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DOE OSTI2015

PROPERTIES OF A CORONAL SHOCK WAVE AS A DRIVER OF EARLY SEP ACCELERATION

Coronal mass ejectmons (CMEs) are thought to drive collisionless shocks in the solar corona, which in turn have been shown to be capable of accelerating solar energetic particles (SEPs) in minutes. It has been notoriously difficult to extract information about energetic particle spectra in the corona, owing to a lack of in situ measurements. It is possible, however, to combine remote observations with data-driven models in order to deduce coronal shock properties relevant to the local acceleration of SEPs and their heliospheric connectivity to near-Earth space. We present such novel analysis applied to the 2011 May 11 CME event on the western solar limb, focusing on the evolution of the eruption-driven, dome-like shock wave observed by the Atmospheric Imaging Assembly (AIA) EUV telescopes on board the Solar Dynamics Observatory spacecraft. We analyze the shock evolution and estimate its strength using emission measure modeling. We apply a new method combining a geometric model of the shock front with a potential field source surface model to estimate time-dependent field-to-shock angles and heliospheric connectivity during shock passage in the low corona. We find that the shock was weak, with an initial speed of ∼450 km s{sup –1}. It was initially mostly quasi-parallel, but a significant portion of it turned quasi-perpendicular later in the event. There was good magnetic connectivity to near-Earth space toward the end of the event as observed by the AIA instrument. The methods used in this analysis hold a significant potential for early characterization of coronal shock waves and forecasting of SEP spectra based on remote observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Heterodyne frequency-domain multispectral diffuse optical tomography of breast cancer in the parallel-plane transmission geometry

Purpose: The authors introduce a state-of-the-art all-optical clinical diffuse optical tomography (DOT) imaging instrument which collects spatially dense, multispectral, frequency-domain breast data in the parallel-plate geometry. Methods: The instrument utilizes a CCD-based heterodyne detection scheme that permits massively parallel detection of diffuse photon density wave amplitude and phase for a large number of source–detector pairs (10{sup 6}). The stand-alone clinical DOT instrument thus offers high spatial resolution with reduced crosstalk between absorption and scattering. Other novel features include a fringe profilometry system for breast boundary segmentation, real-time data normalization, and a patient bed design which permits both axial and sagittal breast measurements. Results: The authors validated the instrument using tissue simulating phantoms with two different chromophore-containing targets and one scattering target. The authors also demonstrated the instrument in a case study breast cancer patient; the reconstructed 3D image of endogenous chromophores and scattering gave tumor localization in agreement with MRI. Conclusions: Imaging with a novel parallel-plate DOT breast imager that employs highly parallel, high-resolution CCD detection in the frequency-domain was demonstrated.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions

Many processes have been put forward to explain the latitudinal gradient in species richness. Here, we use a simulation model to examine four of the most common hypotheses and identify patterns that might be diagnostic of those four hypotheses. The hypotheses examined include (1) tropical niche conservatism, or the idea that the tropics are more diverse because a tropical clade origin has allowed more time for diversification in the tropics and has resulted in few species adapted to extra-tropical climates. (2) The productivity, or energetic constraints, hypothesis suggests that species richness is limited by the amount of biologically available energy in a region. (3) The tropical stability hypothesis argues that major climatic fluctuations and glacial cycles in extratropical regions have led to greater extinction rates and less opportunity for specialization relative to the tropics. (4) Finally, the speciation rates hypothesis suggests that the latitudinal richness gradient arises from a parallel gradient in rates of speciation. We found that tropical niche conservatism can be distinguished from the other three scenarios by phylogenies which are more balanced than expected, no relationship between mean root distance and richness across regions, and a homogeneous rate of speciation across clades and through time. The energy gradient, speciation gradient, and disturbance gradient scenarios all exhibited phylogenies which were more imbalanced than expected, showed a negative relationship between mean root distance and richness, and diversity-dependence of speciation rate estimates through time. Using Bayesian Analysis of Macroevolutionary Mixtures on the simulated phylogenies, we found that the relationship between speciation rates and latitude could distinguish among these three scenarios. We emphasize the importance of considering multiple hypotheses and focusing on diagnostic predictions instead of predictions that are consistent with more than one hypothesis.

biodiversity↗

DOE OSTI2023

In-depth analysis on parallel processing patterns for high-performance Dataframes

