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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

libwfa: Wavefunction analysis tools for excited and open‐shell electronic states

Abstract An open‐source software library for wavefunction analysis, libwfa, provides a comprehensive and flexible toolbox for post‐processing excited‐state calculations, featuring a hierarchy of interconnected visual and quantitative analysis methods. These tools afford compact graphical representations of various excited‐state processes, provide detailed insight into electronic structure, and are suitable for automated processing of large data sets. The analysis is based on reduced quantities, such as state and transition density matrices (DMs), and allows one to distill simple molecular orbital pictures of physical phenomena from intricate correlated wavefunctions. The implemented descriptors provide a rigorous link between many‐body wavefunctions and intuitive physical and chemical models, for example, exciton binding, double excitations, orbital relaxation, and polyradical character. A broad range of quantum‐chemical methods is interfaced with libwfa via a uniform interface layer in the form of DMs. This contribution reviews the structure of libwfa and highlights its capabilities by several representative use cases. This article is categorized under: Software > Quantum Chemistry Theoretical and Physical Chemistry > Spectroscopy

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Hardening of DOE UQ Codes for Ultra-Deep Proactive Geosteering in Oilfield Service

The primary objective of this project was to harden the DOE uncertainty quantification (UQ) code to solve the inverse problem for the geosteering service in the oilfield drilling and exploration. The primary focus is to verify the feasibility of using QUESO to solve geosteering inverse problems through statistical inversion. QUESO is a software library developed by QUEST, a DOE's Scientific Discovery through Advanced Computing (SciDAC) institute. In the process of drilling a borehole, geosteering is the act of adjusting the well trajectory on the fly to reach the geological targets or to keep the wellbore within desired formation. Geosteering inversion is to infer underground formation structure using measurements such as azimuthal resistivity logging data. The geosteering process relies on the real-time reconstruction of the subsurface earth model, and a robust and efficient inversion algorithm is always necessary to satisfy the job requirement. The new generation of azimuthal resistivity geosteering tool is capable of detecting multiple formation boundaries 20-100 ft away, and the corresponding geosteering inversion problem can be very challenging as many parameters need to be inverted within such a large depth of investigation. The success of the project will support US energy security by helping to advance subsurface modeling and characterization technologies in oilfield applications. An effective subsurface inversion algorithm and the implementation as a software package will promote the usage of ultra-deep azimuthal resistivity measurements, which can help well placement in complicated underground environments, reduce costs and risks of drilling, and increase oil and gas production. It will help medium and small size independent service companies and tool manufactures to enter the more advanced and lucrative directional drilling area. In addition, by hardening the QUESO code and building a transparent interface for easy manipulation of the QUESO functions, we provide a user-friendly tool for a larger scientific and industry communities that rely heavily on modeling and simulation tools for forecasting, parameter studies, design, and decision making. These are all activities that can strongly benefit from meaningful representations of modeling uncertainty supported by our product.

58 GEOSCIENCES↗
DOE OSTI2019

Deep learning and radiomics: the utility of Google TensorFlow™ Inception in classifying clear cell renal cell carcinoma and oncocytoma on multiphasic CT

