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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 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

167-PFlops Deep Learning for Electron Microscopy: From Learning Physics to Atomic Manipulation

An artificial intelligence system called MENNDL, which used 25,200 Nvidia Volta GPUs on Oak Ridge National Laboratory’s Summit machine, automatically designed an optimal deep learning network in order to extract structural information from raw atomic-resolution microscopy data. In a few hours, MENNDL creates and evaluates millions of networks using a scalable, parallel, asynchronous genetic algorithm augmented with a support vector machine to automatically find a superior deep learning network topology and hyper-parameter set than a human expert can find in months. For the application of electron microscopy, the system furthers the goal of improving our understanding of the electron-beam-matter interactions and real-time image-based feedback, which enables a huge step beyond human capacity toward nanofabricating materials automatically. Finally, MENNDL has been scaled to the 4,200 available nodes of Summit achieving a measured 152.5 PFlops, with an estimated sustained performance of 167 PFlops when the entire machine is available.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Communication Lower Bounds and Optimal Algorithms for Multiple Tensor-Times-Matrix Computation

Multiple tensor-times-matrix (Multi-TTM) is a key computation in algorithms for computing and operating with the Tucker tensor decomposition, which is frequently used in multidimensional data analysis. Here, we establish communication lower bounds that determine how much data movement is required (under mild conditions) to perform the Multi-TTM computation in parallel. The crux of the proof relies on analytically solving a constrained, nonlinear optimization problem. We also present a parallel algorithm to perform this computation that organizes the processors into a logical grid with twice as many modes as the input tensor. We show that, with correct choices of grid dimensions, the communication cost of the algorithm attains the lower bounds and is therefore communication optimal. Finally, we show that our algorithm can significantly reduce communication compared to the straightforward approach of expressing the computation as a sequence of tensor-times-matrix operations when the input and output tensors vary greatly in size.

HBL-inequalities↗
DOE OSTI2018

Parallel Markov Random Fields for Image Segmentation (PMRF-IS) v1.0

This software performs multi-label segmentation of 2D/3D images. It is highly accurate, results rely on use of an Markov random field (MRF) formulation. It runs in both shared and distributed memory parallel modes. MRF algorithms are powerful tools in image analysis to explore contextual information of data.

Heinemann, Colleen↗
DOE OSTI2017

Genten: Software for Generalized Tensor Decompositions v. 1.0.0

Tensors, or multidimensional arrays, are a powerful mathematical means of describing multiway data. This software provides computational means for decomposing or approximating a given tensor in terms of smaller tensors of lower dimension, focusing on decomposition of large, sparse tensors. These techniques have applications in many scientific areas, including signal processing, linear algebra, computer vision, numerical analysis, data mining, graph analysis, neuroscience and more. The software is designed to take advantage of parallelism present emerging computer architectures such has multi-core CPUs, many-core accelerators such as the Intel Xeon Phi, and computation-oriented GPUs to enable efficient processing of large tensors.

Phipps, EricT.↗
DOE OSTI2022

Advanced architectures for high-performance quantum networking

As practical quantum networks prepare to serve an ever-expanding number of nodes, there has grown a need for advanced auxiliary classical systems that support the quantum protocols and maintain compatibility with the existing fiber-optic infrastructure. We propose and demonstrate a quantum local area network design that addresses current deployment limitations in timing and security in a scalable fashion using commercial off-the-shelf components. First, we employ White Rabbit switches to synchronize three remote nodes with ultra-low timing jitter, significantly increasing the fidelities of the distributed entangled states over previous work with Global Positioning System clocks. Second, using a parallel quantum key distribution channel, we secure the classical communications needed for instrument control and data management. Therefore, the conventional network that manages our entanglement network is secured using keys generated via an underlying quantum key distribution layer, preserving the integrity of the supporting systems and the relevant data in a future-proof fashion.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Human behavior determinants of exposure to Anopheles vectors of malaria in Sumba, Indonesia

