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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

DeePMD-kit v2: A software package for deep potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Streaming Data Reorganization at Scale with DeltaFS Indexed Massive Directories

We report complex storage stacks providing data compression, indexing, and analytics help leverage the massive amounts of data generated today to derive insights. It is challenging to perform this computation, however, while fully utilizing the underlying storage media. This is because, while storage servers with large core counts are widely available, single-core performance and memory bandwidth per core grow slower than the core count per die. Computational storage offers a promising solution to this problem by utilizing dedicated compute resources along the storage processing path. We present DeltaFS Indexed Massive Directories (IMDs), a new approach to computational storage. DeltaFS IMDs harvest available (i.e., not dedicated) compute, memory, and network resources on the compute nodes of an application to perform computation on data. We demonstrate the efficiency of DeltaFS IMDs by using them to dynamically reorganize the output of a real-world simulation application across 131,072 CPU cores. DeltaFS IMDs speed up reads by 1,740x while only slightly slowing down the writing of data during simulation I/O for in situ data processing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Sampling Approaches for Multi-Domain Internet Performance Measurement Infrastructures

The next-generation of high-performance networks being developed in DOE communities are critical for supporting current and emerging data-intensive science applications. The goal of this project is to investigate multi-domain network status sampling techniques and tools to measure/analyze performance, and thereby provide “network awareness” to end-users and network operators in DOE communities. We leverage the infrastructure and datasets available through perfSONAR, which is a multi-domain measurement framework that has been widely deployed in high-performance computing and networking communities; the DOE community is a core developer and the largest adopter of perfSONAR. Our investigations include development of semantic scheduling algorithms, measurement federation policies, and tools to sample multi-domain and multi-layer network status within perfSONAR deployments. We validate our algorithms and policies with end-to-end measurement analysis tools for various monitoring objectives such as network weather forecasting, anomaly detection, and fault-diagnosis. In addition, we develop a multi-domain architecture for an enterprise-specific perfSONAR deployment that can implement monitoring-objective based sampling and that adheres to any domain-specific measurement policies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

An Application Development Platform for Neuromorphic Computing

Dynamic Adaptive Neural Network Arrays (DANNAs) are neuromorphic computing systems developed as a hardware based approach to the implementation of neural networks. They feature highly adaptive and programmable structural elements, which model arti cial neural networks with spiking behavior. We design them to solve problems using evolutionary optimization. In this paper, we highlight the current hardware and software implementations of DANNA, including their features, functionalities and performance. We then describe the development of an Application Development Platform (ADP) to support efficient application implementation and testing of DANNA based solutions. We conclude with future directions.

Dean, Mark↗
DOE OSTI2024

Physics-Guided, Physics-Informed, and Physics-Encoded Neural Networks and Operators in Scientific Computing: Fluid and Solid Mechanics

Abstract Advancements in computing power have recently made it possible to utilize machine learning and deep learning to push scientific computing forward in a range of disciplines, such as fluid mechanics, solid mechanics, materials science, etc. The incorporation of neural networks is particularly crucial in this hybridization process. Due to their intrinsic architecture, conventional neural networks cannot be successfully trained and scoped when data are sparse, which is the case in many scientific and engineering domains. Nonetheless, neural networks provide a solid foundation to respect physics-driven or knowledge-based constraints during training. Generally speaking, there are three distinct neural network frameworks to enforce the underlying physics: (i) physics-guided neural networks (PgNNs), (ii) physics-informed neural networks (PiNNs), and (iii) physics-encoded neural networks (PeNNs). These methods provide distinct advantages for accelerating the numerical modeling of complex multiscale multiphysics phenomena. In addition, the recent developments in neural operators (NOs) add another dimension to these new simulation paradigms, especially when the real-time prediction of complex multiphysics systems is required. All these models also come with their own unique drawbacks and limitations that call for further fundamental research. This study aims to present a review of the four neural network frameworks (i.e., PgNNs, PiNNs, PeNNs, and NOs) used in scientific computing research. The state-of-the-art architectures and their applications are reviewed, limitations are discussed, and future research opportunities are presented in terms of improving algorithms, considering causalities, expanding applications, and coupling scientific and deep learning solvers.

Computer Science↗
DOE OSTI2018

Machine learning for graph-based representations of three-dimensional discrete fracture networks

Structural and topological information play a key role in modeling flow and transport through fractured rock in the subsurface. Discrete fracture network (DFN) computational suites such as dfnWorks (Hyman et al. Comput. Geosci. 84, 10–19 2015) are designed to simulate flow and transport in such porous media. Flow and transport calculations reveal that a small backbone of fractures exists, where most flow and transport occurs. Restricting the flowing fracture network to this backbone provides a significant reduction in the network’s effective size. However, the particle-tracking simulations needed to determine this reduction are computationally intensive. Such methods may be impractical for large systems or for robust uncertainty quantification of fracture networks, where thousands of forward simulations are needed to bound system behavior. In this paper, we develop an alternative network reduction approach to characterizing transport in DFNs, by combining graph theoretical and machine learning methods. We consider a graph representation where nodes signify fractures and edges denote their intersections. Using random forest and support vector machines, we rapidly identify a subnetwork that captures the flow patterns of the full DFN, based primarily on node centrality features in the graph. Our supervised learning techniques train on particle-tracking backbone paths found by dfnWorks, but run in negligible time compared to those simulations. In conclusion, we find that our predictions can reduce the network to approximately 20% of its original size, while still generating breakthrough curves consistent with those of the original network.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

NeRVI: Compressive neural representation of visualization images for communicating volume visualization results

