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At least 1,531 records · Page 85

SpackDev: Multi-Package Development with Spack

High Energy Physics (HEP) software environments often involve ~ hundreds of external packages and libraries, and similar numbers of experiment-specific, science-critical packages—many under continuous development. Managing coherent releases of the external software stack is challenging enough, but managing the highly-collaborative—and distributed—development of a large body of code against such a stack adds even more complexity and room for error. Spack is a popular Python-based package management tool with a specific focus on the needs of High Performance Computing (HPC) systems and system administrators whose strength is orchestrating the discrete download, build, testing, and installation of pre-packaged or tagged third-party software against similarly stable dependencies. As such it is becoming increasingly popular within HEP as that community makes increasing use of HPC facilities, and as efforts to develop future HPC systems utilize Spack to provide scientific software on those platforms. SpackDev is a system to facilitate the simultaneous development of interconnected sets of packages. Intended to handle packages without restriction to one internal build system, SpackDev is integrated with Spack as a command extension in order to leverage features such as dependency calculations and build system configuration, and is generally applicable outside HEP. We describe SpackDev’s features and development over the last two years, initial experience using SpackDev in the context of the LArSoft liquid argon detector toolkit, and work remaining before it can be considered a fully-functional multi-package build system for HEP experiments utilizing Spack.

Green, Chris↗

Span graphics display utilities handbook, first edition

The Space Physics Analysis Network (SPAN) is a computer network connecting scientific institutions throughout the United States. This network provides an avenue for timely, correlative research between investigators, in a multidisciplinary approach to space physics studies. An objective in the development of SPAN is to make available direct and simplified procedures that scientists can use, without specialized training, to exchange information over the network. Information exchanges include raw and processes data, analysis programs, correspondence, documents, and graphite images. This handbook details procedures that can be used to exchange graphic images over SPAN. The intent is to periodically update this handbook to reflect the constantly changing facilities available on SPAN. The utilities described within reflect an earnest attempt to provide useful descriptions of working utilities that can be used to transfer graphic images across the network. Whether graphic images are representative of satellite servations or theoretical modeling and whether graphics images are of device dependent or independent type, the SPAN graphics display utilities handbook will be the users guide to graphic image exchange.

Gallagher, D. L.↗

Inversion methods for satellite studies of the Earth Radiation Budget - Development of algorithms for the ERBE mission

The Earth Radiation Budget Experiment carries a three-channel scanning radiometer and a set of nadir-looking wide and medium field-of-view instruments for measuring the radiation emitted from earth and the solar radiation reflected from earth. This paper describes the algorithms which are used to compute the radiant exitances at a reference level ('top of the atmosphere') from these measurements. Methods used to analyze data from previous radiation budget experiments are reviewed, and the rationale for the present algorithms is developed. The scanner data are converted to radiances by use of spectral factors, which account for imperfect spectral response of the optics. These radiances are converted to radiant exitances at the reference level by use of directional models, which account for anisotropy of the radiation as it leaves the earth. The spectral factors and directional models are selected on the basis of the scene, which is identified on the basis of the location and the long-wave and shortwave radiances. These individual results are averaged over 2.5 x 2.5 deg regions. Data from the wide and medium field-of-view instruments are analyzed by use of the traditional shape factor method and also by use of a numerical filter, which permits resolution enhancement along the orbit track.

Smith, G. L.↗

Evaluation of a nonlinear variational multiscale method for fluid transport problems