The Data Science domain has expanded monumentally in both research and industry communities during the past decade, predominantly owing to the Big Data revolution. Artificial Intelligence (AI) and Machine Learning (ML) are bringing more complexities to data engineering applications, which are now integrated into data processing pipelines to process terabytes of data. Typically, a significant amount of time is spent on data preprocessing in these pipelines, and hence improving its efficiency directly impacts the overall pipeline performance. The community has recently embraced the concept of Dataframes as the de-facto data structure for data representation and manipulation. However, the most widely used serial Dataframes today (R, pandas) experience performance limitations while working on even moderately large data sets. We believe that there is plenty of room for improvement by taking a look at this problem from a high-performance computing point of view. In a prior publication, we presented a set of parallel processing patterns for distributed dataframe operators and the reference runtime implementation, Cylon. In this paper, we are expanding on the initial concept by introducing a cost model for evaluating the said patterns. Furthermore, we evaluate the performance of Cylon on the ORNL Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Asynchronously parallel optimization solver for finding multiple minima

This paper proposes and analyzes an asynchronously parallel optimization algorithm for finding multiple, high-quality minima of nonlinear optimization problems. Our multistart algorithm considers all previously evaluated points when determining where to start or continue a local optimization run. Theoretical results show that, under certain assumptions, the algorithm almost surely starts a finite number of local optimization runs and identifies, or has a single local optimization run converging to, every minimum. The algorithm is applicable to general optimization settings, but our numerical results focus on the case when derivatives are unavailable. In numerical tests, a PYTHON implementation of the algorithm is shown to yield good approximations of many minima (including a global minimum), and this ability scales well with additional resources. Our implementation’s time to solution is shown also to scale well even when the time to evaluate the function evaluation is highly variable.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

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

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

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

High-order matrix-free incompressible flow solvers with GPU acceleration and low-order refined preconditioners

In this work, we present a matrix-free flow solver for high-order finite element discretizations of the incompressible Navier-Stokes and Stokes equations with GPU acceleration. For high polynomial degrees, assembling the matrix for the linear systems resulting from the finite element discretization can be prohibitively expensive, both in terms of computational complexity and memory. For this reason, it is necessary to develop matrix-free operators and preconditioners, which can be used to efficiently solve these linear systems without access to the matrix entries themselves. The matrix-free operator evaluations utilize GPU-accelerated sum-factorization techniques to minimize memory movement and maximize throughput. The preconditioners developed in this work are based on a low-order refined methodology with parallel subspace corrections, as described for diffusion problems in [1]. The saddle-point Stokes system is solved using block-preconditioning techniques, which are robust in mesh size, polynomial degree, time step, and viscosity. For the incompressible Navier-Stokes equations, we make use of projection (fractional step) methods, which require Helmholtz and Poisson solves at each time step. The performance of our flow solvers is assessed on several benchmark problems in two and three spatial dimensions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A fully implicit, asymptotic-preserving, semi-Lagrangian algorithm for the time dependent anisotropic heat transport equation

In this paper, we extend the operator-split asymptotic-preserving, semi-Lagrangian algorithm for time dependent anisotropic heat transport equation proposed in Chacón et al. (2014) [18] to use a fully implicit time integration with backward differentiation formulas. The proposed implicit method can deal with arbitrary heat-transport anisotropy ratios $\mathcal{X}$∥ /$ \mathcal{X}$⟂ $\ggg$ 1 (with $\mathcal{X}$∥, $ \mathcal{X}$⟂ the parallel and perpendicular heat diffusivities, respectively) in complicated magnetic field topologies in an accurate and efficient manner. Further, the implicit algorithm is second-order accurate temporally and demonstrates an accurate treatment at boundary layers (e.g., island separatrices), which was not ensured by the operator-split implementation. The condition number of the resulting algebraic system is independent of the anisotropy ratio, and is inverted with preconditioned GMRES. We propose a simple preconditioner that renders the finite-dimensional linear operator compact, resulting in mesh-independent convergence rates for topologically simple magnetic fields, and convergence rates scaling as ~ (NΔt) 1/4 (with N the total mesh size and Δt the timestep) in topologically complex magnetic-field configurations. We demonstrate the accuracy and performance of the approach with test problems of varying complexity, including an analytically tractable boundary-layer problem in a straight magnetic field, and a topologically complex magnetic field featuring magnetic islands with extreme anisotropy ratios $\mathcal{X}$∥ /$ \mathcal{X}$⟂ = 10 10 ) .

