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At least 361 records · Page 20

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterative workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.

97 MATHEMATICS AND COMPUTING↗

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.

97 MATHEMATICS AND COMPUTING↗

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.

Habib, Salman↗

A comparison of Gaussian processes and neural networks for computer model emulation and calibration

The Department of Energy relies on complex physics simulations for prediction in domains like cosmology, nuclear theory, and materials science. These simulations are often extremely computationally intensive, with some requiring days or weeks for a single simulation. In order to assure their accuracy, these models are calibrated against observational data in order to estimate inputs and systematic biases. Because of their great computational complexity, this process typically requires the construction of an emulator, a fast approximation to the simulation. In this paper, two emulator approaches are compared: Gaussian process regression and neural networks. Their emulation accuracy and calibration performance on three real problems of Department of Energy interest is considered. On these problems, the Gaussian process emulator tends to be more accurate with narrower, but still well-calibrated uncertainty estimates. The neural network emulator is accurate, but tends to have large uncertainty on its predictions. Finally, as a result, calibration with the Gaussian process emulator produces more constrained posteriors that still perform well in prediction.

97 MATHEMATICS AND COMPUTING↗

Daily Ambient Air Pollution Metrics for Five Cities: Evaluation of Data Fusion-Based Estimates and Uncertainties

Spatiotemporal characterization of ambient air pollutant concentrations is increasingly relying on the combination of observations and air quality models to provide well-constrained, spatially and temporally complete pollutant concentration fields. Air quality models, in particular, are attractive, as they characterize the emissions, meteorological, and physiochemical process linkages explicitly while providing continuous spatial structure. However, such modeling is computationally intensive and has biases. The limitations of spatially sparse and temporally incomplete observations can be overcome by blending the data with estimates from a physically and chemically coherent model, driven by emissions and meteorological inputs. We recently developed a data fusion method that blends ambient ground observations and chemical transport-modeled (CTM) data to estimate daily, spatially resolved pollutant concentrations and associatedcorrelations. In this study, we assess the ability of the data fusion method to produce daily metrics (i.e., 1-hr max, 8-hr max, and 24-hr average) of ambient air pollution that capture spatiotemporal air pollution trends for 12 pollutants (CO, NO2, NOx, O3, SO2, PM (sub10), PM (sub 2.5), and five PM (sub 2.5) components) across five metropolitan areas (Atlanta, Birmingham, Dallas, Pittsburgh, and St. Louis), from 2002 to 2008. Three sets of comparisons are performed: (1) the CTM concentrations are evaluated for each pollutant and metropolitan domain, (2) the data fusion concentrations are compared with the monitor data, (3) a comprehensive cross-validation analysis against observed data evaluates the quality of the data fusion model simulations across multiple metropolitan domains. The resulting daily spatial field estimates of air pollutant concentrations and uncertainties are not only consistent with observations, emissions, andmeteorology, but substantially improve CTM-derived results for nearly all pollutants and all cities, with the exception of NO2 for Birmingham. The greatest improvements occur for O3 and PM (sub 2.5). Squared spatiotemporal correlation coefficients range between simulations and observations determined using cross-validation across all cities for air pollutants of secondary and mixed origins are R-squared equal to 0.88-0.93 (O3), 0.81-0.89 (SO4), 0.67-0.83 (PM (sub 2.5)), 0.52-0.72 (NO3), 0.43-0.80 (NH4), 0.32-0.51 (OC), and 0.14-0.71 (PM (sub 10)). Results for relatively homogeneous pollutants of secondary origin, tend to be better than those for more spatially heterogeneous (larger spatial gradients) pollutants of primary origin (NOx, CO, SO2 and EC). Generally, background concentrations and spatial concentration gradients reflect interurban airshed complexity and the effects of regional transport, whereas daily spatial pattern variability shows intra urban consistency in the fused data. With sufficiently high CTM spatial resolution, traffic-related pollutants exhibit gradual concentration gradients that peak toward the urban centers. Ambient pollutant concentration uncertainty estimates for the fused data are both more accurate and smaller than those for either the observations or the model simulations alone.

