research Center's Powered Lift Facility. The model had three parallel flow passages. Each passage was formed by a vaneset consisting of a long and a short vane. The longer vanes controlled the jet vector angle, and the shorter controlled the flow area. Nozzle performance for three nominal flow areas (basic and plus or minus 21 percent of basic area), each at nominal jet vector angles from -20 deg (forward of vertical) to +45 deg (rearward of vertical) are presented. The tests were made with the nozzle mounted on a model tailpipe with a blind flange on the end to simulate a closed cruise nozzle, at tailpipe-to-ambient pressure ratios from 1.8 to 4.0. Also included are jet wake data, single-vaneset vector performance for long/short and equal-length vane designs, and pumping capability. The pumping capability arises from the subambient pressure developed in the cavities between the vanesets, which could be used to aspirate flow from a source such as the engine compartment. Some of the performance characteristics are compared with characteristics of a single-jet nozzle previously reported.

Mcardle, Jack G.↗

Performance characteristics of a variable-area vane nozzle for vectoring an ASTOVL exhaust jet up to 45 deg

Many conceptual designs for advanced short-takeoff, vertical landing (ASTOVL) aircraft need exhaust nozzles that can vector the jet to provide forces and moments for controlling the aircraft's movement or attitude in flight near the ground. A type of nozzle that can both vector the jet and vary the jet flow area is called a vane nozzle. Basically, the nozzle consists of parallel, spaced-apart flow passages formed by pairs of vanes (vanesets) that can be rotated on axes perpendicular to the flow. Two important features of this type of nozzle are the abilities to vector the jet rearward up to 45 degrees and to produce less harsh pressure and velocity footprints during vertical landing than does an equivalent single jet. A one-third-scale model of a generic vane nozzle was tested with unheated air at the NASA Lewis Research Center's Powered Lift Facility. The model had three parallel flow passages. Each passage was formed by a vaneset consisting of a long and a short vane. The longer vanes controlled the jet vector angle, and the shorter controlled the flow area. Nozzle performance for three nominal flow areas (basic and plus or minus 21 percent of basic area), each at nominal jet vector angles from -20 deg (forward of vertical) to +45 deg (rearward of vertical) are presented. The tests were made with the nozzle mounted on a model tailpipe with a blind flange on the end to simulate a closed cruise nozzle, at tailpipe-to-ambient pressure ratios from 1.8 to 4.0. Also included are jet wake data, single-vaneset vector performance for long/short and equal-length vane designs, and pumping capability. The pumping capability arises from the subambient pressure developed in the cavities between the vanesets, which could be used to aspirate flow from a source such as the engine compartment. Some of the performance characteristics are compared with characteristics of a single-jet nozzle previously reported.

Mcardle, Jack G.↗

Adaptive Critical Balance and Firehose Instability in an Expanding, Turbulent, Collisionless Plasma

Abstract Using a hybrid-kinetic particle-in-cell simulation, we study the evolution of an expanding, collisionless, magnetized plasma in which strong Alfvénic turbulence is persistently driven. Temperature anisotropy generated adiabatically by the plasma expansion (and consequent decrease in the mean magnetic-field strength) gradually reduces the effective elasticity of the field lines, causing reductions in the linear frequency and residual energy of the Alfvénic fluctuations. In response, these fluctuations modify their interactions and spatial anisotropy to maintain a scale-by-scale “critical balance” between their characteristic linear and nonlinear frequencies. Eventually the plasma becomes unstable to kinetic firehose instabilities, which excite rapidly growing magnetic fluctuations at ion-Larmor scales. The consequent pitch-angle scattering of particles maintains the temperature anisotropy near marginal stability, even as the turbulent plasma continues to expand. The resulting evolution of parallel and perpendicular temperatures does not satisfy double-adiabatic conservation laws, but is described accurately by a simple model that includes anomalous scattering. Our results have implications for understanding the complex interplay between macro- and microscale physics in various hot, dilute, astrophysical plasmas, and offer predictions concerning power spectra, residual energy, ion-Larmor-scale spectral breaks, and non-Maxwellian features in ion distribution functions that may be tested by measurements taken in high-beta regions of the solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗