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Dissipation of moving vortices in thin films

In this letter, moving vortices in thin superconducting films are considered within the time-dependent London description. The dissipation due to out-of-core normal excitations for two vortices moving together turns out to have a minimum for the separation vector $\textit{a}$ parallel to the velocity and equal to $a_m$ ≈ 2.2 Λ , where Λ is the Pearl length. The minimum entropy production suggests that moving vortices should have a tendency to form chains along the velocity with a period of the order $a_m$.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Modelling a Transition-Edge Sensor X-Ray Microcalorimeter Linear Array for Compton Profile Measurements and Energy Dispersive Diffraction

Transition-edge sensors (TES) are a type of superconducting detector that offers high energy resolution based on their sharp resistance-temperature feature in the superconducting-to-normal transition. TES X-ray microcalorimeters have typically been designed and used for spectroscopic applications. In this work, we present a design optimization for a TES X-ray microcalorimeter array for high-energy scattering and diffraction measurements. Specifically, Compton scattering provides information about the electron momentum distribution, while energy dispersive diffraction provides structural information about dense engineering materials. Compton scattering and energy dispersive diffraction experiments must be conducted in the very hard X-ray regime (~100 keV), demanding a high X-ray stopping power in the detector; therefore, an absorber with a large heat capacity is needed in conjunction with the TES. In addition, both applications would benefit from an array composed of parallel strips. We propose a design for a TES X-ray microcalorimeter optimized for such applications. In particular, we model the longitudinal position dependence due to the finite thermal diffusion time in the absorber.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Rapid Commissioning of Large Machine Tools Using Finite Element-Based Correction of Geometric Errors

Large computer numerical control (CNC) machine tools derive their stiffness from monolithic cast iron bases or weldments that are sometimes integral to machine motion systems like box ways or guideways. However, the sheer size of castings and even floor flatness deviations result in dimensional errors in these systems, which manifest as machine motion errors. Typical geometric alignment processes rely on an iterative approach, where measurements are taken to assess alignment (straightness, squareness, and parallelism), followed by adjustment of the machine supports (fixators or leveling pads), which can take weeks even for an experienced operator. Conversely, a novel method is proposed to shorten the correction time by eliminating the trial-and-error process in favor of a more deterministic approach guided by a finite element (FE) method. A feasibility study is conducted on a CNC polymer hybrid machine, with a steel weldment frame, supported by six leveling pads. An FE model of the frame is utilized to obtain recommended leveling pad adjustments, based on measurement of machine errors taken using a laser tracker. After a single adjustment cycle, measurements reveal that geometric errors of the machine tool are reduced from 2.22 mm of flatness deviation to 0.32 mm, achieving an 85.6% reduction. Furthermore, the entire process including measurement, adjustment, and assessment is completed in just 6 h by two operators who are not professional service engineers. In conclusion, this methodology demonstrates feasibility for scaling up, especially to large, high-precision CNC machine tools with bases mounted by fixators, offering the capability for bidirectional adjustment.

42 ENGINEERING↗

DOE OSTI2016

SU-C-207A-06: On-Line Beam Range Verification with Multiple Scanning Particle Beams: Initial Feasibility Study with Simulations

Purpose: To investigate the feasibility and requirement for intra-fraction on-line multiple scanning particle beam range verifications (BRVs) with in-situ PET imaging, which is beyond the current single-beam BRV with extra factors that will affect the BR measurement accuracy, such as beam diameter, separation between beams, and different image counts at different BRV positions. Methods: We simulated a 110-MeV proton beam with 5-mm diameter irradiating a uniform PMMA phantom by GATE simulation, which generated nuclear interaction-induced positrons. In this preliminary study, we simply duplicated these positrons and placed them next to the initial protons to approximately mimic the two spatially separated positron distributions produced by two beams parallel to each other but with different beam ranges. These positrons were then imaged by a PET (∼2-mm resolution, 10% sensitivity, 320×320×128 mm^3 FOV) with different acquisition times. We calculated the positron activity ranges (ARs) from reconstructed PET images and compared them with the corresponding ARs of original positron distributions. Results: Without further image data processing and correction, the preliminary study show the errors between the measured and original ARs varied from 0.2 mm to 2.3 mm as center-to-center separations and range differences were in the range of 8–12 mm and 2–8 mm respectively, indicating the accuracy of AR measurement strongly depends on the beam separations and range differences. In addition, it is feasible to achieve ≤ 1.0-mm accuracy for both beams with 1-min PET acquisition and 12 mm beam separation. Conclusion: This study shows that the overlap between the positron distributions from multiple scanning beams can significantly impact the accuracy of BRVs of distributed particle beams and need to be further addressed beyond the established method of single-beam BRV, but it also indicates the feasibility to achieve accurate on-line multi-beam BRV with further improved method.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-EF-BRB-08: Robotic Motion Compensation for Radiation Therapy: A 6DOF Phantom Study