Diverse transport problems, especially those based on fluid flow models, are intrinsically multiscale and nonlinear, characteristics that often lead to intricate dynamics such as the development of instabilities and turbulence. Computational simulations that resolve all scales in these problems are often unfeasible, prompting to coarse-grained simulation strategies in which small-scale features are modeled instead of resolved. Variational Multiscale (VMS) methods, and particularly residual-based Large-Eddy Simulation (LES) approaches, have proven effective and robust for the coarse-grained simulation of complex transport problems. VMS methods avoid the assumption of separable nonlinearity and the reliance on empirical small-scale models by using a variational decomposition of scales together with a residual-based approximation of the small-scales. Evaluation of a nonlinear VMS approach, denoted as VMS n , is presented for the coarse-grained simulation of transient-advective-diffusive-reactive (TADR) transport problems arising from fluid flow models. In contrast to classical VMS approaches that neglect the effect of the small scales on the transport operator, VMS n treats the inter-dependence between large- and small-scales upfront. The treatment of inter-scale coupling involves the solution of a local algebraic nonlinear system describing the evolution of the small-scales. The VMS n approach is complemented with two algebraic approximations of the small-scales: one based on the main diagonal of the transport matrices and another that preserves transport fluxes and is suitable for generic TADR systems. The suitability of the VMS n approach for handling general TADR problems and regimes is evaluated with benchmark incompressible, compressible, and magnetohydrodynamic laminar flow problems, the incompressible Taylor-Green vortex flow, the turbulent free jet, and the two-temperature arc in crossflow. Furthermore, simulation results show that VMS n leads to minor improvements in accuracy with respect to the classical VMS for the laminar flow problems, but to significantly greater accuracy for the turbulent flows and the unsteady plasma flow problems, while using the same cohesive numerical formulation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

2p x-ray absorption spectroscopy of 3d transition metal systems

This review provides an overview of the different methods and computer codes that are used to interpret 2p x-ray absorption spectra of 3d transition metal ions. We first introduce the basic parameters and give an overview of the methods used. We start with the semi-empirical multiplet codes and compare the different codes that are available. A special chapter is devoted to the user friendly interfaces that have been written on the basis of these codes. Next we discuss the first principle codes based on band structure, including a chapter on Density Functional theory based approaches. We also give an overview of the first-principle multiplet codes that start from a cluster calculation and we discuss the wavefunction based methods, including multi-reference methods. We end the review with a discussion of the link between theory and experiment and discuss the open issues in the spectral analysis.

36 MATERIALS SCIENCE↗

The Effective Field Theory of Large Scale Structures at two loops

Here, large scale structure surveys promise to be the next leading probe of cosmological information. It is therefore crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbation theory for the weakly non-linear regime of dark matter, where correlation functions are computed in an expansion of the wavenumber k of a mode over the wavenumber associated with the non-linear scale k NL . Since most of the information is contained at high wavenumbers, it is necessary to compute higher order corrections to correlation functions. After the one-loop correction to the matter power spectrum, we estimate that the next leading one is the two-loop contribution, which we compute here. At this order in k/k NL , there is only one counterterm in the EFTofLSS that must be included, though this term contributes both at tree-level and in several one-loop diagrams. We also discuss correlation functions involving the velocity and momentum fields. We find that the EFTofLSS prediction at two loops matches to percent accuracy the non-linear matter power spectrum at redshift zero up to k~ 0.6 h Mpc –1 , requiring just one unknown coefficient that needs to be fit to observations. Given that Standard Perturbation Theory stops converging at redshift zero at k~ 0.1 h Mpc –1 , our results demonstrate the possibility of accessing a factor of order 200 more dark matter quasi-linear modes than naively expected. If the remaining observational challenges to accessing these modes can be addressed with similar success, our results show that there is tremendous potential for large scale structure surveys to explore the primordial universe.