Malaria vector control interventions in Sumba, Indonesia, have not been able to eliminate malaria. Human drivers of exposure to Anopheles bites were investigated as part of a larger clinical trial evaluating the impact of a spatial repellent product on malaria incidence. Human behavioral observations (HBOs) evaluating temporal and spatial presence, sleeping behaviors, and insecticide treated net (ITN) use, were collected parallel to entomological collections—indoor and outdoor human landing catches (HLCs), and house hold surveys. Data demonstrates that mosquito access to humans, enabled by structurally open houses, is evident by the similar entomological landing rates both inside and outside households. The presence of animals inside houses was associated with increased mosquito entry–however, the number of humans present inside houses was not related to increased mosquito landing. Analyzing mosquito landing rates with human behavior data enables the spatial and temporal estimation of exposure to Anopheles bites, accounting for intervention (ITN) presence and usage. Human behavior adjusted exposure to Anopheles bites was found to be highest in the early in the evening, but continued at lower levels throughout the night. Over the night, most exposure (53%) occurred when people were indoors and not under the protection of nets (asleep or awake) followed by exposure outside (44%). Characterized gaps in protection are outdoor exposure as well as exposure indoors–when awake, and when asleep and not using ITNs. Interestingly, in the primary trial, even though there was not a significant impact of the spatial repellent on vector biting rates by themselves (16%), when factoring in human behavior, there was approximately 28% less exposure in the intervention arm than in the placebo arm. The treated arm had less human behavior adjusted bites in all spaces evaluated though there was proportionally higher exposure indoors. This analysis points to the importance of using HBOs both towards understanding gaps in protection as well as how interventions are evaluated. To mitigate ongoing transmission, understanding context specific spatial and temporal exposure based on the interactions of vectors, humans and interventions would be vital for a directed evidence-based control or elimination strategy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Two Delayed Critical 7-Inch-Diameter Interacting Enriched (93.14) Uranium Metal Cylinders without Moderator and Reflector

This report documents very accurately the configuration and the materials for experiments with two unmoderated, unreflected, interacting, coaxial, highly enriched, 7-in.-diameter, uranium metal cylinders performed at the Oak Ridge Critical Experiments Facility (ORCEF) in April 1963 and described in logbook E-19 associated with experiments in the East cell of ORCEF. The information is sufficiently accurate that it can be used as the basis for preparation of benchmarks for International Criticality Safety Benchmark Program (ICSBEP) at Idaho National laboratory. The thickness of the cylinders was varied and the spacing between them was adjusted to achieve a delayed critical configuration. The average enrichment of the uranium metal was 94.15 wt. % 235 U. The heights of the 7-in.-diameter, equal-height cylinders varied from 2 5/8 to 3 1/4 inches. All interacting cylinders were assembled coaxially with their flat faces parallel and their combined masses varied between 62 and 76 kilograms of HEU metal. The data from these six experiments described are judged to be acceptable for use as criticality safety benchmark experiments for the ICSBEP and EURATOM’s Nuclear Energy Agency nuclear criticality safety benchmark program, once the uncertainty analysis is completed. Based on previous ICSBEP benchmarks with this enriched uranium metal at ORCEF, it is expected that the uncertainties in k eff could be as low as ± 0.0002.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2020

Two Delayed Critical 15-Inch-Diameter Interacting Enriched (93.14) Uranium Metal Cylinders without Moderator and Reflector

This report documents very accurately the configuration and the materials for experiments with two unmoderated, unreflected, interacting, coaxial, highly enriched, 15-in.-diameter, uranium metal cylinders performed at the Oak Ridge Critical Experiments Facility (ORCEF) in May to Aug 1963 and described in logbook E-19 and E -20 associated with experiments in the East cell of ORCEF. Measurements were also performed in April and May of 1965 and described in logbooks E-22 and E-23 The information is sufficiently accurate that it can be used as the basis for preparation of benchmarks for International Criticality Safety Benchmark Program (ICSBEP) at Idaho National laboratory. The thickness of the cylinders was varied and the spacing between them was adjusted to achieve a delayed critical configuration. The average enrichment of the uranium metal was 94.14 wt. % 235 U. The heights of the 15-in.-diameter, equal-height cylinders varied from 1-5/8 to 3.0-inches. All interacting cylinders were assembled coaxially with their flat faces parallel and their combined masses varied between 182 and 325 kilograms of HEU metal. The data from these 12 experiments described would be acceptable for use as criticality safety benchmark experiments for the ICSBEP and EURATOM’s Nuclear Energy Agency nuclear criticality safety benchmark program, once the uncertainty analysis is completed. Based on previous ICSBEP benchmarks with this enriched uranium metal at ORCEF, it is expected that the uncertainties in k eff could be as low as ± 0.0002.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Three Delayed Critical 15-Inch-Diameter Interacting Enriched (93.14) Uranium Metal Cylinders Without Moderator and Reflector