spatiotemporal fusion↗

A unifying Bayesian framework for merging X-ray diffraction data

Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as reflections. To compute the electron density of a molecule, the intensity of each reflection must be estimated, and redundant observations reduced to consensus intensities. Systematic effects, however, lead to the measurement of equivalent reflections on different scales, corrupting observation of changes in electron density. Here, we present a modern Bayesian solution to this problem, which uses deep learning and variational inference to simultaneously rescale and merge reflection observations. We successfully apply this method to monochromatic and polychromatic single-crystal diffraction data, as well as serial femtosecond crystallography data. We find that this approach is applicable to the analysis of many types of diffraction experiments, while accurately and sensitively detecting subtle dynamics and anomalous scattering.

59 BASIC BIOLOGICAL SCIENCES↗

Key issues of ultraviolet radiation of OH at high altitudes

Ultraviolet (UV) emissions radiated by hydroxyl (OH) is one of the fundamental elements in the prediction of radiation signature of high-altitude and high-speed vehicle. In this work, the OH A{sup 2}Σ{sup +}→X{sup 2}Π ultraviolet emission band behind the bow shock is computed under the experimental condition of the second bow-shock ultraviolet flight (BSUV-2). Four related key issues are discussed, namely, the source of hydrogen element in the high-altitude atmosphere, the formation mechanism of OH species, efficient computational algorithm of trace species in rarefied flows, and accurate calculation of OH emission spectra. Firstly, by analyzing the typical atmospheric model, the vertical distributions of the number densities of different species containing hydrogen element are given. According to the different dominating species containing hydrogen element, the atmosphere is divided into three zones, and the formation mechanism of OH species is analyzed in the different zones. The direct simulation Monte Carlo (DSMC) method and the Navier-Stokes equations are employed to compute the number densities of the different OH electronically and vibrationally excited states. Different to the previous work, the trace species separation (TSS) algorithm is applied twice in order to accurately calculate the densities of OH species and its excited states. Using a non-equilibrium radiation model, the OH ultraviolet emission spectra and intensity at different altitudes are computed, and good agreement is obtained with the flight measured data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

HAM: Hotspot-Aware Manager for Improving Communications with 3D-Stacked Memory

merging High-Performance Computing (HPC) workloads, such as graph analytics, machine learning, and big data science, are data-intensive. Data-intensive workloads usually present fine-grained memory accesses with limited or no data locality, and thus incur frequent cache misses and low utilization of memory bandwidth. 3D-stacked memory devices such as Hybrid Memory Cube (HMC) and High Bandwidth Memory (HBM) can provide significantly higher bandwidth than conventional memory modules. However, the traditional interfaces and optimization methods for JEDEC DDR devices do not allow to fully exploit the potential performance of 3D-stacked memory with the massive amount of irregular memory accesses of data-intensive applications. In this paper, we propose a novel Hotspot-Aware Manager (HAM) infrastructure for 3D-stacked memory devices capable of optimizing memory access streams via request aggregation, hotspot detection, and in-memory prefetching. %and an associated hotspot-aware page policy. We present the HAM design and implementation, and simulate it on a system using RISC-V embedded cores with attached HMC devices. We extensively evaluate HAM with over 12 benchmarks and applications representing diverse irregular memory access patterns. The results show that, on average, HAM reduces redundant requests by 37.51\% and increases the prefetch buffer hit rate by 4.2 times, compared to a baseline streaming prefetcher. On the selected benchmark set, HAM provides performance gains of 21.81\% in average (up to 34.28\%) and power savings of 35.07\% over a standard 3D-stacked memory.

