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All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Hyperspectral Image Classification Using Graph Clustering Methods

Hyperspectral imagery is a challenging modality due to the dimension of the pixels which can range from hundreds to over a thousand frequencies depending on the sensor. Most methods in the literature reduce the dimension of the data using a method such as principal component analysis, however this procedure can lose information. More recently methods have been developed to address classification of large datasets in high dimensions. This paper presents two classes of graph-based classification methods for hyperspectral imagery. Using the full dimensionality of the data, we consider a similarity graph based on pairwise comparisons of pixels. The graph is segmented using a pseudospectral algorithm for graph clustering that requires information about the eigenfunctions of the graph Laplacian but does not require computation of the full graph. We develop a parallel version of the Nyström extension method to randomly sample the graph to construct a low rank approximation of the graph Laplacian. With at most a few hundred eigenfunctions, we can implement the clustering method designed to solve a variational problem for a graph-cut-based semi-supervised or unsupervised classification problem. We implement OpenMP directive-based parallelism in our algorithms and show performance improvement and strong, almost ideal, scaling behavior. The method can handle very large datasets including a video sequence with over a million pixels, and the problem of segmenting a data set into a pre-determined number of classes.

47 OTHER INSTRUMENTATION↗
DOE OSTI2016

DIRECTED SEARCHES FOR BROADBAND EXTENDED GRAVITATIONAL WAVE EMISSION IN NEARBY ENERGETIC CORE-COLLAPSE SUPERNOVAE

Core-collapse supernovae (CC-SNe) are factories of neutron stars and stellar-mass black holes. SNe Ib/c stand out as potentially originating in relatively compact stellar binaries and they have a branching ratio of about 1% into long gamma-ray bursts. The most energetic events probably derive from central engines harboring rapidly rotating black holes, wherein the accretion of fall-back matter down to the innermost stable circular orbit (ISCO) offers a window into broadband extended gravitational wave emission (BEGE). To search for BEGE, we introduce a butterfly filter in time–frequency space by time-sliced matched filtering. To analyze long epochs of data, we propose using coarse-grained searches followed by high-resolution searches on events of interest. We illustrate our proposed coarse-grained search on two weeks of LIGO S6 data prior to SN 2010br (z = 0.002339) using a bank of up to 64,000 templates of one-second duration covering a broad range in chirp frequencies and bandwidth. Correlating events with signal-to-noise ratios > 6 from the LIGO L1 and H1 detectors reduces the total to a few events of interest. Lacking any further properties reflecting a common excitation by broadband gravitational radiation, we disregarded these as spurious. This new pipeline may be used to systematically search for long-duration chirps in nearby CC-SNe from robotic optical transient surveys using embarrassingly parallel computing.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Simulation Exploration through Immersive Parallel Planes

We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, each individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Branson: A Mini-App for Studying Parallel IMC, Version 1.0

This code solves the gray thermal radiative transfer (TRT) equations in parallel using simple opacities and Cartesian meshes. Although Branson solves the TRT equations it is not designed to model radiation transport: Branson contains simple physics and does not have a multigroup treatment, nor can it use physical material data. The opacities have are simple polynomials in temperature there is a limited ability to specify complex geometries and sources. Branson was designed only to capture the computational demands of production IMC codes, especially in large parallel runs. It was also intended to foster collaboration with vendors, universities and other DOE partners. Branson is similar in character to the neutron transport proxy-app Quicksilver from LLNL, which was recently open-sourced.

Long, Alex↗
DOE OSTI2017

Branson: A Mini-App for Studying Parallel IMC, Version 1.0

This code solves the gray thermal radiative transfer (TRT) equations in parallel using simple opacities and Cartesian meshes. Although Branson solves the TRT equations it is not designed to model radiation transport: Branson contains simple physics and does not have a multigroup treatment, nor can it use physical material data. The opacities have are simple polynomials in temperature there is a limited ability to specify complex geometries and sources. Branson was designed only to capture the computational demands of production IMC codes, especially in large parallel runs. It was also intended to foster collaboration with vendors, universities and other DOE partners. Branson is similar in character to the neutron transport proxy-app Quicksilver from LLNL, which was recently open-sourced.

