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At least 379 records · Page 21

PANDORA: A Parallel Dendrogram Construction Algorithm for Single Linkage Clustering on GPU

This paper introduces Pandora, a parallel algorithm for computing dendrograms, the hierarchical cluster trees for single linkage clustering (SLC). Current parallel approaches construct dendrograms by partitioning a minimum spanning tree and removing edges. However, they struggle with skewed, hard-to-parallelize real-world dendrograms. Consequently, computing dendrograms is the sequential bottleneck in HDBSCAN*[21], a popular SLC variant. Pandora uses recursive tree contraction to address this limitation. Pandora contracts nodes to construct progressively smaller trees. It computes the smallest contracted dendrogram and expands it by inserting contracted edges. This recursive strategy is highly parallel, skew-independent, work-optimal, and well-suited for GPUs and multicores. We develop a performance portable implementation of Pandora in Kokkos[31] and evaluate its performance on multicore CPUs and multi-vendor GPUs (e.g., Nvidia, AMD) for dendrogram construction in HDBSCAN*. Multithreaded Pandora is 2.2x faster than the current best-multithreaded implementation. Our GPU version achieves 6-20x speedup on AMD GPUs and 10-37x on NVIDIA GPUs over multithreaded Pandora. Pandora removes HDBSCAN*’s sequential bottleneck, greatly boosting efficiency, particularly with GPUs.

Sao, Piyush↗

Downstream Effects on Orbiter Leeside Flow Separation for Hypersonic Flows

Discrepancies between experiment and computation for shuttle leeside flow separation, which came to light in the Columbia accident investigation, are resolved. Tests were run in the Langley Research Center 20-Inch Hypersonic CF4 Tunnel with a baseline orbiter model and two extended trailing edge models. The extended trailing edges altered the wing leeside separation lines, moving the lines toward the fuselage, proving that wing trailing edge modeling does affect the orbiter leeside flow. Computations were then made with a wake grid. These calculations more closely matched baseline experiments. Thus, the present findings demonstrate that it is imperative to include the wake flow domain in CFD calculations in order to accurately predict leeside flow separation for hypersonic vehicles at high angles of attack.

Buck, Gregory M.↗

Effect of Dynamic Rolling Oscillations on Twin Tail Buffet Response

The effect of dynamic rolling oscillations of delta-wing/twin-tail configuration on twin-tail buffet response is investigated. The computational model consists of a sharp-edged delta wing of aspect ratio one and swept-back flexible twin tail with taper ratio of 0.23. The configuration model is statically pitched at 30 deg. angle of attack and then forced to oscillate in roll around the symmetry axis at a constant amplitude of 4 deg. and reduced frequency of pi and 2(pi). The freestream Mach number and Reynolds number are 0.3 and 1.25 million, respectively. This multidisciplinary problem is solved using three sets of equations on a dynamic multi-block grid structure. The first set is the unsteady, full Navier-Stokes equations, the second set is the aeroelastic equations for coupled bending and torsion vibrations of the tails, and the third set is the grid-displacement equations. The configuration is investigated for inboard position of the twin tails which corresponds to a separation distance between the twin tails of 33% wing span. The computed results are compared with the results of stationary configuration, which previously have been validated using experimental data. The results conclusively showed that the rolling oscillations of the configuration have led to higher loads, higher deflections, and higher excitation peaks than those of the stationary configuration. Moreover, increasing the reduced frequency has led to higher loads and excitation peaks and lower bending and torsion deflections and acceleration.

Sheta, Essam F.↗

Globus service enhancements for exascale applications and facilities

Many extreme-scale applications require the movement of large quantities of data to, from, and among leadership computing facilities, as well as other scientific facilities and the home institutions of facility users. These applications, particularly when leadership computing facilities are involved, can touch upon edge cases (e.g., terabyte files) that had not been a focus of previous Globus optimization work, which had emphasized rather the movement of many smaller (megabyte to gigabyte) files. We report here on how automated client-driven chunking can be used to accelerate both the movement of large files and the integrity checking operations that have proven to be essential for large data transfers. In conclusion, we present detailed performance studies that provide insights into the benefits of these modifications in a range of file transfer scenarios.