Stable parallel training of Wasserstein conditional generative adversarial neural networks

In this work, we propose a stable, parallel approach to train Wasserstein conditional generative adversarial neural networks (W-CGANs) under the constraint of a fixed computational budget. Differently from previous distributed GANs training techniques, our approach avoids inter-process communications, reduces the risk of mode collapse and enhances scalability by using multiple generators, each one of them concurrently trained on a single data label. The use of the Wasserstein metric also reduces the risk of cycling by stabilizing the training of each generator. We illustrate the approach on the CIFAR10, CIFAR100, and ImageNet1k datasets, three standard benchmark image datasets, maintaining the original resolution of the images for each dataset. Performance is assessed in terms of scalability and final accuracy within a limited fixed computational time and computational resources. To measure accuracy, we use the inception score, the Fréchet inception distance, and image quality. An improvement in inception score and Fréchet inception distance is shown in comparison to previous results obtained by performing the parallel approach on deep convolutional conditional generative adversarial neural networks as well as an improvement of image quality of the new images created by the GANs approach. Weak scaling is attained on both datasets using up to 2000 NVIDIA V100 GPUs on the OLCF supercomputer Summit.

97 MATHEMATICS AND COMPUTING↗

Nanoactuators Based on Electrostatic Forces on Dielectrics

Nanoactuators of a proposed type would exploit the forces exerted by electric fields on dielectric materials. As used here, "nanoactuators" includes motors, manipulators, and other active mechanisms that have dimensions of the order of nanometers and/or are designed to manipulate objects that have dimensions of the order of nanometers. The underlying physical principle can be described most simply in terms of the example of a square parallel-plate capacitor in which a square dielectric plate is inserted part way into the gap between the electrode plates (see Figure Typically, the force is small from our macroscopic human perspective. The above equation shows that the force depends on the ratio between the capacitor dimensions but does not depend on the size. In other words, the force remains the same if the capacitor and the dielectric slab are shrunk to nanometer dimensions. At the same time, the masses of all components are proportional to third power of their linear dimensions. Therefore the force-to-mass ratio (and, consequently, the acceleration that can be imparted to the dielectric slab) is much larger at the nanoscale than at the macroscopic scale. The proposed actuators would exploit this effect. The upper part of Figure 2 depicts a simple linear actuator based on a parallel- plate capacitor similar to Figure 1. In this case, the upper electrode plate would be split into two parts (A and B) and the dielectric slab would be slightly longer than plate A or B. The actuator would be operated in a cycle. During the first half cycle, plate B would be grounded to the lower plate and plate A would be charged to a potential, V, with respect to the lower plate, causing the dielectric slab to be pulled under plate A. During the second half cycle, plate A would be grounded and plate B would be charged to potential V, causing the dielectric slab to be pulled under plate B. The back-and-forth motion caused by alternation of the voltages on plates A and B could be used to drive a nanopump, for example. A rotary motor, shown in the middle part of Figure 2, could include a dielectric rotor sandwiched between a top and a bottom plate containing multiple electrodes arranged symmetrically in a circle. Voltages would be applied sequentially to electrode pairs 1 and 1a, then 2 and 2a, then 3 and 3a in order to attract the dielectric rotor to sequential positions between the electrode pairs.

Wang, Yu↗

Community Detection on the GPU

We present and evaluate a new GPU algorithm based on the Louvain method for community detection. Our algorithm is the first for this problem that parallelizes the access to individual edges. In this way we can fine tune the load balance when processing networks with nodes of highly varying degrees. This is achieved by scaling the number of threads assigned to each node according to its degree. Extensive experiments show that we obtain speedups up to a factor of 270 compared to the sequential algorithm. The algorithm consistently outperforms other recent shared memory implementations and is only one order of magnitude slower than the current fastest parallel Louvain method running on a Blue Gene/Q supercomputer using more than 500K threads.

community detection↗