Long, Alex↗
DOE OSTI2016

TH-AB-201-08: Ion Chamber Dose Measurements - Problems with the Temperature-Pressure Correction Factor

Purpose: To investigate the behavior of ionization chambers over a wide pressure range. Methods: Three cylindrical and two parallel-plate designs of ion chamber were investigated. The ion chambers were placed in vessel where the pressure was varied from atmospheric (101 kPa) down to 5 kPa. Measurements were made using 60Co and high-energy electron beams. The pressure was measured to better than 0.1% and multiple data sets were obtained for each chamber at both polarities to investigate pressure cycling and dependency on the sign of the charge collected. Results: For all types of chamber, the ionization current, corrected using the standard PTP, showed a similar behaviour. Deviations from the standard theory were generally small for Co-60 but very significant for electron beams, up to 20 % below P = 10 kPa. The effect was found to be always larger when collecting negative charge, suggesting a dependence on free-electron collection. The most likely source of such electrons is low-energy electrons emitted from the electrodes. This signal would be independent of air pressure within the chamber cavity. The data was analyzed to extract this signal and it was found to be a non-negligible component of the ionization current at atmospheric pressure. In the case of the parallel plate chambers, the effect was approximately 0.25 %. For the cylindrical chambers the effect was larger - up to 1.2 % - and dependent on the chamber type, which would be consistent with electron emission from different wall materials. For the electron beams, the correction factor was dependent on the electron energy and approximately double that observed in 60Co. Conclusion: Measurements have indicated significant deviations of the standard pressure correction that are consistent with electron emission from chamber electrodes. This has implications for both primary standard and reference ion chamber-based dosimetry.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Memory access optimization for particle operations in computational fluid dynamics-discrete element method simulations

Computational Fluid Dynamics - Discrete Element Method is used to model gas-solid systems in several applications in energy, pharmaceutical and petrochemical industries. Computational performance bottlenecks often limit the problem sizes that can be simulated at industrial scale. The data structures used to store several millions of particles in such large-scale simulations have a large memory footprint that does not fit into the processor cache hierarchies on current high-performance-computing platforms, leading to reduced computational performance. This paper specifically addresses this aspect of memory access bottlenecks in industrial scale simulations. The use of space-filling curves to improve memory access patterns is described and their impact on computational performance is quantified in both shared and distributed memory parallelization paradigms. The Morton space filling curve applied to uniform grids and k-dimensional tree partitions are used to reorder the particle data-structure thus improving spatial and temporal locality in memory. The performance impact of these techniques when applied to two benchmark problems, namely the homogeneous-cooling-system and a fluidized-bed, are presented. We report these optimization techniques lead to approximately two-fold performance improvement in particle focused operations such as neighbor-list creation and data-exchange, with ~ 1.5 times overall improvement in a fluidization simulation with 1.27 million particles.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Scalable hierarchical PDE sampler for generating spatially correlated random fields using nonmatching meshes: Scalable hierarchical PDE sampler using nonmatching meshes

This work describes a domain embedding technique between two nonmatching meshes used for generating realizations of spatially correlated random fields with applications to large-scale sampling-based uncertainty quantification. The goal is to apply the multilevel Monte Carlo (MLMC) method for the quantification of output uncertainties of PDEs with random input coefficients on general and unstructured computational domains. We propose a highly scalable, hierarchical sampling method to generate realizations of a Gaussian random field on a given unstructured mesh by solving a reaction–diffusion PDE with a stochastic right-hand side. The stochastic PDE is discretized using the mixed finite element method on an embedded domain with a structured mesh, and then, the solution is projected onto the unstructured mesh. This work describes implementation details on how to efficiently transfer data from the structured and unstructured meshes at coarse levels, assuming that this can be done efficiently on the finest level. We investigate the efficiency and parallel scalability of the technique for the scalable generation of Gaussian random fields in three dimensions. An application of the MLMC method is presented for quantifying uncertainties of subsurface flow problems. Here, we demonstrate the scalability of the sampling method with nonmatching mesh embedding, coupled with a parallel forward model problem solver, for large-scale 3D MLMC simulations with up to 1.9·109 unknowns.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