97 MATHEMATICS AND COMPUTING↗

Vortical Flow Prediction Using an Adaptive Unstructured Grid Method

A computational fluid dynamics (CFD) method has been employed to compute vortical flows around slender wing/body configurations. The emphasis of the paper is on the effectiveness of an adaptive grid procedure in "capturing" concentrated vortices generated at sharp edges or flow separation lines of lifting surfaces flying at high angles of attack. The method is based on a tetrahedral unstructured grid technology developed at the NASA Langley Research Center. Two steady-state, subsonic, inviscid and Navier-Stokes flow test cases are presented to demonstrate the applicability of the method for solving practical vortical flow problems. The first test case concerns vortex flow over a simple 65 delta wing with different values of leading-edge radius. Although the geometry is quite simple, it poses a challenging problem for computing vortices originating from blunt leading edges. The second case is that of a more complex fighter configuration. The superiority of the adapted solutions in capturing the vortex flow structure over the conventional unadapted results is demonstrated by comparisons with the wind-tunnel experimental data. The study shows that numerical prediction of vortical flows is highly sensitive to the local grid resolution and that the implementation of grid adaptation is essential when applying CFD methods to such complicated flow problems.

Pirzadeh, Shahyar Z.↗

Vortical Flow Prediction using an Adaptive Unstructured Grid Method

A computational fluid dynamics (CFD) method has been employed to compute vortical flows around slender wing/body configurations. The emphasis of the paper is on the effectiveness of an adaptive grid procedure in "capturing" concentrated vortices generated at sharp edges or flow separation lines of lifting surfaces flying at high angles of attack. The method is based on a tetrahedral unstructured grid technology developed at the NASA Langley Research Center. Two steady-state, subsonic, inviscid and Navier-Stokes flow test cases are presented to demonstrate the applicability of the method for solving vortical flow problems. The first test case concerns vortex flow over a simple 65 delta wing with different values of leading-edge radius. Although the geometry is quite simple, it poses a challenging problem for computing vortices originating from blunt leading edges. The second case is that of a more complex fighter configuration. The superiority of the adapted solutions in capturing the vortex flow structure over the conventional unadapted results is demonstrated by comparisons with the wind-tunnel experimental data. The study shows that numerical prediction of vortical flows is highly sensitive to the local grid resolution and that the implementation of grid adaptation is essential when applying CFD methods to such complicated flow problems.

Pirzadeh, Shahyar Z.↗

Stress Concentration Around an Open Circular Hole in a Plate Subjected to Bending Normal to the Plane of the Plate

An aluminum-alloy plate containing an open circular hole of diameter large compared with the thickness of the plate was subjected to bending forces normal to the plane of the plate. Deflection and strain measurements were taken for two different loads. Stress concentrations occurred at the edge of the hole and the maximum stresses were tangential to the hole at the ends of the transverse diameter. The maximum stress at the edge of the hole was 1.59 times the computed stress on the net section and 1.85 times the computed stress in a solid plate of the same dimensions subjected to the same bending forces. The maximum deflections were about 20 percent greater than the corresponding deflection for a solid plate of the same size subjected to the same bending forces. The smallest edge distance was equal to 2-1/2 times the diameter of the hole and the stress concentration on this side of the hole was the same as on the side where the edge distance was about 4-1/2 diameters. A theoretical analysis of the problem shows that, for an aluminum plate of infinite width, the stress concentration at the edge of the hole would be 1.87 times the stress in a solid plate, which is substantially the same relation obtained for the plate tested.