79 ASTRONOMY AND ASTROPHYSICS↗

Thermal Radiator Pointing for International Space Station

In order to provide thermal radiation environments that result in adequate beat rejection, the single-phase, liquid ammonia (NH3) heat rejection system on the International Space Station (ISS) requires that its two thermal radiator wings be dynamically rotated as the ISS travels through its orbit. This paper discusses the closed-loop, thermal radiator pointing system that is used on ISS to ensure adequate heat rejection by the radiators, while preventing freezing of the ammonia under low heat loads and cold-environmental conditions. Although initial designs used an open-loop approach for radiator pointing, concerns about performance robustness, algorithm complexity, memory requirements, and sustaining support drove the development of a more robust, simpler, closed-loop system. Hence, the challenge of the closed-loop system was to utilize existing sensors, actuators and computers to fit into the existing hardware and software architecture of the ISS. Using a proportional-integral (PI) control architecture with limited output and an anti-windup integrator, the temperature of the ammonia coming out of the radiator is measured and controlled by adjusting the radiator wing orientation. The radiator wing orientation for the local minimum environment is fed forward to the control system, and the closed-loop controller is used to generate a bias off of that local minimum environment in order to heat up the ammonia when necessary to avoid freezing. In the earth's shadow, the controller is suspended and the radiator wing is oriented to face the earth, the local maximum thermal environment which further prevents freezing of the ammonia. This control architecture is shown to provide adequate heat rejection and avoid freezing of the ammonia, even though the physical system consists of large transport delays and time-varying dynamics which change dramatically due to orbit motion and variable heat loads.

Green, Scott↗

The distribution and mechanism of pore formation in copper foams fabricated by Lost Carbonate Sintering method

In this research, utilizing X-ray computed tomography (XCT), geometrical characterization, and pore formation mechanisms of highly porous copper foams manufactured by powder metallurgical (PM) process are investigated. Open-cell copper foams with porosity percentages of 60% and 80% and with a pore size within the range of 300–600 μm were manufactured by using potassium carbonate as a space holder agent via the Lost Carbonate Sintering (LCS) technique. XCT and SEM were also employed to investigate the three-dimensional structure of foams and to find the effect of the parameters of the space holders on the structural properties of copper foams. The result showed an excellent correlation between the structural properties of the foams including the size and shape of the pores, porosity percentage, volume percentage, particle size, and the shape of the sacrificial agent used. Also, the advanced image analysis of XCT images indicated fluctuations up to ± 10% in porosity distribution across different cross-sections of the foams. Simultaneous thermal analysis (STA: DTA–TG) was also used to study the thermal history of the powders used during the manufacturing process of the foams. The results indicated that the melting and thermal decomposition of the potassium carbonate occurred simultaneously at 920 °C and created the porous structure of the foams. By combining the STA result with the result of the tension analysis of cell walls, the mechanisms of open-pore formation were suggested. In fact, most open pores in the samples were formed due to the direct contact of potassium carbonate particles with each other in green compact. Also, it was found that the thermal decomposition of potassium carbonate particles into gaseous CO{sub 2} led to the production of gas pressure inside the closed pores, which eventually caused the creation of cracks on the cell walls and the opening of the pores in foam's structure. - Highlights: • Structural characterization of copper foam produced by LCS method is investigated by tomography images. • The ability of LCS technique to control structural features of produced foams was proved. • The mechanisms of open pores formation were presented.

36 MATERIALS SCIENCE↗

THE LBT BOOeTES FIELD SURVEY. I. THE REST-FRAME ULTRAVIOLET AND NEAR-INFRARED LUMINOSITY FUNCTIONS AND CLUSTERING OF BRIGHT LYMAN BREAK GALAXIES AT Z {approx} 3

We present a deep LBT/LBC U{sub spec}-band imaging survey (9 deg{sup 2}) covering the NOAO Booetes field. A total of 14,485 Lyman break galaxies (LBGs) at z {approx} 3 are selected, which are used to measure the rest-frame UV luminosity function (LF). The large sample size and survey area reduce the LF uncertainties due to Poisson statistics and cosmic variance by {>=}3 compared to previous studies. At the bright end, the LF shows excess power compared to the best-fit Schechter function, which can be attributed to the contribution of z {approx} 3 quasars. We compute the rest-frame near-infrared LF and stellar mass function (SMF) of z {approx} 3 LBGs based on the R-band and [4.5 {mu}m]-band flux relation. We investigate the evolution of the UV LFs and SMFs between z {approx} 7 and z {approx} 3, which supports a rising star formation history in the LBGs. We study the spatial correlation function of two bright LBG samples and estimate their average host halo mass. We find a tight relation between the host halo mass and the galaxy star formation rate (SFR), which follows the trend predicted by the baryonic accretion rate onto the halo, suggesting that the star formation in LBGs is fueled by baryonic accretion through the cosmic web. By comparing the SFRs with the total baryonic accretion rates, we find that cosmic star formation efficiency is about 5%-20% and it does not evolve significantly with redshift, halo mass, or galaxy luminosity.