A performance study of the time-varying cache behavior: a study on APEX, Mantevo, NAS, and PARSEC

Cache has long been used to minimize the latency of main memory accesses by storing frequently used data near the processor. Processor performance depends on the underlying cache performance. Therefore, significant research has been done to identify the most crucial metrics of cache performance. Although the majority of research focuses on measuring cache hit rates and data movement as the primary cache performance metrics, cache utilization is significantly important. We investigate the application’s locality using cache utilization metrics. In addition, we present cache utilization and traditional cache performance metrics as the program progresses providing detailed insights into the dynamic application behavior on parallel applications from four benchmark suites running on multiple cores. We explore cache utilization for APEX, Mantevo, NAS, and PARSEC, mostly scientific benchmark suites. Our results indicate that 40% of the data bytes in a cache line are accessed at least once before line eviction. Also, on average a byte is accessed two times before the cache line is evicted for these applications. Moreover, we present runtime cache utilization, as well as, conventional performance metrics that illustrate a holistic understanding of cache behavior. To facilitate this research, we build a memory simulator incorporated into the Structural Simulation Toolkit (Rodrigues et al. in SIGMETRICS Perform Eval Rev 38(4):37–42, 2011). Finally, our results suggest that variable cache line size can result in better performance and can also conserve power.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The Optimized Parallel MOC module in Code cosLATC

A new neutron transport lattice physics code, cosLATC, which is an essential part in COSINE (Core and System Integrated Engine) code package, has been developed by SPICRI. It is mainly used for 2-D transport calculations on Pressurized Water Reactor (PWR) assemblies or pin cells. cosLATC generates few group constants for the core physics code cosCORE in COSINE package. With regards to cross-section data, WIMS-D 69 and 281 energy groups library is employed currently. cosLATC also has capability of resonance treatment, depletion and fuel temperature calculation. cosLATC uses modular tracking and parallelization technique in MOC transport calculation, which can save lots of memory and running time. In this paper, MOC module in cosLATC are introduced, the accuracy and efficiency of the module are verified by C5G7 benchmark and a PWR typical assembly. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

A massively-parallel, unstructured overset method for mesh connectivity

Here we present a method that dynamically and efficiently performs connectivity calculations between many O(10 5 ) moving, unstructured overset meshes in parallel. In order to connect overset meshes, elements exterior to the solution domain must be removed from the simulation. In regions with many overlapping meshes, elements must be selectively removed to reduce redundancy while maintaining a solution over the entire domain. Around masked regions interpolation partner pairing is required between meshes to provide boundary conditions. For general unstructured meshes, these steps involve challenging computational geometry calculations which must be efficient and automatic. For many moving meshes each step must be massively parallelized and scalable to large numbers of computational cores. To establish communication patterns a parallelized master/slave algorithm is used which minimizes global communication and storage. To remove elements a parallel ‘Forest Fire’ flood-fill algorithm is used to set a masking variable. For interpolation partner pairing, and other necessary searches, k-dimensional tree data structures (k-d trees) are extensively used. Often in a calculation, the connectivity between overset meshes remains largely the same between time steps. The temporal coherence of the various objects in the connectivity calculation is directly used to only update necessary information with time, resulting in substantial cost savings. Details of the different algorithms are presented. Resulting connectivity and timings are shown for complex geometries. Parallel scaling is demonstrated for 100,000 spherical particles within a channel up to 492,000 processors.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Real-time and post-hoc compression for data from Distributed Acoustic Sensing

