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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Manycore Parallel Computing for a Hybridizable Discontinuous Galerkin Nested Multigrid Method

In this work, we present a parallel computing strategy for a hybridizable discontinuous Galerkin (HDG) nested geometric multigrid (GMG) solver. Parallel GMG solvers require a combination of coarse-grain and fine-grain parallelism to improve time-to-solution performance. In this work we focus on fine-grain parallelism. We use Intel's second generation Xeon Phi (Knights Landing) manycore processor. The GMG method achieves ideal convergence rates of 0.2 or less, for high polynomial orders. A matrix free (assembly free) technique is exploited to save considerable memory usage and increase arithmetic intensity. HDG enables static condensation, and due to the discontinuous nature of the discretization, we developed a matrix vector multiply routine that does not require any costly synchronizations or barriers. Our algorithm is able to attain 80% of peak bandwidth performance for higher order polynomials. This is possible due to the data locality inherent in the HDG method. Very high performance is realized for high order schemes, due to good arithmetic intensity, which declines as the order is reduced.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Prospective Validation of a High Dimensional Shape Model for Organ Motion in Intact Cervical Cancer

Purpose: Validated models are needed to justify strategies to define planning target volumes (PTVs) for intact cervical cancer used in clinical practice. Our objective was to independently validate a previously published shape model, using data collected prospectively from clinical trials. Methods and Materials: We analyzed 42 patients with intact cervical cancer treated with daily fractionated pelvic intensity modulated radiation therapy and concurrent chemotherapy in one of 2 prospective clinical trials. We collected online cone beam computed tomography (CBCT) scans before each fraction. Clinical target volume (CTV) structures from the planning computed tomography scan were cast onto each CBCT scan after rigid registration and manually redrawn to account for organ motion and deformation. We applied the 95% isodose cloud from the planning computed tomography scan to each CBCT scan and computed any CTV outside the 95% isodose cloud. The primary aim was to determine the proportion of CTVs that were encompassed within the 95% isodose volume. A 1-sample t test was used to test the hypothesis that the probability of complete coverage was different from 95%. We used mixed-effects logistic regression to assess effects of time and patient variability. Results: The 95% isodose line completely encompassed 92.3% of all CTVs (95% confidence interval, 88.3%-96.4%), not significantly different from the 95% probability anticipated a priori (P=.19). The overall proportion of missed CTVs was small: the grand mean of covered CTVs was 99.9%, and 95.2% of misses were located in the anterior body of the uterus. Time did not affect coverage probability (P=.71). Conclusions: With the clinical implementation of a previously proposed PTV definition strategy based on a shape model for intact cervical cancer, the probability of CTV coverage was high and the volume of CTV missed was low. This PTV expansion strategy is acceptable for clinical trials and practice; however, we recommend daily image guidance to avoid systematic large misses in select patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Kernels for scalable data analysis in science: Towards an architecture-portable future

In this paper, we pose and address some of the unique challenges in the analysis of scientific Big Data on supercomputing platforms. Our approach identifies, implements and scales numerical kernels that are critical to the instantiation of theory-inspired analytic workflows on modern computing architectures. We present the benefits of scalable kernels towards constructing algorithms such as principal component analysis and non-negative matrix factorization on an image-analysis use case at the Oak Ridge Leadership Computing Facility (OLCF). Based on experience with the use-case, we conclude that piecing scalable analytic kernels into user-defined analytic workflows are a flexible, modular and agile way to enable architecture-portable productivity for the data-intensive sciences.

Sukumar, Sreenivas R.↗
DOE OSTI2015

Single Vocal Cord Irradiation: Image Guided Intensity Modulated Hypofractionated Radiation Therapy for T1a Glottic Cancer: Early Clinical Results