79 ASTRONOMY AND ASTROPHYSICS↗

A self-consistent method to assess air quality co-benefits from U.S. climate policies

Air quality co-benefits can possibly reduce the costs of greenhouse gas mitigation. However, whereas many studies of the cost of greenhouse gas mitigation model the macroeconomic welfare impacts of mitigation, most studies of air quality co-benefits do not. We enable a U.S. computable general equilibrium economic model previously linked to an air quality modeling system and enhance it to represent the economy-wide welfare impacts of fine particulate matter. We introduce a first application of this method to explore the efficiency and distributional implications of a Clean Energy Standard (CES) and a Cap and Trade (CAT) program that both reduce CO 2 emissions by 10% in 2030 relative to 2006. We find that co-benefits from fine particulate matter reduction (median $\$$6; $\$$2 to $\$$10/tCO 2 ) completely offset policy costs by 110% (40% to 190%), transforming the net welfare impact of the CAT into a gain of $\$$1 (-$\$$5 to $\$$7) billion 2005 $\$$. For the CES, the corresponding co-benefit (median $\$$8; $\$$3 to $\$$14/tCO 2 ) is a smaller fraction (median 5%; 2% to 9%) of its higher policy cost. The eastern United States garners 78% and 71% of co-benefits for the CES and CAT, respectively. By representing the effects of pollution-related morbidities and mortalities as an impact to labor and the demand for health services, we find that the welfare impact per unit of reduced pollution varies by region. These interregional differences can enhance the preference of some regions, such as Texas, for a CAT over a CES, or switch the calculation of which policy yields higher co-benefits, compared with an approach that uses one valuation for all regions. This framework could be applied to quantify consistent air quality impacts of other pricing instruments, subnational trading programs, or green tax swaps.

54 ENVIRONMENTAL SCIENCES↗

An example of scaling MST Doppler spectra using median spectra, spectral smoothing, and velocity tracing

Although automatic, computer scaling methods appeared at the start of the MST (mesosphere stratosphere troposphere) radar technique, there is a continuing need for scaling algorithms that perform editing functions and increase the sensitivity of radar by post processing. The scaling method presented is an adaptation of the method of scaling MST Doppler spectra presented by Rastogi (1984). A brief overview of this method is as follows: a median spectrum is calculated from several sequential spectra; the median noise value is subtracted from this derived spectrum; the median spectrum is smoothed; the detection/nondetection decision is made by comparing the smoothed spectrum to the variance of the smoothed noise; and if a signal is detected, then the half-power points of the smoothed echo spectrum are used to place limits on the evaluation of the first two moments of the unsmoothed median spectrum. In all of the above steps, the algorithm is guided by tracing the expected velocity range upward from the lowest range as far as possible. The method is discussed in more detail.

Green, J. L.↗

Semantic segmentation with a sparse convolutional neural network for event reconstruction in MicroBooNE

We present the performance of a semantic segmentation network, SparseSSNet, that provides pixel-level classification of MicroBooNE data. The MicroBooNE experiment employs a liquid argon time projection chamber for the study of neutrino properties and interactions. SparseSSNet is a submanifold sparse convolutional neural network, which provides the initial machine learning based algorithm utilized in one of MicroBooNE's ν e -appearance oscillation analyses. The network is trained to categorize pixels into five classes, which are re-classified into two classes more relevant to the current analysis. The output of SparseSSNet is a key input in further analysis steps. This technique, used for the first time in liquid argon time projection chambers data and is an improvement compared to a previously used convolutional neural network, both in accuracy and computing resource utilization. Here, the accuracy achieved on the test sample is ≥ 99%. For full neutrino interaction simulations, the time for processing one image is ≈ 0.5 sec, the memory usage is at 1 GB level, which allows utilization of most typical CPU worker machine.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