Dumont, C↗

HDBind: encoding of molecular structure with hyperdimensional binary representations

Traditional methods for identifying “hit” molecules from a large collection of potential drug-like candidates rely on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have a significant limitation in that they require exceptional computing capabilities for even relatively small collections of molecules. Increasingly large and complex state-of-the-art deep learning approaches have gained popularity with the promise to improve the productivity of drug design, notorious for its numerous failures. However, as deep learning models increase in their size and complexity, their acceleration at the hardware level becomes more challenging. Hyperdimensional Computing (HDC) has recently gained attention in the computer hardware community due to its algorithmic simplicity relative to deep learning approaches. The HDC learning paradigm, which represents data with high-dimension binary vectors, allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas (computer vision, bioinformatics, mass spectrometery, remote sensing, edge devices, etc.). To the best of our knowledge, our work is the first to consider HDC for the task of fast and efficient screening of modern drug-like compound libraries. We also propose the first HDC graph-based encoding methods for molecular data, demonstrating consistent and substantial improvement over previous work. We compare our approaches to alternative approaches on the well-studied MoleculeNet dataset and the recently proposed LIT-PCBA dataset derived from high quality PubChem assays. We demonstrate our methods on multiple target hardware platforms, including Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs), showing at least an order of magnitude improvement in energy efficiency versus even our smallest neural network baseline model with a single hidden layer. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools. We make our code publicly available at https://github.com/LLNL/hdbind.

59 BASIC BIOLOGICAL SCIENCES↗

A translational registration system for LANDSAT image segments

The use of satellite images obtained from various dates is essential for crop forecast systems. In order to make possible a multitemporal analysis, it is necessary that images belonging to each acquisition have pixel-wise correspondence. A system developed to obtain, register and record image segments from LANDSAT images in computer compatible tapes is described. The translational registration of the segments is performed by correlating image edges in different acquisitions. The system was constructed for the Burroughs B6800 computer in ALGOL language.

Parada, N. D. J.↗

Turbulence modeling for computational aerodynamics

The status of turbulence modeling for external aerodynamic flows is reviewed, and closure concepts for the compressible form of the Reynolds-averaged Navier-Stokes equations are briefly outlined to establish a framework for comparison. The importance of experimental requirements for developing and verifying turbulence models is emphasized. Attention is then given to three important flow categories: attached flows, separating and reattaching flows, and trailing-edge flows. Examples of comparisons between experiments and computations for twoand three-dimensional flows are presented to illustrate the status of modeling. It is shown that, for most two-dimensional attached flows, eddy viscosity concepts will probably be adequate. For attached three-dimensional flows, however, eddy-viscosity and Reynolds-stress models are both deficient, failing to predict the proper surface shear-stress in rapidly skewing boundary layers, regardless of whether they are pressure driven or strain driven.

Marvin, J. G.↗

Three-Dimensional Ignition and Flame Propagation Above Liquid Fuel Pools: Computational Analysis

A three-dimensional unsteady reactive Navier-Stokes code is developed to study the ignition and flame spread above liquid fuels initially below the flashpoint temperature. Opposed air flow to the flame spread due to forced and/or natural convection is considered. Pools of finite width and length are studied in air channels of prescribed height and width. Three-dimensional effects of the flame front near the edge of the pool are captured in the computation. The formation of a recirculation zone in the gas phase similar to that found in two-dimensional calculations is also present in the three-dimensional calculations. Both uniform spread and pulsating spread modes are found in the calculated results.

Cai, Jinsheng↗

Prediction of unsteady aerodynamic loadings caused by trailing edge control surface motions in subsonic compressible flow: Analysis and results

A theoretical analysis and a computer program have been developed for the prediction of unsteady lifting surface loadings caused by motions of trailing edge control surfaces having sealed gaps. The final form of the downwash integral equation has been formulated by isolating the singularities from the non-singular terms and establishing a preferred solution process to remove and evaluate the downwash discontinuities in a systematic manner. Comparisons of theoretical and experimental pressure data are made for several control surface configurations. The comparisons indicate that reasonably accurate theoretical pressure distributions and generalized forces may be obtained for a wide variety of control surface configurations. Spanwise symmetry or antisymmetry of motion, and up to four control surfaces on each half span can be accommodated.