Purpose: To report, from a retrospective analysis of prospectively collected data, on the feasibility, outcome, toxicity, and voice-handicap index (VHI) of patients with T1a glottic cancer treated by a novel intensity modulated radiation therapy technique developed at our institution to treat only the involved vocal cord: single vocal cord irradiation (SVCI). Methods and Materials: Thirty patients with T1a glottic cancer were treated by means of SVCI. Dose prescription was set to 16 × 3.63 Gy (total dose 58.08 Gy). The clinical target volume was the entire vocal cord. Setup verification was done by means of an online correction protocol using cone beam computed tomography. Data for voice quality assessment were collected prospectively at baseline, end of treatment, and 4, 6, and 12 weeks and 6, 12, and 18 months after treatment using VHI questionnaires. Results: After a median follow-up of 30 months (range, 7-50 months), the 2-year local control and overall survival rates were 100% and 90% because no single local recurrence was reported and 3 patients died because of comorbidity. All patients have completed the intended treatment schedule; no treatment interruptions and no grade 3 acute toxicity were reported. Grade 2 acute dermatitis or dysphagia was reported in only 5 patients (17%). No serious late toxicity was reported; only 1 patient developed temporary grade 2 laryngeal edema, and responded to a short-course of corticosteroid. The VHI improved significantly, from 33.5 at baseline to 9.5 and 10 at 6 weeks and 18 months, respectively (P<.001). The control group, treated to the whole larynx, had comparable local control rates (92.2% vs 100%, P=.24) but more acute toxicity (66% vs 17%, P<.0001) and higher VHI scores (23.8 and 16.7 at 6 weeks and 18 months, respectively, P<.0001). Conclusion: Single vocal cord irradiation is feasible and resulted in maximal local control rate at 2 years. The deterioration in VHI scores was slight and temporary and subsequently improved to normal levels. Long-term follow-up is needed to consolidate these promising results.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Sparse-view proton computed tomography using modulated proton beams

Purpose: Proton imaging that uses a modulated proton beam and an intensity detector allows a relatively fast image acquisition compared to the imaging approach based on a trajectory tracking detector. In addition, it requires a relatively simple implementation in a conventional proton therapy equipment. The model of geometric straight ray assumed in conventional computed tomography (CT) image reconstruction is however challenged by multiple-Coulomb scattering and energy straggling in the proton imaging. Radiation dose to the patient is another important issue that has to be taken care of for practical applications. In this work, the authors have investigated iterative image reconstructions after a deconvolution of the sparsely view-sampled data to address these issues in proton CT. Methods: Proton projection images were acquired using the modulated proton beams and the EBT2 film as an intensity detector. Four electron-density cylinders representing normal soft tissues and bone were used as imaged object and scanned at 40 views that are equally separated over 360°. Digitized film images were converted to water-equivalent thickness by use of an empirically derived conversion curve. For improving the image quality, a deconvolution-based image deblurring with an empirically acquired point spread function was employed. They have implemented iterative image reconstruction algorithms such as adaptive steepest descent-projection onto convex sets (ASD-POCS), superiorization method–projection onto convex sets (SM-POCS), superiorization method–expectation maximization (SM-EM), and expectation maximization-total variation minimization (EM-TV). Performance of the four image reconstruction algorithms was analyzed and compared quantitatively via contrast-to-noise ratio (CNR) and root-mean-square-error (RMSE). Results: Objects of higher electron density have been reconstructed more accurately than those of lower density objects. The bone, for example, has been reconstructed within 1% error. EM-based algorithms produced an increased image noise and RMSE as the iteration reaches about 20, while the POCS-based algorithms showed a monotonic convergence with iterations. The ASD-POCS algorithm outperformed the others in terms of CNR, RMSE, and the accuracy of the reconstructed relative stopping power in the region of lung and soft tissues. Conclusions: The four iterative algorithms, i.e., ASD-POCS, SM-POCS, SM-EM, and EM-TV, have been developed and applied for proton CT image reconstruction. Although it still seems that the images need to be improved for practical applications to the treatment planning, proton CT imaging by use of the modulated beams in sparse-view sampling has demonstrated its feasibility.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

High Energy Physics Research: Experimental & Theoretical (Final Report)

The research at the energy frontier was to explore high energy and luminosity collisions at the LHC using the ATLAS and CMS detectors to lead physics analyses in characterization of the Higgs Boson, to search for its potential partners, to lead searches for Dark Matter and to make extensive studies of Electroweak phenomena. The objectives are also to operate and upgrade the ATLAS and CMS detectors and their computing to optimize their physics performance in the present data taking and to enable the full exploitation of planned High Luminosity LHC. The research for the theory frontier was to analyze and interpret the new data from the experimental frontiers: energy, cosmic and intensity (Phenomenology), to investigate new theories of high energy physics extending the standard model by including gravity within consistent frameworks such as string theory, and examine their phenomenological and cosmological implications (String Theory and Theoretical Cosmology.)