Purpose: Currently, all solid enhancing renal masses without microscopic fat are considered malignant until proven otherwise and there is substantial overlap in the imaging findings of benign and malignant renal masses, particularly between clear cell RCC (ccRCC) and benign oncocytoma (ONC). Radiomics has attracted increased attention for its utility in pre-operative work-up on routine clinical images. Radiomics based approaches have converted medical images into mineable data and identified prognostic imaging signatures that machine learning algorithms can use to construct predictive models by learning the decision boundaries of the underlying data distribution. The TensorFlow™ framework from Google is a state-of-the-art open-source software library that can be used for training deep learning neural networks for performing machine learning tasks. The purpose of this study was to investigate the diagnostic value and feasibility of a deep learning-based renal lesion classifier using open-source Google TensorFlow™ Inception in differentiating ccRCC from ONC on routine four-phase MDCT in patients with pathologically confirmed renal masses. Methods: With institutional review board approval for this 1996 Health Insurance Portability and Accountability Act compliant retrospective study and a waiver of informed consent, we queried our institution’s pathology, clinical, and radiology databases for histologically proven cases of ccRCC and ONC obtained between January 2000 and January 2016 scanned with a an intravenous contrast-enhanced four-phase renal mass protocol (unenhanced (UN), corticomedullary (CM), nephrographic (NP), and excretory (EX) phases). To extract features to be used for the machine learning model, the entire renal mass was contoured in the axial plane in each of the four phases, resulting in a 3D volume of interest (VOI) representative of the entire renal mass. We investigated thirteen different approaches to convert the acquired VOI data into a set of images that adequately represented each tumor which was used to train the final layer of the neural network model. Training was performed over 4000 iterations. In each iteration, 90% of the data were designated as training data and the remaining 10% served as validation data and a leave-one-out cross-validation scheme was implemented. Accuracy, sensitivity, specificity, positive (PPV) and negative predictive (NPV) values, and CIs were calculated for the classification of the thirteen processing modes. Results: We analyzed 179 consecutive patients with 179 lesions (128 ccRCC and 51 ONC). The ccRCC cohort had a mean size of 3.8 cm (range 0.8–14.6 cm) and the ONC cohort had a mean lesion size of 3.9 cm (range 1.0–13.1 cm). The highest specificity and PPV (52.9% and 80.3%, respectively) were achieved in the EX phase when we analyzed the single mid-slice of the tumor in the axial, coronal and sagittal plane, and when we increased the number of mid-slices of the tumor to three, with an accuracy of 75.4%, which also increased the sensitivity to 88.3% and the PPV to 79.6%. Using the entire tumor volume also showed that classification performance was best in the EX phase with an accuracy of 74.4%, a sensitivity of 85.8% and a PPV of 80.1%. When the entire tumor volume, plus mid-slices from all phases and all planes presented as tiled images, were submitted to the final layer of the neural network we achieved a PPV of 82.5%. Conclusions: The best classification result was obtained in the EX phase among the thirteen classification methods tested. Our proof of concept study is the first step towards understanding the utility of machine learning in the differentiation of ccRCC from ONC on routine CT images. We hope this could lead to future investigation into the development of a multivariate machine learning model which may augment our ability to accurately predict renal lesion histology on imaging.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

A parallel and performance portable implementation of a full-field crystal plasticity model

We have developed a parallel implementation of an Elasto-Viscoplastic Fast Fourier Transform-based (EVPFFT) micromechanical solver to enable computationally efficient crystal plasticity modeling for polycrystalline materials. Our primary focus lies in achieving performance portability, allowing a single EVPFFT implementation to run optimally on various homogeneous architectures, including multi-core Central Processing Units (CPUs), as well as on heterogeneous computer architectures comprising multi-core CPUs and Graphics Processing Units (GPUs) from different vendors. To accomplish this goal, we have leveraged MATAR, a C++ software library that simplifies the creation and utilization of multidimensional dense or sparse matrix and array data structures. These data structures are designed to be portable across diverse architectures through the use of Kokkos, a performance-portable library. Additionally, we have employed the Message Passing Interface (MPI) to efficiently distribute the computational workload among processors. The heFFTe (Highly Efficient FFT for Exascale) library is used to facilitate the performance portability of the fast Fourier transforms (FFTs) computation. The computational performance of EVPFFT is evaluated and presented in terms of parallel scalability and simulation runtime on different high-performance computing (HPC) architectures. As a result, the utility of the developed framework to efficiently simulate the micro-mechanical fields in polycrystalline microstructures in engineering applications is discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2021

MATAR: A performance portability and productivity implementation of data-oriented design with Kokkos