Rowe, W. S.↗

Experimental Space Shuttle Orbiter Studies to Acquire Data for Code and Flight Heating Model Validation

In an experimental study to obtain detailed heating data over the Space Shuttle Orbiter, CUBRC has completed an extensive matrix of experiments using three distinct models and two unique hypervelocity wind tunnel facilities. This detailed data will be employed to assess heating augmentation due to boundary layer transition on the Orbiter wing leading edge and wind side acreage with comparisons to computational methods and flight data obtained during the Orbiter Entry Boundary Layer Flight Experiment and HYTHIRM during STS-119 reentry. These comparisons will facilitate critical updates to be made to the engineering tools employed to make assessments about natural and tripped boundary layer transition during Orbiter reentry. To achieve the goals of this study data was obtained over a range of Mach numbers from 10 to 18, with flight scaled Reynolds numbers and model attitudes representing key points on the Orbiter reentry trajectory. The first of these studies were performed as an integral part of Return to Flight activities following the accident that occurred during the reentry of the Space Shuttle Columbia (STS-107) in February of 2003. This accident was caused by debris, which originated from the foam covering the external tank bipod fitting ramps, striking and damaging critical wing leading edge heating tiles that reside in the Orbiter bow shock/wing interaction region. During investigation of the accident aeroheating team members discovered that only a limited amount of experimental wing leading edge data existed in this critical peak heating area and a need arose to acquire a detailed dataset of heating in this region. This new dataset was acquired in three phases consisting of a risk mitigation phase employing a 1.8% scale Orbiter model with special temperature sensitive paint covering the wing leading edge, a 0.9% scale Orbiter model with high resolution thin-film instrumentation in the span direction, and the primary 1.8% scale Orbiter model with detailed thin-film resolution in both the span and chord direction in the area of peak heating. Additional objectives of this first study included: obtaining natural or tripped turbulent wing leading edge heating levels, assessing the effectiveness of protuberances and cavities placed at specified locations on the orbiter over a range of Mach numbers and Reynolds numbers to evaluate and compare to existing engineering and computational tools, obtaining cavity floor heating to aid in the verification of cavity heating correlations, acquiring control surface deflection heating data on both the main body flap and elevons, and obtain high speed schlieren videos of the interaction of the orbiter nose bow shock with the wing leading edge. To support these objectives, the stainless steel 1.8% scale orbiter model in addition to the sensors on the wing leading edge was instrumented down the windward centerline, over the wing acreage on the port side, and painted with temperature sensitive paint on the starboard side wing acreage. In all, the stainless steel 1.8% scale Orbiter model was instrumented with over three-hundred highly sensitive thin-film heating sensors, two-hundred of which were located in the wing leading edge shock interaction region. Further experimental studies will also be performed following the successful acquisition of flight data during the Orbiter Entry Boundary Layer Flight Experiment and HYTHIRM on STS-119 at specific data points simulating flight conditions and geometries. Additional instrumentation and a protuberance matching the layout present during the STS-119 boundary layer transition flight experiment were added with testing performed at Mach number and Reynolds number conditions simulating conditions experienced in flight. In addition to the experimental studies, CUBRC also performed a large amount of CFD analysis to confirm and validate not only the tunnel freestream conditions, but also 3D flows over the orbiter acreage, wing leading edge, and controlurfaces to assess data quality, shock interaction locations, and control surface separation regions. This analysis is a standard part of any experimental program at CUBRC, and this information was of key importance for post-test data quality analysis and understanding particular phenomena seen in the data. All work during this effort was sponsored and paid for by the NASA Space Shuttle Program Office at the Johnson Space Center in Houston, Texas.

Wadhams, T. P.↗

Improved sonic-box computer program for calculating transonic aerodynamic loads on oscillating wings with thickness

A computer program was developed to account approximately for the effects of finite wing thickness in transonic potential flow over an oscillation wing of finite span. The program is based on the original sonic box computer program for planar wing which was extended to account for the effect of wing thickness. Computational efficiency and accuracy were improved and swept trailing edges were accounted for. Account for the nonuniform flow caused by finite thickness was made by application of the local linearization concept with appropriate coordinate transformation. A brief description of each computer routine and the applications of cubic spline and spline surface data fitting techniques used in the program are given, and the method of input was shown in detail. Sample calculations as well as a complete listing of the computer program listing are presented.

