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At least 415 records · Page 23

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DOE OSTI2014

Beam dynamics in an ultra-low energy storage rings (review of existing facilities and feasibility studies for future experiments)

Storage rings operating at ultra-low energies and in particular electrostatic storage rings have proven to be invaluable tools for atomic and molecular physics. Due to the mass independence of the electrostatic rigidity, these machines are able to store a wide range of different particles, from light ions to heavy singly charged bio-molecules. However, earlier measurements showed strong limitations on beam intensity, fast decay of ion current, reduced life time etc. The nature of these effects was not fully understood. Also a large variety of experiments in future generation ultra-low energy storage and decelerator facilities including in-ring collision studies with a reaction microscope require a comprehensive investigation of the physical processes involved into the operation of such rings. In this paper, we present review of non-linear and long term beam dynamics studies on example of the ELISA, AD Recycler, TSR and USR rings using the computer codes BETACOOL, OPERA-3D and MAD-X. The results from simulations were benchmarked against experimental data of beam losses in the ELISA storage ring. We showed that decay of beam intensity in ultra-low energy rings is mainly caused by ion losses on ring aperture due to multiple scattering on residual gas. Beam is lost on ring aperture due to small ring acceptance. Rate of beam losses increases at high intensities because of the intra-beam scattering effect adds to vacuum losses. Detailed investigations into the ion kinetics under consideration of the effects from electron cooling and multiple scattering of the beam on a supersonic gas jet target have been carried out as well. The life time, equilibrium momentum spread and equilibrium lateral spread during collisions with this internal gas jet target were estimated. In addition, the results from experiments at the TSR ring, where low intensity beam of CF{sup +} ions at 93 keV/u has been shrunk to extremely small dimensions have been reproduced. Based on these simulations, conditions for stable ring operation with extremely low emittance beam are presented. Finally, results from studies into the interaction of ions with a gas jet target at 3–30 keV energy range are summarized.

43 PARTICLE ACCELERATORS↗

DOE OSTI2012

Radiation modeling using the Uintah heterogeneous CPU/GPU runtime system. In: XSEDE '12 Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond, Article No. 4

The Uintah Computational Framework was developed to provide an environment for solving fluid-structure interaction problems on structured adaptive grids on large-scale, long-running, data-intensive problems. Uintah uses a combination of fluid-flow solvers and particle-based methods for solids, together with a novel asynchronou task-based approach with fully automated load balancing. Uintah demonstrates excellent weak and strong scalability at full machine capacity on XSEDE resources such as Ranger and Kraken, and through the use of a hybrid memory approach based on a combination of MPI and Pthreads, Uintah now runs on up to 262k cores on the DOE Jaguar system. In order to extend Uintah to heterogeneous systems, with ever-increasing CPU core counts and additional on-node GPUs, a new dynamic CPU-GPU task scheduler is designed and evaluated in this study. This new scheduler enables Uintah to fully exploit these architectures with support for asynchronous, out-of-order scheduling of both CPU and GPU computational tasks. A new runtime system has also been implemented with an added multi-stage queuing architecture for efficient scheduling of CPU and GPU tasks. This new runtime system automatically handles the details of asynchronous memory copies to and from the GPU and introduces a novel method of pre-fetching and preparing GPU memory prior to GPU task execution. In this study this new design is examined in the context of a developing, hierarchical GPU-based ray tracing radiation transport model that provides Uintah with additional capabilities for heat transfer and electromagnetic wave propagation. The capabilities of this new scheduler design are tested by running at large scale on the modern heterogeneous systems, Keeneland and TitanDev, with up to 360 and 960 GPUs respectively. On these systems, we demonstrate significant speedups per GPU against a standard CPU core for our radiation problem.