There is a need for simple, fast, and memory-efficient multidimensional data structures for dense and sparse storage that arise with numerical methods and in software applications. The data structures must perform equally well across multiple computer architectures, including CPUs and GPUs. For this purpose, we developed MATAR, a C++ software library that allows for simple creation and use of intricate data structures that is also portable across disparate architectures using Kokkos. Here, the performance aspect is achieved by forcing contiguous memory layout (or as close to contiguous as possible) for multidimensional and multi-size dense or sparse MATrix and ARray (hence, MATAR) types. Our results show that MATAR has the capability to improve memory utilization, performance, and programmer productivity in scientific computing. This is achieved by fitting more work into the available memory, minimizing memory loads required, and by loading memory in the most efficient order. This document describes the purpose of the work, the implementation of each of the data types, and the resulting performance both in some simple baseline test cases and in an application code.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Minimizing development costs for efficient many-core visualization using MCD3

Scientific visualization software increasingly needs to support many-core architectures. However, development time is a significant challenge due to the breadth and diversity of both visualization algorithms and architectures. With this work, we introduce a development environment for visualization algorithms on many-core devices that extends the traditional data-parallel primitive (DPP) approach with several existing constructs and an important new construct: meta-DPPs. We refer to our approach as MCD 3 — Meta-DPPs, Convenience routines, Data management, DPPs, and Devices. The twin goals of MCD 3 are to reduce developer time and to deliver efficient performance on many-core architectures, and our evaluation considers both of these goals. For development time, we study 57 algorithms implemented in the VTK-m software library and determine that MCD 3 leads to significant savings. For efficient performance, we survey ten studies looking at individual algorithms and determine that the MCD 3 hardware-agnostic approach leads to performance comparable to hardware-specific approaches: sometimes better, sometimes worse, and better in the aggregate. In total, we find that MCD 3 is an effective approach for scientific visualization libraries to support many-core architectures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Combustion machine learning: Principles, progress and prospects

Progress in combustion science and engineering has led to the generation of large amounts of data from large-scale simulations, high-resolution experiments, and sensors. This corpus of data offers enormous opportunities for extracting new knowledge and insights—if harnessed effectively. Machine learning (ML) techniques have demonstrated remarkable success in data analytics, thus offering a new paradigm for data-intense analyses and scientific investigations through combustion machine learning (CombML). While data-driven methods are utilized in various combustion areas, recent advances in algorithmic developments, the accessibility of open-source software libraries, the availability of computational resources, and the abundance of data have together rendered ML techniques ubiquitous in scientific analysis and engineering. This article examines ML techniques for applications in combustion science and engineering. Starting with a review of sources of data, data-driven techniques, and concepts, we examine supervised, unsupervised, and semi-supervised ML methods. Various combustion examples are considered to illustrate and to evaluate these methods. Next, we review past and recent applications of ML approaches to problems in combustion, spanning fundamental combustion investigations, propulsion and energy-conversion systems, and fire and explosion hazards. Challenges unique to CombML are discussed and further opportunities are identified, focusing on interpretability, uncertainty quantification, robustness, consistency, creation and curation of benchmark data, and the augmentation of ML methods with prior combustion-domain knowledge.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Applications of “Synchrotron Radiation Workshop” Code

The “Synchrotron Radiation Workshop” (SRW) computer code was started in the group of Insertion Devices of the European Synchrotron Radiation Facility in 1997. The idea behind it was to combine in one software library electrodynamics methods for calculating electric fields (and derived characteristics) of synchrotron radiation (SR) generated by relativistic electrons moving in magnetic fields of nearly arbitrary configuration with wave-optics methods for simulating propagation of radiation through optical elements of beamlines. Further, the use of this general approach was initially driven by applications in electron beam diagnostics using SR. However, with time it started to be used for more complicated beamlines of synchrotron light sources, and the use of the code for these applications continues to increase, with the new light sources offering brighter and more coherent x ray beams for wide ranges of experiments in different areas of science.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Progress toward Accelogic compression in ROOT