Distributed Acoustic Sensing (DAS) is an emerging sensing technology that records the strain-rate along fiber optic cables at high spatial and temporal resolution. This technique is becoming a popular tool in seismology, hydrology, and other subsurface monitoring applications. However, due to the large coverage (10’s of km) and high density of measurements (1m spacing at 100’s of Hz), a DAS installation could produce terabytes of data records per day. Because many DAS instruments are deployed in remote locations, this large data size poses significant challenges to its transfer and storage. In this paper, we explore lossless compression methods to reduce the storage requirement in both real-time and post-hoc scenarios. Here we propose a two-stage compression method to improve the compression ratio and compression speed. This two-stage compression method could reduce the storage requirement by 40%, which is 20% more than other lossless methods, such as ZSTD. We demonstrate that the compression method could complete its operation well before the DAS instrument needs to output the next file, making it suitable for real-time DAS acquisition. We also implement a parallel compression method for a post-hoc scenario and demonstrate that our method could effectively utilize a parallel computer. With 256 CPU cores, our parallel compression method achieves the speed of 26GB/second.

58 GEOSCIENCES↗
DOE OSTI2020

Hubble constant difference between CMB lensing and BAO measurements

We apply a tension metric QUDM, the update difference in mean parameters, to understand the source of the difference in the measured Hubble constant H0 inferred with cosmic microwave background lensing measurements from the Planck satellite (H 0 = $67.9$ $^{+1.1}_{–1.3}$ km/s/Mpc) and from the South Pole Telescope (H 0 = $72.0$ $^{+2.1}_{–2.5}$ km/s/Mpc) when both are combined with baryon acoustic oscillation (BAO) measurements with priors on the baryon density (BBN). Q UDM isolates the relevant parameter directions for tension or concordance where the two data sets are both informative, and aids in the identification of subsets of data that source the observed tension. With Q UDM , we uncover that the difference in H 0 is driven by the tension between Planck lensing and BAO+BBN, at probability-to-exceed of 6.6%. Most of this mild tension comes from the galaxy BAO measurements parallel to the line of sight in the redshift range 0.2 < z < 0.75. Here, the redshift dependence of the parallel BAOs pulls both the matter density Ω m and H 0 high in Λ CDM, but these parameter anomalies are usually hidden when the BAO measurements are combined with other cosmological data sets with much stronger Ω m constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

The high level trigger and express data production at STAR

To meet the demands of the Beam Energy Scan phase-II (BES-II) program, the STAR experiment at the Relativistic Heavy Ion Collider (RHIC) developed a dual real-time framework consisting of a High Level Trigger (HLT) and an Express Data Production system (xProduction). The HLT operates online within the Data Acquisition (DAQ) chain on a dedicated multi-core CPU cluster with the option to offload compute-intensive kernels to Xeon Phi coprocessors. It uses parallelized algorithms, such as the Cellular Automaton (CA) Track Finder, to perform rapid tracking, vertexing, and event filtering. This allows it to select events of interest in real time and provide immediate feedback on detector and beam conditions. In contrast, the xProduction workflow runs concurrently and independently of the DAQ loop. It applies near offline-quality calibration and reconstruction within hours of data collection. The xProduction input is the express data stream, whose content can be enriched by HLT trigger/priority selections under DAQ/HLT resource constraints, and it uses the STAR calibration/conditions framework, incorporating online calibration/QA information when available. This enables early preliminary physics analysis, including the reconstruction of rare signals, such as hyperons and hypernuclei. It also provides collaboration-wide access to analysis-ready datasets. Together, the HLT and xProduction systems form a complementary architecture: the HLT performs online event selection while the xProduction chain delivers high-quality results within a short amount of time. This integrated framework has enabled the prompt reconstruction of the $^5_Λ$ He hypernucleus with high statistical significance and the efficient processing of hundreds of millions of heavy-ion collision events. In conclusion, its demonstrated scalability and robustness establish a model for future high-luminosity experiments requiring both online event filtering and rapid access to analysis-quality data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Part-scale microstructure prediction for laser powder bed fusion Ti-6Al-4V using a hybrid mechanistic and machine learning model