Ruo, S. Y.↗

Liquid lithium divertor analysis using coupled plasma material interaction model

A liquid lithium divertor can improve performance of future fusion devices by creating efficient power exhaust and improving the energy confinement via pumping of the hydrogen isotopes. In addition, significantly higher heat fluxes can be handled if controlled vapor shielding is used to redistribute the divertor heat flux over a wider area. Design and optimization of such a system calls for an analysis model which includes a strong two-way coupling between the plasma and divertor material. The incoming plasma heat and particle flux will affect the divertor surface temperature, which is a defining factor of the lithium evaporative and sputtered flux going into the plasma. Results of the coupled model based on the plasma edge code SOLPS-ITER and the computational fluid dynamics (CFD) code ANSYS-CFX will be presented for different configurations. An analytical slab flow model is used as a heat transfer boundary condition for SOLPS, defining particle flux from the wall via calculation of the surface temperature. At the final step, results of the SOLPS analysis are verified using a 3D CFD magnetohydrodynamics (MHD) analysis which uses heat and particle flux from SOLPS as a boundary condition. In addition to plasma heat flux, both analytical and CFD temperature models include several plasma material interaction effects, such as lithium evaporation, condensation and sputtering based on deuterium target flux. New adatom sputtering model based on the available experimental data is presented. Analytical model is expanded to include free surface axisymmetric configurations. Results of parametric studies of the divertor configurations with different lithium inlet temperature and velocity will be presented leading to the optimal design resulting in the lowest possible lithium contamination in the core.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The Heterogeneous Integration of Electronic Components

Heterogeneous integration (HI) of electronics components is broadly recognized as a powerful and crucial enabler for the continued growth of computing and communication. From 2010 onwards, the value of HI is increasingly visible in the advanced packaging used in artificial intelligence, high-performance computing, smartphones and communications product implementations. In this Perspective, we argue that HI is crucial to semiconductors and more broadly to the continued evolution of computing and communications. We use leading-edge advanced packaging examples to represent the value, advancements and opportunities for HI. To succeed, it is critical to develop comprehensive HI roadmaps that inform collaborations across the design, manufacturing and reliability spectrum between systems architects, packaging and semiconductor technologists to common goals. Although this article does not provide a full roadmap, we instead detail additional parameters for artificial intelligence, smartphone and other cellular communication devices, and their constituent building blocks including interconnects, power electronics, photonics, thermal management, reliability, modelling and co-design, to foster greater collaboration opportunities among academia, research laboratories and industry.

42 ENGINEERING↗

Cyclically symmetric radially self-similar phononic pseudocrystal isolator for broadband, ultrasonic vibration bandstop filtering

A 2D phononic pseudocrystal isolator exhibiting cyclic symmetry and radial self-similarity is measured and demonstrated to block a wide range of ultrasonic vibration. Measurements of longitudinal and shear wave blocking effects are made and compared with computational results. The use of the bandgap edge ratio is recommended for quantifying suppression in very-wide-bandgap materials. In conclusion, the upper-to-lower suppression edge frequency ratios of 3–4 are remarkably large for shear waves and even larger for longitudinal waves upper-to-lower suppression ratio (13 at 5 dB), such that 92.5% of frequencies in that range experience ≥ 5 dB of suppression.

Acoustic metamaterial↗

Bayesian chain graph models to characterize microbe-environment dynamics

Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is problematic given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence, thus agreeing with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via the Bayesian linear regression (LASSO). In addition, we propose an adaptive extension so that different shrinkages can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting, and compositional responses via an appropriate hierarchical structure. We test the performance of our model in a variety of simulated datasets, thereby showing superior performance to state-of-the-art approaches. We further apply our model to human gut and soil microbial compositional datasets, and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data.

compositional data↗