For the last 7 years, Accelogic pioneered and perfected a radically new theory of numerical computing codenamed “Compressive Computing”, which has an extremely profound impact on real-world computer science [1]. At the core of this new theory is the discovery of one of its fundamental theorems which states that, under very general conditions, the vast majority (typically between 70% and 80%) of the bits used in modern large-scale numerical computations are absolutely irrelevant for the accuracy of the end result. This theory of Compressive Computing provides mechanisms able to identify (with high intelligence and surgical accuracy) the number of bits (i.e., the precision) that can be used to represent numbers without affecting the substance of the end results, as they are computed and vary in real time. The bottom-line outcome will be to provide state-of-the-art compression algorithms --and accompanying software libraries-- able to surpass the performance of the compression engines currently available in the ROOT [7] framework. The resulting technology has the capability to enable substantial economic and operational gains (including speedup) for High Energy and Nuclear Physics data storage/analysis. In our initial studies, a factor of nearly x4 (3.9) compression was achieved with RHIC/STAR data where ROOT compression managed only x1.4 [6].As a collaboration of experimental scientists, private industry, and the ROOT Team, our aim is to capitalize on the substantial success delivered by the initial effort and produce a robust technology properly packaged as an open-source tool that could be used by virtually every experiment around the world as means for improving data management and accessibility.In this contribution, we will present our efforts integrating our concepts of “functionally lossless compression” within the ROOT framework implementation, with the purpose of producing a basic solution readily integrated into HENP applications. We will also present our progress applying this compression through realistic examples of analysis from both the STAR and CMS experiments.

Canal, Ph.↗
DOE OSTI2022

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Scalable Static and Dynamic Community Detection Using Grappolo

Graph clustering, popularly known as community detection, is a fundamental kernel for several applications of relevance to the Defense Advanced Research Projects Agency’s (DARPA) Hierarchical Identify Verify Exploit (HIVE) Pro- gram. Clusters or communities represent natural divisions within a network that are densely connected within a cluster and sparsely connected to the rest of the network. The need to compute clustering on large scale data necessitates the development of efficient algorithms that can exploit modern architectures that are fundamentally parallel in nature. How- ever, due to their irregular and inherently sequential nature, many of the current algorithms for community detection are challenging to parallelize. In response to the HIVE Graph Challenge, we present several parallelization heuristics for fast community detection using the Louvain method as the serial template. We implement all the heuristics in a software library called Grappolo. Using the inputs from the HIVE Challenge, we demonstrate superior performance and high quality solutions based on four parallelization heuristics. We use Grappolo on static graphs as the first step towards community detection on streaming graphs.

Community Detection↗
DOE OSTI2025

Towards Automatically Matching Security Advisories to CPEs: String Similarity-based Vendor Matching

When a vulnerability is reported by the National Vulnerability Database (NVD), affected products are listed in the structured Common Platform Enumeration (CPE) format. Unfortunately, if the vulnerability is in a software library (e.g., Log4j), it will not include CPEs for each product containing that library. In these cases, security operators need to manually read the vendor's or third-party security advisories to see if their product is affected. However, these advisories do not report affected products in a structured format, which prevents automated processing, This paper makes the first effort towards automatically constructing structured CPEs for the vulnerable products in a non-NVD security advisory from the unstructured data in the advisory. Since this is a very challenging problem, this paper specifically focuses on the initial but key step of matching the un-structured vendor names in security advisories to the structured vendor representations in the standard CPE format. We explore the feasibility of using string similarity to solve the problem. The basic idea is to compare a vendor name from the non-NVD advisory with each vendor in the official CPE dictionary. The CPE vendor with the highest similarity score to the advisory's vendor will be considered as the match. We first conduct an experimental, comparative study of multiple mainstream string similarity metrics for this matching problem. To improve the performance, we then design a new string similarity metric that is adapted from an existing metric by weighing different tokens in the advisory's vendor name differently.