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

New hardware and software platform for experiments on a HUBER-5042 X-ray diffractometer with a DISPLEX DE-202 helium cryostat in the temperature range of 20–300 K

Huber-5042 diffractometer with a closed-cycle Displex DE-202 helium cryostat is a unique scientific instrument for carrying out X-ray diffraction experiments when studying the single crystal structure in the temperature range of 20–300 K. To make the service life longer and develop new experimental techniques, the diffractometer control is transferred to a new hardware and software platform. To this end, a modern computer; a new detector reader unit; and new control interfaces for stepper motors, temperature controller, and cryostat vacuum pumping system are used. The system for cooling the X-ray tube, the high-voltage generator, and the helium compressor and pump for maintaining the desired vacuum in the cryostat are replaced. The system for controlling the primary beam shutter is upgraded. A biological shielding is installed. The new program tools, which use the Linux Ubuntu operating system and SPEC constructor, include a set of drivers for control units through the aforementioned interfaces. A program for searching reflections from a sample using fast continuous scanning and a priori information about crystal is written. Thus, the software package for carrying out the complete cycle of precise diffraction experiment (from determining the crystal unit cell to calculating the integral reflection intensities) is upgraded. High quality of the experimental data obtained on this equipment is confirmed in a number of studies in the temperature range from 20 to 300 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Introduction to Special Section: Machine Learning for Image-based Geologic Interpretation

Image-based geological interpretation has been a labor-intensive and time-consuming process because it requires well-trained geoscientists to identify geological structures, features, and textures from various types of images. These images include scanning electron microscopic images, optical microscopic images, optical photos, resistivity images, seismic volumes, remote-sensing images, etc. With fast-evolving machine learning (ML) technology and computing power in recent decades, computers can achieve nearhuman-level to super-human-level performance with scalable high efficiency in the computer vision field. These technological revolutions facilitated image-based geological interpretation in petroleum exploration and production. For example, a fault picking method applied to 3-D seismic volume data using deep learning can achieve superior performance in comparison to conventional auto-picking methods. In addition, under the new normal of low oil prices, the petroleum industry seeks cost-effective strategies such as automating traditionally labor-intensive processes. Nevertheless, the potential of applying ML to geological image interpretation is still facing a few key challenges including data scarcity, data distribution, poor data and/or label quality, data leakage, learning algorithms, model architecture, training methodologies, testing and evaluation metrics, hyper-parameters optimization, model drift, production deployment, and the like.

58 GEOSCIENCES↗
DOE OSTI2014

Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane

Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm{sup −1}, and 0.5 km mol{sup −1}, for bond lengths, angles, wavenumbers, and IR intensities, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

An Eigenvector-Based Method of Radio Array Calibration and Its Application to the Tianlai Cylinder Pathfinder

We propose an eigenvector-based formalism for the calibration of radio interferometer arrays. In the presence of a strong dominant point source, the complex gains of the array can be obtained by taking the first eigenvector of the visibility matrix. We use the stable principle component analysis method to help separate outliers and noise from the calibrator signal to improve the performance of the method. This method can be applied with poorly known beam model of the antenna, is insensitive to outliers or imperfections in the data, and has low computational complexity. It thus is particularly suitable for the initial calibration of the array, which can serve as the initial point for more accurate calibrations. We demonstrate this method by applying it to the cylinder pathfinder of the Tianlai experiment, which aims to measure the dark energy equation of state using the baryon acoustic oscillation features in the large-scale structure by making intensity mapping observation of the redshifted 21 cm emission of the neutral hydrogen (H i). The complex gain of the array elements and the beam profile in the east–west direction (short axis of the cylinder) are successfully obtained by applying this method to the transit data of bright radio sources.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

An Eigenvector-based Method of Radio Array Calibration and Its Application to the Tianlai Cylinder Pathfinder