This report documents very accurately the configuration and the materials for experiments with three unmoderated, unreflected, interacting, coaxial, highly enriched, 15-in.-diameter, uranium metal cylinders performed at the Oak Ridge Critical Experiments Facility (ORCEF) in August and September 1963 and described in logbook E 20 associated with experiments in the East cell of ORCEF. The information is sufficiently accurate that it can be used as the basis for preparation of benchmarks for International Criticality Safety Benchmark Program (ICSBEP) at Idaho National laboratory. The thickness of the cylinders was varied and the spacing between them was adjusted to achieve a delayed critical configuration. The average enrichment of the uranium metal was 94.14 wt. % 235U. The heights of the 15-in.-diameter, equal-height cylinders varied from 1-1/8to 2.00 inches. All interacting cylinders were assembled coaxially with their flat faces parallel and their combined masses varied between 182 and 325 kilograms of HEU metal. The data from these six experiments described are judged to be acceptable for use as criticality safety benchmark experiments for the ICSBEP and EURATOM’s Nuclear Energy Agency nuclear criticality safety benchmark program, once the uncertainty analysis is completed. Based on previous ICSBEP benchmarks with this enriched uranium metal at ORCEF, it is expected that the uncertainties in measured keff could be as low as ± 0.0002.

36 MATERIALS SCIENCE↗
DOE OSTI2018

167-PFlops deep learning for electron microscopy: from learning physics to atomic manipulation

An artificial intelligence system called MENNDL, which used 25,200 NVIDIA Volta GPUs on Oak Ridge National Laboratory's Summit machine, automatically designed an optimal deep learning network in order to extract structural information from raw atomic-resolution microscopy data. In a few hours, MENNDL creates and evaluates millions of networks using a scalable, parallel, asynchronous genetic algorithm augmented with a support vector machine to automatically find a superior deep learning network topology and hyper-parameter set than a human expert can find in months. For the application of electron microscopy, the system furthers the goal of improving our understanding of the electron-beam-matter interactions and real-time image-based feedback, which enables a huge step beyond human capacity towards nanofabricating materials automatically. MENNDL has been scaled to the 4,200 available nodes of Summit achieving a measured 152.5 PFlops, with an estimated sustained performance of 167 PFlops when the entire machine is available.

Patton, Robert↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here. In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry. Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2015

Oxygen transport properties estimation by classical trajectory–direct simulation Monte Carlo

Coupling direct simulation Monte Carlo (DSMC) simulations with classical trajectory calculations is a powerful tool to improve predictive capabilities of computational dilute gas dynamics. The considerable increase in computational effort outlined in early applications of the method can be compensated by running simulations on massively parallel computers. In particular, Graphics Processing Unit acceleration has been found quite effective in reducing computing time of classical trajectory (CT)-DSMC simulations. The aim of the present work is to study dilute molecular oxygen flows by modeling binary collisions, in the rigid rotor approximation, through an accurate Potential Energy Surface (PES), obtained by molecular beams scattering. The PES accuracy is assessed by calculating molecular oxygen transport properties by different equilibrium and non-equilibrium CT-DSMC based simulations that provide close values of the transport properties. Comparisons with available experimental data are presented and discussed in the temperature range 300–900 K, where vibrational degrees of freedom are expected to play a limited (but not always negligible) role.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

A Computational Approach for Modeling Neutron Scattering Data from Lipid Bilayers

Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to signficant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally. Importantly, computer simulations are starting to play a more prominent role in interpreting experimental results, enabling a molecular under- standing of lipid membranes. Particularly, the synergy between scattering experiments and simulations offers opportunities for new discoveries in membrane physics, as the length and time scales probed by molecular dynamics (MD) simulations parallel those of experiments. We also describe a coarse-grained MD simulation approach that mimics neutron scattering data from large unilamellar lipid vesicles over a range of bilayer rigidity. Specfically, we simulate vesicle form factors and membrane thickness fluctuations determined from small angle neutron scattering (SANS) and neutron spin echo (NSE) experiments, respectively. Our simulations accurately reproduce trends from experiments and lay the groundwork for investigations of more complex membrane systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nonparallel transcriptional divergence during parallel adaptation

Abstract How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies ( Poecilia reticulata ) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high‐ and low‐predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high‐ and low‐predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Fischer, Eva K.↗
DOE OSTI2015

WE-EF-207-02: The Rotate-Plus-Shift C-Arm Trajectory: Theory and First Clinical Results