McClanahan, Kylie↗
DOE OSTI2023

ExTreeM: Scalable Augmented Merge Tree Computation via Extremum Graphs

Over the last decade merge trees have been proven to support a plethora of visualization and analysis tasks since they effectively abstract complex datasets. Here, this paper describes the ExTreeM-Algorithm: A scalable algorithm for the computation of merge trees via extremum graphs. The core idea of ExTreeM is to first derive the extremum graph G of an input scalar field f defined on a cell complex K, and subsequently compute the unaugmented merge tree of f on G instead of K; which are equivalent. Any merge tree algorithm can be carried out significantly faster on G, since K in general contains substantially more cells than G. To further speed up computation, ExTreeM includes a tailored procedure to derive merge trees of extremum graphs. The computation of the fully augmented merge tree, i.e., a merge tree domain segmentation of K, can then be performed in an optional post-processing step. All steps of ExTreeM consist of procedures with high parallel efficiency, and we provide a formal proof of its correctness. Our experiments, performed on publicly available datasets, report a speedup of up to one order of magnitude over the state-of-the-art algorithms included in the TTK and VTK-m software libraries, while also requiring significantly less memory and exhibiting excellent scaling behavior.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Network Uncertainty Quantification for Analysis of Multi-Component Systems

To impact physical mechanical system design decisions and realize the full promise of high-fidelity computational tools, simulation results must be integrated at the earliest stages of the design process. This is particularly challenging when dealing with uncertainty and optimizing for system-level performance metrics, as full-system models (often notoriously expensive and time-consuming to develop) are generally required to propagate uncertainties to system-level quantities of interest. Methods for propagating parameter and boundary condition uncertainty in networks of interconnected components hold promise for enabling design under uncertainty in real-world applications. These methods avoid the need for time consuming mesh generation of full-system geometries when changes are made to components or subassemblies. Additionally, they explicitly tie full-system model predictions to component/subassembly validation data which is valuable for qualification. These methods work by leveraging the fact that many engineered systems are inherently modular, being comprised of a hierarchy of components and subassemblies that are individually modified or replaced to define new system designs. By doing so, these methods enable rapid model development and the incorporation of uncertainty quantification earlier in the design process. The resulting formulation of the uncertainty propagation problem is iterative. We express the system model as a network of interconnected component models, which exchange solution information at component boundaries. We present a pair of approaches for propagating uncertainty in this type of decomposed system and provide implementations in the form of an open-source software library. We demonstrate these tools on a variety of applications and demonstrate the impact of problem-specific details on the performance and accuracy of the resulting UQ analysis. This work represents the most comprehensive investigation of these network uncertainty propagation methods to date.

42 ENGINEERING↗
DOE OSTI2023

A New Semistructured Algebraic Multigrid Method

Multigrid methods are well suited to large massively parallel computer architectures because they are mathematically optimal and display good parallelization properties. Since current architecture trends are favoring regular compute patterns to achieve high performance, the ability to express structure has become much more important. The hypre software library provides high-performance multigrid preconditioners and solvers through conceptual interfaces, including a semistructured interface that describes matrices primarily in terms of stencils and logically structured grids. This paper presents a new semistructured algebraic multigrid (SSAMG) method built on this interface. The numerical convergence and performance of a CPU implementation of this method are evaluated for a set of semistructured problems. In conclusion, SSAMG achieves significantly better setup times than hypre’s unstructured AMG solvers and comparable convergence. In addition, the new method is capable of solving more complex problems than hypre’s structured solvers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Progress Version 1.0

Software library for parallel rapid order N and graph-based recursive electronic structure solvers with applications to material science, chemistry, and molecular biology.

Niklasson, AndersM.↗
DOE OSTI2017

Portage, Version 2.0

Portage is a software library system for physics remapping (mapping physics variables from one computational mesh to another) either within a single simulation code or between two disparate simulation codes. Portage is designed to utilize advanced-architecture compute platforms and to be easily extensible by third parties.

Herring, Angela↗