Humphrey, Alan↗

DOE OSTI2011

A report documenting the completion of the Los Alamos National Laboratory portion of the ASC level II milestone ""Visualization on the supercomputing platform

This report provides documentation for the completion of the Los Alamos portion of the ASC Level II 'Visualization on the Supercomputing Platform' milestone. This ASC Level II milestone is a joint milestone between Sandia National Laboratory and Los Alamos National Laboratory. The milestone text is shown in Figure 1 with the Los Alamos portions highlighted in boldfaced text. Visualization and analysis of petascale data is limited by several factors which must be addressed as ACES delivers the Cielo platform. Two primary difficulties are: (1) Performance of interactive rendering, which is the most computationally intensive portion of the visualization process. For terascale platforms, commodity clusters with graphics processors (GPUs) have been used for interactive rendering. For petascale platforms, visualization and rendering may be able to run efficiently on the supercomputer platform itself. (2) I/O bandwidth, which limits how much information can be written to disk. If we simply analyze the sparse information that is saved to disk we miss the opportunity to analyze the rich information produced every timestep by the simulation. For the first issue, we are pursuing in-situ analysis, in which simulations are coupled directly with analysis libraries at runtime. This milestone will evaluate the visualization and rendering performance of current and next generation supercomputers in contrast to GPU-based visualization clusters, and evaluate the perfromance of common analysis libraries coupled with the simulation that analyze and write data to disk during a running simulation. This milestone will explore, evaluate and advance the maturity level of these technologies and their applicability to problems of interest to the ASC program. In conclusion, we improved CPU-based rendering performance by a a factor of 2-10 times on our tests. In addition, we evaluated CPU and CPU-based rendering performance. We encourage production visualization experts to consider using CPU-based rendering solutions when it is appropriate. For example, on remote supercomputers CPU-based rendering can offer a means of viewing data without having to offload the data or geometry onto a CPU-based visualization system. In terms of comparative performance of the CPU and CPU we believe that further optimizations of the performance of both CPU or CPU-based rendering are possible. The simulation community is currently confronting this reality as they work to port their simulations to different hardware architectures. What is interesting about CPU rendering of massive datasets is that for part two decades CPU performance has significantly outperformed CPU-based systems. Based on our advancements, evaluations and explorations we believe that CPU-based rendering has returned as one viable option for the visualization of massive datasets.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

A fast band–Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors

We introduce a new iterative Krylov subspace-based eigensolver for the simulation of macromolecular motions on desktop multithreaded platforms equipped with multicore processors and, possibly, a graphics accelerator (GPU). The method consists of two stages, with the original problem first reduced into a simpler band-structured form by means of a high-performance compute-intensive procedure. This is followed by a memory-intensive but low-cost Krylov iteration, which is off-loaded to be computed on the GPU by means of an efficient data-parallel kernel. The experimental results reveal the performance of the new eigensolver. Concretely, when applied to the simulation of macromolecules with a few thousands degrees of freedom and the number of eigenpairs to be computed is small to moderate, the new solver outperforms other methods implemented as part of high-performance numerical linear algebra packages for multithreaded architectures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

Power and Performance Trade-offs for Space Time Adaptive Processing

Computational efficiency – performance relative to power or energy – is one of the most important concerns when designing RADAR processing systems. This paper analyzes power and performance trade-offs for a typical Space Time Adaptive Processing (STAP) application. We study STAP implementations for CUDA and OpenMP on two computationally efficient architectures, Intel Haswell Core I7-4770TE and NVIDIA Kayla with a GK208 GPU. We analyze the power and performance of STAP’s computationally intensive kernels across the two hardware testbeds. We also show the impact and trade-offs of GPU optimization techniques. We show that data parallelism can be exploited for efficient implementation on the Haswell CPU architecture. The GPU architecture is able to process large size data sets without increase in power requirement. The use of shared memory has a significant impact on the power requirement for the GPU. A balance between the use of shared memory and main memory access leads to an improved performance in a typical STAP application.

Gawande, Nitin A.↗

DOE OSTI2025

Real-Time FPGA Implementation For Frequency Sweep Interferometry In The LBNF Complex