Purpose: The proposed method enables the acquisition of a complete dataset for 3D reconstruction of C-Arm data using less than 180° rotation. Methods: Typically a C–arm cone–beam CT scan is performed using a circle–like trajectory around a region of interest. Therefore an angular range of at least 180° plus fan–angle must be covered to ensure a completely sampled data set. This fact defines some constraints on the geometry and technical specifications of a C–arm system, for example a larger C radius or a smaller C opening respectively. This is even more important for mobile C-arm devices which are typically used in surgical applications.To overcome these limitations we propose a new trajectory which requires only 180° minusfan–angle of rotation for a complete data set. The trajectory consists of three parts: A rotation of the C around a defined iso–center and two translational movements parallel to the detector plane at the begin and at the end of the rotation (rotate plus shift trajectory). This enables the acquisition of a completely sampled dataset using only 180° minus fan–angle of rotation. Results: For the evaluation of the method we show simulated and measured data. The results show, that the rotate plus shift scan yields equivalent image quality compared to the short scan which is assumed to be the gold standard for C-arm CT today. Compared to the pure rotational scan over only 165°, the rotate plus shift scan shows strong improvements in image quality. Conclusion: The proposed method makes 3D imaging using C–arms with less than 180° rotation range possible. This enables integrating full 3D functionality into a C- arm device without any loss of handling and usability for 2D imaging.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Juggler: a dependence-aware task-based execution framework for GPUs

Scientific applications with single instruction, multiple data (SIMD) computations show considerable performance improvements when run on today's graphics processing units (GPUs). However, the existence of data dependences across thread blocks may significantly impact the speedup by requiring global synchronization across multiprocessors (SMs) inside the GPU. To efficiently run applications with interblock data dependences, we need fine-granular task-based execution models that will treat SMs inside a GPU as stand-alone parallel processing units. Such a scheme will enable faster execution by utilizing all internal computation elements inside the GPU and eliminating unnecessary waits during device-wide global barriers.In this paper, we propose Juggler, a task-based execution scheme for GPU workloads with data dependences. The Juggler framework takes applications embedding OpenMP 4.5 tasks as input and executes them on the GPU via an efficient in-device runtime, hence eliminating the need for kernel-wide global synchronization. Juggler requires no or little modification to the source code, and once launched, the runtime entirely runs on the GPU without relying on the host through the entire execution. We have evaluated Juggler on an NVIDIA Tesla P100 GPU and obtained up to 31% performance improvement against global barrier based implementation, with minimal runtime overhead.

Belviranli, Mehmet E.↗
DOE OSTI2017

GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

Computer Science↗
DOE OSTI2022

Distributed Real-time Plume Monitoring for Deep Sea Mineral Extraction​

In the emerging industry of deep-sea mining for minerals and deposits (e.g. polymetallic nodules for nickel, cobalt, copper, and manganese), more data is required to understand the effects of sediment plume generation and predict the distribution of disturbed sediment. There are two main sources of plume generation, the first being at the active mining site where the “collector” directly removes the top layer of the sea floor. The other is the “midwater plume” consisting of unwanted sediment that was collected during extraction that is pumped back into the aphotic zone. The vast majority of plume generation is caused by the collector, causing detrimental and long-lasting impacts on seafloor ecosystems due to the lack of wave activity or strong currents at the sea floor. Therefore, it is crucial to invest in the infrastructure to support the study and constant monitoring over a large area of the sea floor where plume generation is present. Due to the limited number of usable channels and power requirements, current subsea wireless communications technologies are not well suited to instrumenting the large areas of the sea floor needed to monitor plume migration. The scope of this effort is to transition experimental demonstrations of high-bandwidth, full-duplex scalable underwater laser communications to the seafloor in an open ocean environment. Specifically tackling challenges associated with the dynamic nature of the subsea world, including but not limited to, deployment logistics, sustainability, and range. The goal is to enable the internet of underwater things for deep sea industries by broadening the capabilities of subsea communications. By using high-precision laser transmitters, many of the challenges current subsea optical systems face can be circumvented, such as power consumption, interference, and bandwidth limitations. This approach lends itself to wireless interlinking multi-node networks, in series or parallel, facilitating the implementation of a wide array of sensor types. This interlinking allows all the data gathered from the network to be processed through a single hardline uplink to the surface, lowering the complexity required for near real-time data processing. Additionally, the laser control systems produce metadata that can be used to help characterize the water column between the nodes. Combining data from various sensors such as turbidity, temperature, current velocity with metadata such as beam attenuation and deflection can produce a high-resolution model of sea floor conditions around an active mining zone. The resulting near real-time model can be used to optimize location and flow rate of the mining operation to minimize and quantify the environmental impact.

Mons, Ishan↗