Wang, Xi↗

Stress intensities for cracks emanating from pin-loaded holes

A series of stress freezing photoelastic experiments were conducted on large plates containing central holes with cracks emanating from the edge formed by the intersection of the hole with the plate surface. Loads were applied through rigid pins with neat fits in the holes. Stress-intensity factors (SIF) were estimated by a computer assisted least squares analysis of the photoelastic data taken from slices near the points of intersection of the flaw border with the hole boundary and the plate surface. Results indicate that the local mode of loading changes from Mode 1 near the hole boundary to mixed mode near the plate surface. The analysis is extended to include mixed mode loading, and results are compared with an existing approximate theory.

Smith, C. W.↗

Estimating vegetation coverage in St. Joseph Bay, Florida with an airborne multispectral scanner

A four-channel multispectral scanner (MSS) carried aboard an aircraft was used to collect data along several flight paths over St. Joseph Bay, FL. Various classifications of benthic features were defined from the results of ground-truth observations. The classes were statistically correlated with MSS channel signal intensity using multivariate methods. Application of the classification measures to the MSS data set allowed computer construction of a detailed map of benthic features of the bay. Various densities of segrasses, various bottom types, and algal coverage were distinguished from water of various depths. The areal vegetation coverage of St. Joseph Bay was not significantly different from the results of a survey conducted six years previously, suggesting that seagrasses are a very stable feature of the bay bottom.

Savastano, K. J.↗

Studies of extended planetary atmospheres

There was a theoretical study of physical and chemical processes in the stratosphere, later broadened to include the mesosphere. Particular emphasis was laid on testing of proposed height profiles of the eddy diffusion coefficient against observed tracer data. Eventually the effort shifted to study of ozone time series in satellite data, and interpretation in terms of aeronomical processes. Since all this work is computer-intensive, the first year of funding also contributed to the acquisition of a powerful minicomputer system, in collaboration with several other faculty members. This proved to be highly successful and cost effective.

Hunten, D. M.↗

Surface pressure field mapping using luminescent coatings

In recent experiments we demonstrated the feasibility of using the oxygen dependence of luminescent molecules for surface pressure measurement in aerodynamic testing. This technique is based on the observation that for many luminescent molecules the light emitted increases as the oxygen partial pressure, and thus the air pressure, the molecules see decreases. In practice the surface to be observed is coated with an oxygen permeable polymer containing a luminescent molecule and illuminated with ultraviolet radiation. The airflow induced surface pressure field is seen as a luminescence intensity distribution which can be measured using quantitative video techniques. Computer processing converts the video data into a map of the surface pressure field. The experiments consisted of evaluating a trial luminescent coating in measuring the static surface pressure field over a two-dimensional NACA-0012 section model airfoil for Mach numbers ranging from 0.3 and 0.66. Comparison of the luminescent coating derived pressures were made to those obtained from conventional pressure taps. The method along with the experiment and its results will be described.

Mclachlan, B. G.↗

Stresses Produced in Airplane Wings by Gusts

Accurate prediction of gust stress being out of the question because of the multiplicity of the free air movements, the exploration of gust stress is restricted to static method which must be based upon: 1) stress measurements in free flight; 2) check of design specifications of approved type airplanes. With these empirical data the stress must be compared which can be computed for a gust of known intensity and structure. This "maximum gust" then must be so defined as to cover the whole ambit of empiricism and thus serve as prediction for new airplane designs.

Kussner, Hans Georg↗

CART and GSFC raman lidar measurements of atmospheric aerosol backscattering and extinction profiles for EOS validation and ARM radiation studies