The Long Baseline Neutrino Facility (LBNF) will deliver a 2.4 MW muon neutrino beam from Fermilab to the Deep Underground Neutrino Experiment (DUNE), requiring unprecedented precision in beamline alignment to achieve DUNE's neutrino oscillation measurement goals. Vertical misalignments of beamline components as small as 0.5 mm can contribute 6-7\% uncertainty in predicted neutrino flux, necessitating sub-0.1 mm alignment monitoring capabilities. The Horn Location Sensor (HLS) system employs frequency sweep interferometry (FSI) in a distributed hydrostatic leveling network to achieve the required precision under harsh radiation conditions up to 5000 kRad/year. Traditional FSI implementations suffer from laser sweep nonlinearities that degrade resolution and require computationally intensive post-processing corrections using gas reference cells. This work presents a real-time FPGA-based implementation of the HLS data acquisition and processing system using a sweep tracker interferometer for dynamic sweep linearization. The system utilizes a PYNQ-Z2 FPGA with programmable logic implementing parallel 16k-point FFT processing across four channels, synchronized by the sweep tracker signal to eliminate post-processing requirements. Spectral performance testing demonstrates significant improvements in peak sharpness compared to traditional fixed-frequency digitization. The FPGA implementation enables real-time displacement monitoring with processing speeds orders of magnitude faster than software-based approaches, essential for the operational requirements of LBNF's eventual distributed sensor network. This advancement in real-time FSI processing directly supports DUNE's precision neutrino physics program by providing the rapid feedback necessary for maintaining stringent beamline alignment tolerances during high-power beam operations.

Rossel, A. Jacob [Fermilab; Unlisted]↗

DOE OSTI2014

A Compute Capable SSD Architecture for Next-Generation Non-volatile Memories

Existing storage technologies (e.g., disks and ash) are failing to cope with the processor and main memory speed and are limiting the overall perfor- mance of many large scale I/O or data-intensive applications. Emerging fast byte-addressable non-volatile memory (NVM) technologies, such as phase-change memory (PCM), spin-transfer torque memory (STTM) and memristor are very promising and are approaching DRAM-like performance with lower power con- sumption and higher density as process technology scales. These new memories are narrowing down the performance gap between the storage and the main mem- ory and are putting forward challenging problems on existing SSD architecture, I/O interface (e.g, SATA, PCIe) and software. This dissertation addresses those challenges and presents a novel SSD architecture called XSSD. XSSD o oads com- putation in storage to exploit fast NVMs and reduce the redundant data tra c across the I/O bus. XSSD o ers a exible RPC-based programming framework that developers can use for application development on SSD without dealing with the complication of the underlying architecture and communication management. We have built a prototype of XSSD on the BEE3 FPGA prototyping system. We implement various data-intensive applications and achieve speedup and energy ef- ciency of 1.5-8.9 and 1.7-10.27 respectively. This dissertation also compares XSSD with previous work on intelligent storage and intelligent memory. The existing ecosystem and these new enabling technologies make this system more viable than earlier ones.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Airborne LiDAR to Improve Canopy Fuels Mapping for Wildfire Modeling

Increasing conflict between wildfire and the built environment has increased the need for more up-to-date and finer resolution canopy fuels data to improve wildfire modeling and associated risk forecasts. The US Forest Service and US Department of the Interior’s LANDFIRE product, which provides 30-m resolution canopy fuels data for the entire US, is one of the most widely used sources of fuels data. However, the last complete mapping effort for LANDFIRE is based on 2016 conditions, and subsequent updates reflect disturbances 1-2 years behind the release year. Airborne systems equipped with Light Detection and Ranging (LiDAR) sensors can be deployed to actively sense canopy structure and estimate canopy fuels data (cover, height, base height, bulk density) at finer resolutions. Canopy base height (CBH) and canopy bulk density (CBD) are difficult to measure both in the field and in LiDAR point clouds. Still, they are important for accurately modeling crown fires, which are often intense and difficult to contain. Additionally, point cloud datasets are large, and calculations require efficient utilization of computational resources. To address these challenges, we are working on an approach that uses openly available National Ecological Observatory Network (NEON) airborne LiDAR data, with calculations processed in the R programming language and parallelized through the lidR package. CBH and CBD are often derived from tree height, diameter at breast height, and species-specific allometries using the Fire and Fuels Extension of the Forest Vegetation Simulator (FFE-FVS). We aim to test if airborne LiDAR can estimate CBH and CBD without the use of empirical equations. Reliable estimates of canopy fuels data directly from airborne LiDAR could streamline quick, fine-resolution updates for use in wildfire behavior models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Turbulence-parameter estimation for current-energy converters using surrogate model optimization