We propose an eigenvector-based formalism for the calibration of radio interferometer arrays. In the presence of a strong dominant point source, the complex gains of the array can be obtained by taking the first eigenvector of the visibility matrix. We use the stable principle component analysis (SPCA) method to help separate outliers and noise from the calibrator signal to improve the performance of the method. This method can be applied with poorly known beam model of the antenna, and is insensitive to outliers or imperfections in the data, and has low computational complexity. It thus is particularly suitable for the initial calibration of the array, which can serve as the initial point for more accurate calibrations. We demonstrate this method by applying it to the cylinder pathfinder of the Tianlai experiment, which aims to measure the dark energy equation of state using the baryon acoustic oscillation (BAO) features in the large scale structure by making intensity mapping observation of the redshifted 21~cm emission of the neutral hydrogen (HI). The complex gain of the array elements and the beam profile in the East-West direction (short axis of the cylinder) are successfully obtained by applying this method to the transit data of bright radio sources.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Employing artificial intelligence to steer exascale workflows with colmena

Computational workflows are a common class of application on supercomputers, yet the loosely coupled and heterogeneous nature of workflows often fails to take full advantage of their capabilities. We created Colmena to leverage the massive parallelism of a supercomputer by using Artificial Intelligence (AI) to learn from and adapt a workflow as it executes. Colmena allows scientists to define how their application should respond to events (e.g., task completion) as a series of cooperative agents. In this paper, we describe the design of Colmena, the challenges we overcame while deploying applications on exascale systems, and the science workflows we have enhanced through interweaving AI. The scaling challenges we discuss include developing steering strategies that maximize node utilization, introducing data fabrics that reduce communication overhead of data-intensive tasks, and implementing workflow tasks that cache costly operations between invocations. These innovations coupled with a variety of application patterns accessible through our agent-based steering model have enabled science advances in chemistry, biophysics, and materials science using different types of AI. In conclusion, our vision is that Colmena will spur creative solutions that harness AI across many domains of scientific computing.

Workflows↗
DOE OSTI2024

GPU-enabled extreme-scale turbulence simulations: Fourier pseudo-spectral algorithms at the exascale using OpenMP offloading

Fourier pseudo-spectral methods for nonlinear partial differential equations are of wide interest in many areas of advanced computational science, including direct numerical simulation of three-dimensional (3-D) turbulence governed by the Navier-Stokes equations in fluid dynamics. This paper presents a new capability for simulating turbulence at a new record resolution up to 35 trillion grid points, on the world's first exascale computer, Frontier, comprising AMD MI250x GPUs with HPE's Slingshot interconnect and operated by the US Department of Energy's Oak Ridge Leadership Computing Facility (OLCF). Key programming strategies designed to take maximum advantage of the machine architecture involve performing almost all computations on the GPU which has the same memory capacity as the CPU, performing all-to-all communication among sets of parallel processes directly on the GPU, and targeting GPUs efficiently using OpenMP offloading for intensive number-crunching including 1-D Fast Fourier Transforms (FFT) performed using AMD ROCm library calls. With 99% of computing power on Frontier being on the GPU, leaving the CPU idle leads to a net performance gain via avoiding the overhead of data movement between host and device except when needed for some I/O purposes. Memory footprint including the size of communication buffers for MPI_ALLTOALL is managed carefully to maximize the largest problem size possible for a given node count. Detailed performance data including separate contributions from different categories of operations to the elapsed wall time per step are reported for five grid resolutions, from 2048 3 on a single node to 32768 3 on 4096 or 8192 nodes out of 9408 on the system. Both 1D and 2D domain decompositions which divide a 3D periodic domain into slabs and pencils respectively are implemented. The present code suite (labeled by the acronym GESTS, GPUs for Extreme Scale Turbulence Simulations) achieves a figure of merit (in grid points per second) exceeding goals set in the Center for Accelerated Application Readiness (CAAR) program for Frontier. The performance attained is highly favorable in both weak scaling and strong scaling, with notable departures only for 2048 3 where communication is entirely intra-node, and for 32768 3 , where a challenge due to small message sizes does arise. Communication performance is addressed further using a lightweight test code that performs all-to-all communication in a manner matching the full turbulence simulation code. Performance at large problem sizes is affected by both small message size due to high node counts as well as dragonfly network topology features on the machine, but is consistent with official expectations of sustained performance on Frontier. Overall, although not perfect, the scalability achieved at the extreme problem size of 32768 3 (and up to 8192 nodes — which corresponds to hardware rated at just under 1 exaflop/sec of theoretical peak computational performance) is arguably better than the scalability observed using prior state-of-the-art algorithms on Frontier's predecessor machine (Summit) at OLCF. New science results for the study of intermittency in turbulence enabled by this code and its extensions are to be reported separately in the near future.