Purpose: The high accuracy of frame-based stereotactic radiosurgery (SRS), which uses a rigid frame fixed to the patient’s skull, is offset by potential drawbacks of poor patient compliance and clinical workflow restrictions. Recent research into frameless SRS has so far resulted in reduced accuracy. In this study, we investigate the use of a novel 6 degree-of-freedom (6DOF) robotic head motion cancellation system that continuously detects and compensates for patient head motions during a SRS delivery. This approach has the potential to reduce invasiveness while still achieving accuracies better or equal to traditional frame-based SRS. Methods: A 6DOF parallel kinematics robotics stage was constructed, and controlled using an inverse kinematics-based motion compensation algorithm. A 6DOF stereoscopic infrared (IR) marker tracking system was used to monitor real-time motions at sub-millimeter and sub-degree levels. A novel 6DOF calibration technique was first applied to properly orient the camera coordinate frame to match that of the LINAC and robotic control frames. Simulated head motions were measured by the system, and the robotic stage responded to these 6DOF motions automatically, returning the reflective marker coordinate frame to its original position. Results: After the motions were introduced to the system in the phantom-based study, the robotic stage automatically and rapidly returned the phantom to LINAC isocenter. When errors exceeded the compensation lower threshold of 0.25 mm or 0.25 degrees, the system registered the 6DOF error and generated a cancellation trajectory. The system responded in less than 0.5 seconds and returned all axes to less than 0.1 mm and 0.1 degree after the 6DOF compensation was performed. Conclusion: The 6DOF real-time motion cancellation system was found to be effective at compensating for translational and rotational motions to current SRS requirements. This system can improve frameless SRS by automatically returning patients to isocenter with high 6DOF accuracy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

On the Strong Scaling of the Spectral Element Solver Nek5000 on Petascale Systems. In: EASC '16 Proceedings of the Exascale Applications and Software Conference 2016, Article No. 5

The present work is targeted at performing a strong scaling study of the high-order spectral element fluid dynamics solver Nek5000. Prior studies such as [5] indicated a recommendable metric for strong scalability from a theoretical viewpoint, which we test here extensively on three parallel machines with different performance characteristics and interconnect networks, namely Mira (IBM Blue Gene/Q), Beskow (Cray XC40) and Titan (Cray XK7). The test cases considered for the simulations correspond to a turbulent flow in a straight pipe at four different friction Reynolds numbers Reτ = 180, 360, 550 and 1000. Considering the linear model for parallel communication we quantify the machine characteristics in order to better assess the scaling behaviors of the code. Subsequently sampling and profiling tools are used to measure the computation and communication times over a large range of compute cores. We also study the effect of the two coarse grid solvers XXT and AMG on the computational time. Super-linear scaling due to a reduction in cache misses is observed on each computer. The strong scaling limit is attained for roughly 5000-10,000 degrees of freedom per core on Mira, 30,000 - 50,0000 on Beskow, with only a small impact of the problem size for both machines, and ranges between 10,000 and 220,000 depending on the problem size on Titan. This work aims at being a reference for Nek5000 users and also serves as a basis for potential issues to address as the community heads towards exascale supercomputers.

Offermans, Nicolas↗

DOE OSTI2017

TCP Throughput Profiles Using Measurements over Dedicated Connections

Wide-area data transfers in high-performance computing infrastructures are increasingly being carried over dynamically provisioned dedicated network connections that provide high capacities with no competing traffic. We present extensive TCP throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs). Contrary to the general expectation, they show significant statistical and temporal variations, in addition to the overall dependencies on the congestion control mechanism, buffer size, and the number of parallel streams. We analyze several throughput profiles that have highly desirable concave regions wherein the throughput decreases slowly with RTTs, in stark contrast to the convex profiles predicted by various TCP analytical models. We present a generic throughput model that abstracts the ramp-up and sustainment phases of TCP flows, which provides insights into qualitative trends observed in measurements across TCP variants: (i) slow-start followed by well-sustained throughput leads to concave regions; (ii) large buffers and multiple parallel streams expand the concave regions in addition to improving the throughput; and (iii) stable throughput dynamics, indicated by a smoother Poincare map and smaller Lyapunov exponents, lead to wider concave regions. These measurements and analytical results together enable us to select a TCP variant and its parameters for a given connection to achieve high throughput with statistical guarantees.

