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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
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 OSTI2015

Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors

Accurate representation of intermolecular forces has been the central task of classical atomic simulations, known as molecular mechanics. Recent advancements in molecular mechanics models have put forward the explicit representation of permanent and/or induced electric multipole (EMP) moments. The formulas developed so far to calculate EMP interactions tend to have complicated expressions, especially in Cartesian coordinates, which can only be applied to a specific kernel potential function. For example, one needs to develop a new formula each time a new kernel function is encountered. The complication of these formalisms arises from an intriguing and yet obscured mathematical relation between the kernel functions and the gradient operators. Here, I uncover this relation via rigorous derivation and find that the formula to calculate EMP interactions is basically invariant to the potential kernel functions as long as they are of the form f(r), i.e., any Green’s function that depends on inter-particle distance. I provide an algorithm for efficient evaluation of EMP interaction energies, forces, and torques for any kernel f(r) up to any arbitrary rank of EMP moments in Cartesian coordinates. The working equations of this algorithm are essentially the same for any kernel f(r). Recently, a few recursive algorithms were proposed to calculate EMP interactions. Depending on the kernel functions, the algorithm here is about 4–16 times faster than these algorithms in terms of the required number of floating point operations and is much more memory efficient. I show that it is even faster than a theoretically ideal recursion scheme, i.e., one that requires 1 floating point multiplication and 1 addition per recursion step. This algorithm has a compact vector-based expression that is optimal for computer programming. The Cartesian nature of this algorithm makes it fit easily into modern molecular simulation packages as compared with spherical coordinate-based algorithms. A software library based on this algorithm has been implemented in C++11 and has been released.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2015

Extrapolating W -associated jet-production ratios at the LHC

Electroweak vector-boson production, accompanied by multiple jets, is an important background to searches for physics beyond the standard model. A precise and quantitative understanding of this process is helpful in constraining deviations from known physics. We study four key ratios in W + n -jet production at the LHC. We compute the ratio of cross sections for W + n - to W + (n-1)-jet production as a function of the minimum jet transverse momentum. We also study the ratio differentially, as a function of the W-boson transverse momentum; as a function of the scalar sum of the jet transverse energy, H$jets\atop{T}$; and as a function of certain jet transverse momenta. We show how to use such ratios to extrapolate differential cross sections to W + 6 -jet production at next-to-leading order, and we cross-check the method against a direct calculation at leading order. We predict the differential distribution in H$jets\atop{T}$ for W + 6 jets at next-to-leading order using such an extrapolation. We use the BlackHat software library together with SHERPA to perform the computations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Collaborative Computational Project for Electron cryo-Microscopy

The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Exploring Hardware Support For Scaling Irregular Applications on Multi-node Multi-core Architectures

With the recent emergence of large-scale knowledge dis- covery, data mining and social network analysis, irregular applications have gained renewed interest. Classic cache-based high-performance architectures do not provide optimal performances with such kind of workloads, mainly due to the very low spatial and temporal locality of the irregular control and memory access patterns. In this paper, we present a multi-node, multi-core, fine-grained multi-threaded shared-memory system architecture specifically designed for the execution of large-scale irregular applications, and built on top of three pillars, that we believe are fundamental to support these workloads. First, we offer transparent hardware support for Partitioned Global Address Space (PGAS) to provide a large globally-shared address space with no software library overhead. Second, we employ multi-threaded multi-core processing nodes to achieve the necessary latency tolerance required by accessing global memory, which potentially resides in a remote node. Finally, we devise hardware support for inter-thread synchronization on the whole global address space. We first model the performances by using an analytical model that takes into account the main architecture and application characteristics. We describe the hardware design of the proposed cus- tom architectural building blocks that provide support for the above- mentioned three pillars. Finally, we present a limited-scale evaluation of the system on a multi-board FPGA prototype with typical irregular kernels and benchmarks. The experimental evaluation demonstrates the architecture performance scalability for different configurations of the whole system.

FPGA↗
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 OSTI2014

Physics Integration KErnels (PIKE)

Pike is a software library for coupling and solving multiphysics applications. It provides basic interfaces and utilities for performing code-to-code coupling. It provides simple "black-box" Picard iteration methods for solving the coupled system of equations including Jacobi and Gauss-Seidel solvers. Pike was developed originally to couple neutronics and thermal fluids codes to simulate a light water nuclear reactor for the Consortium for Simulation of Light-water Reactors (CASL) DOE Energy Innovation Hub. The Pike library contains no physics and just provides interfaces and utilities for coupling codes. It will be released open source under a BSD license as part of the Trilinos solver framework (trilinos.org) which is also BSD. This code provides capabilities similar to other open source multiphysics coupling libraries such as LIME, AMP, and MOOSE.

Pawlowski, Roger↗