Laser powder bed fusion (LPBF) Ti-6Al-4V is widely studied for use in structural applications in aerospace and medical industries, but mechanical anisotropy and microstructural inhomogeneity prohibits its wider adoption. Although successful microstructure prediction models have been developed, a remaining challenge is their limited integration across length/time scales and validation by experimental studies. Here, this work proposes a physics-augmented machine learning surrogate model to unite predictions of LPBF temperature, β phase morphology and texture, and α/α’ formation into a single framework that is calibrated and validated with experiments. First, a phase field (PF) model of the martensitic β→α’ transformation is developed and calibrated using data from in-situ synchrotron cyclic heating/cooling studies quantifying the variation of α phase fraction with time. In parallel, an established finite difference-Monte Carlo (FDMC) model predicts the part-scale temperature profile and β grain formation during solidification. A dataset is developed using LPBF cyclic temperature descriptors from the FDMC model as inputs and corresponding α/α’ phase fraction and width from the PF model as outputs. Five machine learning (ML) regression models are tested and optimized, having mean absolute error in testing ≤ 4 %, and the k-nearest neighbors (KNN) model is selected as the best performing. The KNN model is called at the nodal level during post-processing of the FDMC model to replace and downscale the response of the PF model. The combined agility and accuracy of the hybrid FDMC-ML model enables part-scale microstructure predictions that can be further used for property predictions to accelerate AM process optimization.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Effective g factor of low-density two-dimensional holes in a Ge quantum well

Here we report the measurements of the effective g factor of low-density two-dimensional holes in a Ge quantum well. Using the temperature dependence of the Shubnikov-de Haas oscillations, we extract the effective g factor in a magnetic field perpendicular to the sample surface. Very large values of the effective g factor, ranging from ~13 to ~28, are observed in the density range of 1.4×10 10 cm -2 – 1.4×10 11 cm -2 . When the magnetic field is oriented parallel to the sample surface, the effective g factor is obtained from a protrusion in the magneto-resistance data that signify full spin polarization. In the latter orientation, a small effective g factor, ~1.3-1.4, is measured in the density range of 1.5×10 10 cm -2 –2×10 10 cm -2 . Finally, this very strong anisotropy is consistent with theoretical predictions and previous measurements in other 2D hole systems, such as InGaAs and GaSb.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Orbital orientation mapping of V 2 O 5 thin films

We report the effects of growth methods on the orbital orientation in vanadium pentoxide (V 2 O 5 ) thin films, an important factor to consider when selecting growth techniques for highly selective catalysts and devices. Thermal evaporation and sol-gel methods were used to synthesize the V 2 O 5 films. The surface morphology, roughness, and orientation of the films were characterized by atomic force microscopy and x-ray diffraction. Surface electronic properties and oxidation states were assessed by x-ray photoemission spectroscopy. Polarized x-ray absorption spectroscopy demonstrated that the thermally evaporated film [which was in the (001) orientation] exhibited greater anisotropy than the (100) oriented sol-gel film. The observed increase in anisotropy agrees well with computational findings which revealed that more vanadyl bonds are present at the surface of the thermally evaporated film than at the surface of the sol-gel film. The same computational study also found that the orientation of these bonds is more parallel to the film surface in the thermally evaporated film than in the sol-gel film. Finally, the data suggest that the method of growth may be used as a controlled variable to select key film characteristics for potential applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Modeling of a chain of three plasma accelerator stages with the WarpX electromagnetic PIC code on GPUs

The fully electromagnetic particle-in-cell code WarpX is being developed by a team of the U.S. DOE Exascale Computing Project (with additional non-U.S. collaborators on part of the code) to enable the modeling of chains of tens to hundreds of plasma accelerator stages on exascale supercomputers, for future collider designs. The code is combining the latest algorithmic advances (e.g., Lorentz boosted frame and pseudo-spectral Maxwell solvers) with mesh refinement and runs on the latest computer processing unit and graphical processing unit (GPU) architectures. In this paper, we summarize the strategy that was adopted to port WarpX to GPUs, report on the weak parallel scaling of the pseudo-spectral electromagnetic solver, and then present solutions for decreasing the time spent in data exchanges from guard regions between subdomains. In Sec. IV, we demonstrate the simulations of a chain of three consecutive multi-GeV laser-driven plasma accelerator stages.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