Rao, Nageswara S.↗

DOE OSTI2016

Chromospheric condensation and quasi-periodic pulsations in a circular-ribbon flare

In this paper, we report our multiwavelength observations of the C3.1 circular-ribbon flare SOL2015-10-16T10:20 in active region (AR) 12434. The flare consisted of a circular flare ribbon (CFR), an inner flare ribbon (IFR) inside it, and a pair of short parallel flare ribbons (PFRs). The PFRs located to the north of the IFR were most striking in the Interface Region Imaging Spectrograph (IRIS) 1400 and 2796 Å images. For the first time, we observed the circular-ribbon flare in the Ca ii H line of the Solar Optical Telescope on board Hinode, which has a similar shape as observed in the Atmospheric Imaging Assembly 1600 Å on board the Solar Dynamic Observatory (SDO). Photospheric line-of-sight magnetograms from the Helioseismic and Magnetic Imager on board SDO show that the flare is associated with positive polarities with a negative polarity inside. The IFR and CFR were cospatial with the negative polarity and positive polarities, implying the existence of a magnetic null point (B=0) and a dome-like spine–fan topology. During the impulsive phase of the flare, “two-step” raster observations of IRIS with a cadence of 6 s and an exposure time of 2 s showed plasma downflow at the CFR in the Si iv λ1402.77 line (logT≈4.8), suggesting chromospheric condensation. The downflow speeds first increased rapidly from a few km s{sup −1} to the peak values of 45–52 km s{sup −1}, before decreasing gradually to the initial levels. The decay timescales of condensation were 3–4 minutes, indicating ongoing magnetic reconnection. Interestingly, the downflow speeds are positively correlated with the logarithm of the Si iv line intensity and time derivative of the GOES soft X-ray (SXR) flux in 1–8 Å. The radio dynamic spectra are characterized by a type III radio burst associated with the flare, which implies that the chromospheric condensation was most probably driven by nonthermal electrons. Using an analytical expression and the peak Doppler velocity, we derive the lower limit of energy flux of the precipitating electrons, i.e., 0.65 × 10{sup 10} erg cm{sup −2} s{sup −1}. The Si iv line intensity and SXR derivative show quasi-periodic pulsations with periods of 32–42 s, which are likely caused by intermittent null-point magnetic reconnections modulated by the fast wave propagating along the fan surface loops at a phase speed of 950–1250 km s{sup −1}. Periodic accelerations and precipitations of the electrons result in periodic heating observed in the Si iv line and SXR.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Dynamic Equivalence of Large-Scale Power Systems Based on Boundary Measurements

Parallel computing helped speed up many tasks that can be done independently. The advance in gaming industry did not produce a technology that helps the power industry to reduce the computation time for dynamic simulation in individual cases. To perform faster than real-time simulation for the purpose of predicting power system dynamic trajectory, power industry continues to struggle to reduce the system size and simulation time of large-scale power systems while keeping its dynamic behavior under various disturbances. There is also an acute need for real-time dynamic model reduction as more renewables enter the generation mix with dramatic changes in the generation outputs. All existing model reduction solutions are based on having access to a detailed dynamic model of the system. The system changes by the minutes, dynamic models are only updated annually. To solve this problem, wide-area measurements obtained by the phasor measurement unit (PMU) at the boundaries between the reduced system and the study system is used to represent the external area. An artificial neuro-fuzzy inference system (ANFIS) is established to perform the mapping of the measurement to the external equivalent model. Here the external area is regarded as a black-box. Model reduction studies are conducted on the Northeast Power Coordinating Council (NPCC) under various types of contingencies, by using a co-simulation approach between PSS/E and MATLAB. The results look very promising and will be discussed in this paper.

Tong, Ning↗

DOE OSTI2021

Double-sided electrodynamic screen films

An electrode film includes a first electrode pattern having a first set of parallel conductive electrodes and a second electrode pattern having a second set of parallel conductive electrodes disposed on a first surface of a transparent film, wherein elements of the first electrode pattern do not cross over elements of the second electrode pattern. A third electrode pattern having a third set of parallel conductive electrodes is disposed on a second surface of the transparent film, wherein the first, second and third sets of parallel conductive electrodes are arranged in an interlaced pattern. The electrode patterns are configured to be connected to respective power sources of electrical power supplying respective waveforms to generate a time-varying electric field pattern above a surface of the electrode film.

Tombs, Thomas Nathaniel↗