Surrogate models maximize information utility by building predictive models in place of computational or experimentally expensive model runs. Marine hydrokinetic current energy converters require large-domain simulations to estimate array efficiencies and environmental impacts. Meso-scale models typically represent turbines as actuator discs that act as momentum sinks and sources of turbulence and its dissipation. An OpenFOAM model was developed where actuator disc k-ε turbulence was characterized using an approach developed for flows through vegetative canopies. Turbine-wake data from laboratory flume experiments collected at two influent turbulence intensities were used to calibrate parameters in the turbulence-source terms in the k-ε equations. Additionally, parameter influences on longitudinal wake profiles were estimated using Gaussian process regression with subsequent optimization minimizing the objective function within 3.1% of those obtained using the full model representation, but for 74% of the computational cost (far fewer model runs). This framework facilitates more efficient parameterization of the turbulence-source equations using turbine-wake data.

16 TIDAL AND WAVE POWER↗

DOE OSTI2021

Flexible‐rate optoelectronic wireless transmission system at 101 GHz using multiband CAP‐PAM modulation and envelope detection

Abstract In this paper, we have experimentally demonstrated the first flexible‐rate optoelectronic terahertz wireless transmission system at 101 GHz based on multiband CAP‐PAM modulation and cost‐efficient envelope detection. Instead of traditional M‐QAM mapping, PAM‐N mapping is used in CAP modulation with low‐computational complexity. The system performances and optimal capacity in both single‐band case and multiband case are intensively investigated. The results show that the highest data rate for single‐band system is 13.35 Gbit/s with CAP‐PAM‐5 modulation, while the optimum aggregate transmission line rate of 8.49 Gbit/s can be obtained with 4‐sub‐bands CAP‐PAM‐{5,3,2,2} modulation under 7% FEC limit of 3.8 × 10 −3 for four‐user access.

Zhang, Jiao↗

DOE OSTI2020

Machine learning and ligand binding predictions: A review of data, methods, and obstacles

We report that computational predictions of ligand binding is a difficult problem, with more accurate methods being extremely computationally expensive. The use of machine learning for drug binding predictions could possibly leverage the use of biomedical big data in exchange for time-intensive simulations. This paper reviews current trends in the use of machine learning for drug binding predictions, data sources to develop machine learning algorithms, and potential problems that may lead to overfitting and ungeneralizable models. A few popular datasets that can be used to develop virtual high-throughput screening models are characterized using spatial statistics to quantify potential biases. We can see from evaluating some common benchmarks that good performance correlates with models with high-predicted bias scores and models with low bias scores do not have much predictive power. A better understanding of the limits of available data sources and how to fix them will lead to more generalizable models that will lead to novel drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Highly-scalable, physics-informed GANs for learning solutions of stochastic PDEs

Uncertainty quantification for forward and inverse problems is a central challenge across physical and biomedical disciplines. We address this challenge for the problem of modeling subsurface flow at the Hanford Site by combining stochastic computational models with observational data using physics-informed GAN models. The geographic extent, spatial heterogeneity, and multiple correlation length scales of the Hanford Site require training a computationally intensive GAN model to thousands of dimensions. We develop a highly optimized implementation that scales to {\herogpucount} NVIDIA Volta GPUs. We develop a hierarchical scheme based on a multi-player game-theoretic approach for exploiting domain parallelism, map discriminators and generators to multiple GPUs, and employ efficient communication schemes to ensure training stability and convergence. Our implementation scales to {\heronodecount} nodes on the Summit supercomputer with a \weakscalingeff\% scaling efficiency, achieving peak and sustained half-precision rates of {\heropeakperf} PF/s and {\herosustainedperf} PF/s.

physics informed ML, machine learning, generative ↗

DOE OSTI2012

Use of scaled BWR lower plenum boron mixing tests to qualify the boron transport model used in TRACG