3D fast Fourier transform↗
DOE OSTI2022

Circular Trajectory Approach for Online Sinusoidal Signal Distortion Monitoring and Visualization

The increasing complexity and uncertainties of modern power systems are placing significant demands on signal monitoring techniques. This work proposes the Circular Trajectory Approach (CTA) for online sinusoidal signal distortion monitoring and visualization. CTA can detect distortions of a sinusoidal signal. Compared with existing waveform anomaly detection techniques, CTA is faster in detection and less computation intensive. It thus supports edge devices and online applications. CTA also offers a new means of sinusoidal signal distortion visualization. It can reveal the distorted sections in a sinusoidal cycle and clearly display the distortions. The proposed approach is tested on real data from an open source EPRI dataset.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

Template Interfaces for Agile Parallel Data-Intensive Science

Tigres provides a programming library to compose and execute large-scale data-intensive scientific workflows from desktops to supercomputers. DOE User Facilities and large science collaborations are increasingly generating large enough data sets that it is no longer practical to download them to a desktop to operate on them. They are instead stored at centralized compute and storage resources such as high performance computing (HPC) centers. Analysis of this data requires an ability to run on these facilities, but with current technologies, scaling an analysis to an HPC center and to a large data set is difficult even for experts. Tigres is addressing the challenge of enabling collaborative analysis of DOE Science data through a new concept of reusable "templates" that enable scientists to easily compose, run and manage collaborative computational tasks. These templates define common computation patterns used in analyzing a data set.

Ramakrishnan, Lavanya↗
DOE OSTI2019

Preservation of Alcator C-Mod Data and Support of ITER Research Through ITPA Participation (Final Technical Report)

This grant supported two primary activities at the MIT Plasma Science and Fusion Center. First, personnel support, hardware upgrades, and software development were used to maintain the C-Mod data archive set. This highly valuable repository contains all of the data generated from operation of the Alcator C-Mod FES User Facility, covering first operation in 1992 through completion of the final experimental campaign on Sept 30, 2016. The archive, stored using the MDSplus architecture, also includes all of the data analysis, which is ongoing, and most of the results of computer modeling of the data. Second, this grant supported activities related to participation of the C-Mod team in the International Tokamak Physics Activites (ITPA), which includes analysis of C-Mod data, in conjunction with data from tokamaks operated around the world, with intense coordination of joint experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Scalable, In-situ Data Clustering Data Analysis for Extreme Scale Scientific Computing (Final Report)

The objective of this project is to address challenges in the design and development of scalable in-situ data clustering and analytics algorithms and software. Our goal is to develop parallel software consisting of a set of spatio-temporal data clustering and anomaly detection functions, both of which are very important for large-scale analysis and have wide applicability for in-situ runs as well as post-processing analysis. Our design principles for in-situ analysis consider the following: (1) identify parts of the computation can be done close to the data within the nodes, while it is still in memory; (2) extract analysis components can (and should) be performed in remote staging and analysis nodes; (3) develop error-bound approximation methods for applications tolerable for small errors; (4) identify the type of derived distributions and statistics, for spatio-temporal data, that can be kept locally in order to both accelerate computations and meet energy constraints in subsequent iterations and phases; (5) use a self-describing data format so that data can be consistent and understood among local storage (memory and SSDs) and at staging and analysis nodes, thereby providing portability and flexibility; (6) develop service-oriented functions that can schedule in-situ and post-hoc analysis tasks based on the dynamic requirements of applications. Our development focus is to produce the parallel data analysis software/library that will be scalable, reusable, extensible, and generic for applications in different disciplines. The software will be able to run in-situ with the simulations as well as post-hoc analysis. This approach will satisfy many synergistic requirements for data intensive applications executed on data coming from instruments and experiments. In particular, the proposed multilevel approach is directly applicable to perform design tradeoffs for running part of the algorithms near the instruments and the rest on remote (analysis) systems.

97 MATHEMATICS AND COMPUTING↗