The aerosol retrieval algorithms used by the Moderate-Resolution Imaging Spectroradiometer (MODIS) and Multi-Angle Imaging SpectroRadiometer (MISR) sensors on the Earth Observing Satellite (EOS) AM-1 platform operate by comparing measured radiances with tabulated radiances that have been computed for specific aerosol models. These aerosol models are based almost entirely on surface and/or column averaged measurements and so may not accurately represent the ambient aerosol properties. Therefore, to validate these EOS algorithms and to determine the effects of aerosols on the clear-sky radiative flux, we have begun to evaluate the vertical variability of ambient aerosol properties using the aerosol backscattering and extinction profiles measured by the Cloud and Radiation Testbed (CART) and NASA Goddard Space Flight Center (GSFC) Raman Lidars. Using the procedures developed for the GSFC Scanning Raman Lidar (SRL), we have developed and have begun to implement algorithms for the CART Raman Lidar to routinely provide profiles of aerosol extinction and backscattering during both nighttime and ,daytime operations. Aerosol backscattering and extinction profiles are computed for both lidar systems using data acquired during the 1996 and 1997 Water Vapor Intensive Operating Periods (IOPs). By integrating these aerosol extinction profiles, we derive measurements of aerosol optical thickness and compare these with coincident sun photometer measurements. We also use these measurements to measure the aerosol extinction/backscatter ratio S(sub a) (i.e. 'lidar ratio'). Furthermore, we use the simultaneous water vapor measurements acquired by these Raman lidars to investigate the effects of water vapor on aerosol optical properties.

Ferrare, R. A.↗

Predictions of Separated and Transitional Boundary Layers Under Low-Pressure Turbine Airfoil Conditions Using an Intermittency Transport Equation

A new transport equation for the intermittency factor was proposed to predict separated and transitional boundary layers under low-pressure turbine airfoil conditions. The intermittent behavior of the transitional flows is taken into account and incorporated into computations by modifying the eddy viscosity, mu(sub t), with the intermittency factor, gamma. Turbulent quantities are predicted by using Menter's two-equation turbulence model (SST). The intermittency factor is obtained from a transport equation model, which not only can reproduce the experimentally observed streamwise variation of the intermittency in the transition zone, but also can provide a realistic cross-stream variation of the intermittency profile. In this paper, the intermittency model is used to predict a recent separated and transitional boundary layer experiment under low pressure turbine airfoil conditions. The experiment provides detailed measurements of velocity, turbulent kinetic energy and intermittency profiles for a number of Reynolds numbers and freestream turbulent intensity conditions and is suitable for validation purposes. Detailed comparisons of computational results with experimental data are presented and good agreements between the experiments and predictions are obtained.

Suzen, Y. Bora↗

Predictions of Separated and Transitional Boundary Layers Under Low-Pressure Turbine Airfoil Conditions Using an Intermittency Transport Equation

A new transport equation for the intermittency factor was proposed to predict separated and transitional boundary layers under low-pressure turbine airfoil conditions. The intermittent behavior of the transitional flows is taken into account and incorporated into computations by modifying the eddy viscosity, t , with the intermittency factor, y. Turbulent quantities are predicted by using Menter s two-equation turbulence model (SST). The intermittency factor is obtained from a transport equation model, which not only can reproduce the experimentally observed streamwise variation of the intermittency in the transition zone, but also can provide a realistic cross-stream variation of the intermittency profile. In this paper, the intermittency model is used to predict a recent separated and transitional boundary layer experiment under low pressure turbine airfoil conditions. The experiment provides detailed measurements of velocity, turbulent kinetic energy and intermittency profiles for a number of Reynolds numbers and freestream turbulent intensity conditions and is suitable for validation purposes. Detailed comparisons of computational results with experimental data are presented and good agreements between the experiments and predictions are obtained.

Suzen, Y. B.↗

An integrated decision support system for TRAC: A proposal

Optimal allocation and usage of resources is a key to effective management. Resources of concern to TRAC are: Manpower (PSY), Money (Travel, contracts), Computing, Data, Models, etc. Management activities of TRAC include: Planning, Programming, Tasking, Monitoring, Updating, and Coordinating. Existing systems are insufficient, not completely automated, manpower intensive, and has the potential for data inconsistency exists. A system is proposed which suggests a means to integrate all project management activities of TRAC through the development of a sophisticated software and by utilizing the existing computing systems and network resources. The systems integration proposal is examined in detail.

Mukkamala, Ravi↗