An Investigation of Parallel Programming Techniques Applied to Monte Carlo Simulations for Post-Flight Reconstruction of Spacecraft Trajectory

Parallelizing software to execute on multi-core central processing units (CPUs) and graphics processing units (GPUs) can be challenging. For some fields outside of Computer Science, this transition comes with new issues. For example, memory limitations can require modifications to code not initially developed to run on GPUs. This work applies the Open Multi-Processing (OpenMP) and Open Accelerators (OpenACC) directive-based parallelization strategies on a Monte Carlo simulation approach for trajectory reconstruction enabling it to run on multi-core CPUs and GPUs. Large matrix operations are the most common use of GPUs, which are not present in this algorithm; however, the natural parallelism of independent trajectories in Monte Carlo simulations is exploited. Benchmarking data are presented comparing execution times of the software for single-thread CPUs, multi-thread CPUs with OpenMP, and multi-thread GPUs using OpenACC. These data were collected using nodes with Intel® Xeon® E5-2670 (Sandy Bridge) CPUs enhanced with NVIDIA® Tesla® K40 GPUs on the Pleiades Supercomputer cluster at the National Aeronautics and Space Administration (NASA) Ames Research Center (ARC) and a local Intel® Xeon Phi™ node at NASA Langley Research Center (LaRC).

Williams, R. Anthony↗

Elk: A New MOOSE Framework Application for Radio-frequency Electromagnetics

A new tool in-development for general electromagnetic (EM) simulation for modeling radio-frequency (rf) systems is presented. The primary motivation for development of this tool is to leverage the flexibility and high-performance-computing capability of the Multiphysics Object-Oriented Simulation Environment (MOOSE) Framework developed by Idaho National Laboratory (INL) for complex EM problems. A MOOSE application (or MOOSE App) enables the end user to create a fully-functional simulation scenario without needing explicit knowledge of the underlying finite-element weak form implementation. MOOSE combines the libMesh library and the PetSc suite as the finite element and solver libraries, giving a robust platform for solving highly non-linear, coupled sets of PDEs such as those found in EM and plasma physics problems. Initial validation efforts have included standard waveguide and antenna benchmarks with the current focus being field validation against the well-known capacitively-coupled GEC Reference Cell (GEC-CCP). The results of this effort will be outlined and discussed. Future work plans including cold-plasma rf wave propagation studies and coupling to the plasma fluid MOOSE App, Zapdos [Lindsay et al 2016 J. Phys. D: Appl. Phys. 49 235204], will also be discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Organic Matrix Derived from Host–Microbe Interplay Contributes to Pathological Renal Biomineralization

Matrix stones are a rare form of kidney stones. They feature a high percentage of hydrogel-like organic matter, and their formation is closely associated with urinary tract infections. Herein, comprehensive materials and biochemical approaches were taken to map the organic-inorganic interface and gather insights into the host-microbe interplay in pathological renal biomineralization. Surgically extracted soft and slimy matrix stones were examined using micro-X-ray computed tomography and various microspectroscopy techniques. Higher-mineral-density laminae were positive for calcium-bound Alizarin red. Lower-mineral-density laminae revealed periodic acid-Schiff-positive organic filamentous networks of varied thickness. These organic filamentous networks, which featured a high polysaccharide content, were enriched with zinc, carbon, and sulfur elements. Neutrophil extracellular traps (NETs) along with immune response-related proteins, including calprotectin, myeloperoxidase, CD63, and CD86, also were identified in the filamentous networks. Expressions of NETs and upregulation of polysaccharide-rich mucin secretion are proposed as a part of the host immune defense to "trap" pathogens. These host-microbe derived organic matrices can facilitate heterogeneous nucleation and precipitation of inorganic particulates, resulting in macroscale aggregates known as "matrix stones". These insights into the plausible aggregation of constituents through host-microbe interplay underscore the unique "double-edged sword" effect of the host immune response to pathogens and the resulting renal biominerals.