In 2001 GEH applied best estimate methods combined with a statistical methodology to determine upper bound limits for key licensing parameters for anticipated operation occurrence (AOO) transient and anticipated transients without scram (ATWS) overpressure analyses for operating Boiling Water Reactors (BWRs). The methodology was subsequently extended for ESBWR AOO, ATWS, loss of coolant, and stability analyses. GEH is extending the methodology to long-term ATWS analyses for the operating BWRs. A long-term ATWS scenario uses injection of borated water to achieve reactor shutdown. Predicting the mixing and transport of boron is important for calculating the impact on the key licensing parameters. For the many operating BWRs where the denser boron solution is injected into the lower plenum, stratification may occur, delaying boron transport to the core region. CFD modeling can be used to model the stratification and mixing of the boron solution, but such calculations are extremely computer intensive and not cost effective; therefore, a more-empirical approach supported by a theoretical scaling of the dominant phenomena and backed by test data and benchmark calculations is used. The paper presents the TRACG lower plenum boron transport model qualification effort. The scaling basis used to implement the TRACG boron transport model for BWR applications is discussed. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2018

Blazing Signature Filter: a library for fast pairwise similarity comparisons

Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phenotype, the underlying computational task is often a multi-dimensional similarity test. As datasets continue to grow, improvements to the efficiency, sensitivity or specificity of such computation will have broad impacts as it allows scientists to more completely explore the wealth of scientific data. A significant practical drawback of large-scale data mining is the vast majority of pairwise comparisons are unlikely to be relevant, meaning that they do not share a signature of interest. It is therefore essential to efficiently identify these unproductive comparisons as rapidly as possible and exclude them from more time-intensive similarity calculations. The Blazing Signature Filter (BSF) is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time. The algorithm transforms datasets into binary metrics, allowing it to utilize the computationally efficient bit operators and provide a coarse measure of similarity. As a result, the BSF can scale to high dimensionality and rapidly filter unproductive pairwise comparison. Furthermore, two bioinformatics applications of the tool are presented to demonstrate the ability to scale to billions of pairwise comparisons and the usefulness of this approach.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Recommended Nuclear Structure and Decay Data for A=206 Isobars

Here, evaluated nuclear structure and decay data for all nuclei with mass number A=206 ( 206 Pt, 206 Au, 206 Hg, 206 Tl, 206 Pb, 206 Bi, 206 Po, 206 At, 206 Rn, 206 Fr, 206 Ra and 206 Ac), are presented. All available experimental data are compiled and evaluated, and best values for level and γ-ray energies, quantum numbers, lifetimes, γ-ray intensities and transition probabilities, as well as other nuclear properties, are recommended. Inconsistencies and discrepancies that exist in the literature are discussed. A number of computer codes (https://www-nds.iaea.org/public/ensdf_pgm/) developed by members of the NSDD network were used during the evaluation process. This work supersedes the earlier evaluation by F.G. Kondev (2008Ko21), published in Nuclear Data Sheets 109, 1527 (2008).

Kondev, F. G. [Argonne National Laboratory (ANL), ↗

DOE OSTI2016

HIGH-RESOLUTION ROTATIONAL SPECTRUM, DUNHAM COEFFICIENTS, AND POTENTIAL ENERGY FUNCTION OF NaCl

We report laboratory spectroscopy for the first time of the J = 1–0 and J = 2–1 lines of Na{sup 35}Cl and Na{sup 37}Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δ v = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

McStas Analysis of Monoenergetic Thermal Neutron Beam Generation for Total Cross Section Measurements

The thermal neutron scattering law (TSL) of a given material represents data that is essential for assessing the criticality safety of a neutronic system in which this material is utilized. Traditionally, the TSL is developed through elaborate calculations that combine input and models based on condensed matter physics and scattering theory. Nonetheless, measurements of key parameters (e.g., the total cross section at low energies) can help in benchmarking and validating TSL libraries such as those used in the ENDF/B database. In this work, the setup of experiments, at the PULSTAR reactor of North Carolina State University (NCSU), for creating monoenergetic thermal neutron beams in support of total scattering cross section measurements in the thermal energy range is explored using McStas simulations and experimental verification. A McStas model has been established of the NPD facility at the NCSU PULSTAR reactor to explore the production of monoenergetic thermal neutron beams in support of various applications including total cross section measurements. The McStas results clearly demonstrate the viability of six monochromatic thermal neutron beams with substantial intensities that allow future applications at the NPD facility. The experimental results reasonably support the computational model predictions. Based on these results, transmission thermal neutron experiments can be conducted for data validation studies. Furthermore, the model also allows the evaluation of design changes to expand the portfolio of available monoenergetic thermal neutron beams. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