We present NeRVI, a new deep-learning approach that compresses a large collection of visualization images generated from time-varying data for communicating volume visualization results. Based on an image-based implicit neural representation, our approach represents tens of thousands of high-resolution rendering images parametrized by different parameters via a hybrid model of multilayer perceptrons and convolutional neural networks. Here, our model predicts images and corresponding masks, and the masks are utilized for loss computation and network training to capture fine structural details and small components. In conjunction with model quantization and weight encoding, NeRVI yields highly compact compressive neural representations while preserving the image fidelity well. We demonstrate the effectiveness of NeRVI with isosurface rendering and direct volume rendering images generated from multiple data sets and compare NeRVI with other state-of-the-art deep learning-based (InSituNet, SIREN, NeRF, and NeRV) methods. Quantitative and qualitative results show that NeRVI provides an alternative solution that augments domain scientists' ability to manage, represent, and communicate scientific visualization output.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Attention-based convolutional capsules for evapotranspiration estimation at scale

Evapotranspiration (ET) measures the amount of water lost from the Earth's surface to the atmosphere and is an integral metric for both agricultural and environmental sciences. Understanding and quantifying ET is critical for achieving effective management of freshwater and irrigation systems. However, current ET estimation models suffer from a trade-off between accuracy and spatial coverage. In this study, we introduce our model Quench, a neural network architecture that achieves highly-accurate ET estimates over large continuous spatial extents. Quench uses our novel Attention-Based Convolutional Capsule for its neural network layers to identify areas of focus and efficiently extract ET information from satellite imagery. Benchmarks that profile our model's performance show substantive improvements in accuracy, with up to 128% increase in accuracy compared to traditional convolutional-based and process-based models. Finally, Quench also demonstrates consistent model performance over high geospatial variability and a diverse array of regions, seasons, climates, and vegetations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

An efficient algorithm for pairwise local alignment of protein interaction networks

Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Comput Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Dispersion and Mixing in Three-Dimensional Discrete Fracture Networks: Nonlinear Interplay Between Structural and Hydraulic Heterogeneity: DISPERSION AND MIXING-REGULAR VERSUS DISORDERED NETWORKS

We investigate the relative impact of topological, geometric, and hydraulic heterogeneity on transport processes in three-dimensional fracture networks. Focusing on the two largest scales of heterogeneity in these systems, individual fracture and network structure, we compare transport through analogous structured and disordered three-dimensional fracture networks with varying degrees of hydraulic heterogeneity. For the moderate levels of hydraulic heterogeneity we consider, network structure is the dominant control of transport through the networks. Less dispersion, both longitudinal and transverse, is observed in structured networks than in disordered networks, due in part to the higher connectivity in the former, independent of the level of hydraulic heterogeneity. However, increases in dispersion with higher hydraulic heterogeneity are larger in the disordered networks than in the structured networks, thereby indicating that the interplay between structural and hydraulic heterogeneity is nonlinear. Here, we propose a measure of disorder in fracture networks by computing the Shannon entropy of the spectrum of the Laplacian of a weighted graph representation of the networks, where the weights are given by a combination of topological, geometric, and hydraulic properties. Finally, this metric, as a relative indicator by comparison between two networks, is a first approach to the dispersion potential and “mixing capacity” of a fracture network.

58 GEOSCIENCES↗
DOE OSTI2016

Real-time data-intensive computing

Today users visit synchrotrons as sources of understanding and discovery—not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a “super-facility”, giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data—despite its high rate and volume—is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Abisko: Deep codesign of an architecture for spiking neural networks using novel neuromorphic materials

The Abisko project aims to develop an energy-efficient spiking neural network (SNN) computing architecture and software system capable of autonomous learning and operation. The SNN architecture explores novel neuromorphic devices that are based on resistive-switching materials, such as memristors and electrochemical RAM. Equally important, Abisko uses a deep codesign approach to pursue this goal by engaging experts from across the entire range of disciplines: materials, devices and circuits, architectures and integration, software, and algorithms. Here, the key objectives of our Abisko project are threefold. First, we are designing an energy-optimized high-performance neuromorphic accelerator based on SNNs. This architecture is being designed as a chiplet that can be deployed in contemporary computer architectures and we are investigating novel neuromorphic materials to improve its design. Second, we are concurrently developing a productive software stack for the neuromorphic accelerator that will also be portable to other architectures, such as field-programmable gate arrays and GPUs. Third, we are creating a new deep codesign methodology and framework for developing clear interfaces, requirements, and metrics between each level of abstraction to enable the system design to be explored and implemented interchangeably with execution, measurement, a model, or simulation. As a motivating application for this codesign effort, we target the use of SNNs for an analog event detector for a high-energy physics sensor.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Making Advanced Scientific Algorithms and Big Scientific Data Management More Accessible

Synchrotrons such as the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory are known as user facilities. They are sources of extremely bright X-ray beams, and scientists come from all over the world to perform experiments that require these beams. As the complexity of experiments has increased, and the size and rates of data sets has exploded, managing, analyzing and presenting the data collected at synchrotrons has been an increasing challenge. The ALS has partnered with high performance computing, fast networking, and applied mathematics groups to create a"super-facility", giving users simultaneous access to the experimental, computational, and algorithmic resources to overcome this challenge. This combination forms an efficient closed loop, where data despite its high rate and volume is transferred and processed, in many cases immediately and automatically, on appropriate compute resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beam-time. In this paper, We will present work done on advanced tomographic reconstruction algorithms to support users of the 3D micron-scale imaging instrument (Beamline 8.3.2, hard X-ray micro-tomography).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Berkeley Lab 2nd Grader Outreach

The Berkeley Lab IT Department sponsored a community outreach program aimed at teaching young children about computers and networks. Second graders from LeConte Elementary School joined Lab IT Staff for a day of in-depth exercises and fun.

99 GENERAL AND MISCELLANEOUS↗