59 BASIC BIOLOGICAL SCIENCES↗

Network-Level Traffic Signal Cooperation: A Higher-Order Conflict Graph Approach

Traffic signal control and cooperation are extremely important to alleviate traffic congestion in a large traffic network. This study develops a higher-order conflict graph approach for network-wide traffic signal control and cooperation. A conflict graph is applied to model the traffic signal configurations, which identifies the conflict and unconflicted movements for each intersection. In conflict graph, the node represents each movement. The weight of each node can be defined as traffic volume, queue length, fuel consumption, or any weighted combinations of these measurements. The calculation of the optimal green light duration and green light sequence (for different movements) is equivalent to sequentially finding the maximum weight independent set (MWIS) in the conflict graph. The conflict graph also provides a uniform and efficient way to connect traffic signal operations among nearby intersections spatially. Then, we introduced the concept of the k -th order neighborhood to model the degree of connectivity between each movement to the movements at upstream or downstream intersections. The weight of each node in the higher-order conflict graph not only represents its own congestion level, but also relates to the traffic conditions of nearby intersections. Through this approach, the cooperation of multiple intersections can be realized by incorporating their spatial connectivity into conflict graph and solving the MWIS problem. A simulation network is built in SUMO to test the effectiveness of the proposed method. Results suggested that the proposed model outperformed other state-of-the-art signal control methods. Also, the scheme maintains good performance under varying traffic demands.

42 ENGINEERING↗

SU-E-E-06: Teaching About the Gamma Camera and Ultrasound Imaging

Purpose: Instructional modules on applications of physics in medicine are being developed. The target audience consists of students who have had an introductory undergraduate physics course. This presentation will concentrate on an active learning approach to teach the principles of the gamma camera. There will also be a description of an apparatus to teach ultrasound imaging. Methods: Since a real gamma camera is not feasible in the undergraduate classroom, we have developed two types of optical apparatus that teach the main principles. To understand the collimator, LEDS mimic gamma emitters in the body, and the photons pass through an array of tubes. The distance, spacing, diameter, and length of the tubes can be varied to understand the effect upon the resolution of the image. To determine the positions of the gamma emitters, a second apparatus uses a movable green laser, fluorescent plastic in lieu of the scintillation crystal, acrylic rods that mimic the PMTs, and a photodetector to measure the intensity. The position of the laser is calculated with a centroid algorithm.To teach the principles of ultrasound imaging, we are using the sound head and pulser box of an educational product, variable gain amplifier, rotation table, digital oscilloscope, Matlab software, and phantoms. Results: Gamma camera curriculum materials have been implemented in the classroom at Loyola in 2014 and 2015. Written work shows good knowledge retention and a more complete understanding of the material. Preliminary ultrasound imaging materials were run in 2015. Conclusion: Active learning methods add another dimension to descriptions in textbooks and are effective in keeping the students engaged during class time. The teaching apparatus for the gamma camera and ultrasound imaging can be expanded to include more cases, and could potentially improve students’ understanding of artifacts and distortions in the images.

60 APPLIED LIFE SCIENCES↗

Remote sensing of gene expression in Planta: transgenic plants as monitors of exogenous stress perception in extraterrestrial environments

Transgenic arabidopsis plants containing the alcohol dehydrogenase (Adh) gene promoter fused to the green fluorescent protein (GFP) reporter gene were developed as biological sensors for monitoring physiological responses to unique environments. Plants were monitored in vivo during exposure to hypoxia, high salt, cold, and abcissic acid in experiments designed to characterize the utility and responses of the Adh/GFP biosensors. Plants in the presence of environmental stimuli that induced the Adh promoter responded by expressing GFP, which in turn generated a detectable fluorescent signal. The GFP signal degraded when the inducing stimulus was removed. Digital imaging of the Adh/GFP plants exposed to each of the exogenous stresses demonstrated that the stress-induced gene expression could be followed in real time. The experimental results established the feasibility of using a digital monitoring system for collecting gene expression data in real time from Transgenic Arabidopsis Gene Expression System (TAGES) biosensor plants during space exploration experiments.

NASA Discipline Plant Biology↗