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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Oxidation Behavior and Property Degradation of Nuclear Graphites

During its multidecade operation in the core of nuclear reactors, graphite components are subjected to aggressive and continuous exposure to a high field of ionizing and neutron irradiation, high temperature, and various types of present and postulated chemical attacks. High density, high crystallinity polygranular synthetic graphite is unique among other materials for its extraordinary capacity of resisting and adapting to the aggression inflicted by high temperature, high energy neutron bombardment and ionizing gamma radiation. But, as a carbonaceous material, even though of very high purity, graphite is reactive towards common oxidizing agents: oxygen, carbon dioxide, water. Safe operation of HTGRs relies, among other aspects, on engineered safeguard systems for efficient and continuous protection of graphite components against oxidation. Graphite oxidation behavior was, and continues to be, an important direction of theoretical and experimental research, engineering analyses, models and simulations, and design and safety regulations. The avalanche of publications, reports, experimental data, computer codes, and regulatory documents related to oxidation behavior of nuclear graphite is now accelerating to new levels, prompted by the increased interest for nuclear energy as a clean, carbon-free energy source. Even though public’s perception of nuclear energy advantages may still be influenced by the memories of past accidents of nuclear reactors from generations II and III, the community of informed scientists and engineers, regulators and statemen knows that generation IV of nuclear reactors is designed at very high safety standards, doubled by great advances of scientific knowledge and technological progress. One of routes of these recent advances is directed at better understanding of graphite oxidation behavior, its relationship with graphite manufacturing and microstructural properties, along with the effects of various environmental factors and process variables. Together, the recent progress in manufacturing, properties characterization, and modeling of intricated physical and chemical processes that concur to the oxidation behavior led to development of powerful simulation codes able to analyze various scenarios of normal operation and hypothetical off-normal events, and thus to clearly specify the allowable parameters envelopes for the designers, constructors, and operators of current and future modular HTGRs. This review begins with an introduction on manufacturing methods, structure, and properties of nuclear graphite, including basic requirements that this specialty graphite type must satisfy for nuclear use. It continues with a chapter on environmental effects on nuclear graphite, where emphasis is placed less on irradiation and much more on oxidation phenomena, their safety implications, and the basic traits of chronic and acute oxidation by air (oxygen) and water (humidity, steam). Particular attention is placed on the three graphite grades of interest for this document (IG-110, NBG-18, PCEA). A chapter on properties degradation induced by oxidation follows, with focus on density, dimensional, and mechanical properties changes. The next chapter is intended as a brief review of various approaches used for modeling of graphite oxidation behavior. It summarizes the progress of oxidation models, from the early attempts to complex computational approaches interfaced with specialized computer codes designed for nuclear reactor simulations. Last, a list is presented of knowledge gaps where more research is needed. A short summary concludes the review.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Accelerating large scale de novo metagenome assembly using GPUs

Metagenomic workflows involve studying uncultured microorganisms directly from the environment. These environmental samples when processed by modern sequencing machines yield large and complex datasets that exceed the capabilities of metagenomic software. The increasing sizes and complexities of datasets make a strong case for exascale-capable metagenome assemblers. However, the underlying algorithmic motifs are not well suited for GPUs. This poses a challenge since the majority of next-generation supercomputers will rely primarily on GPUs for computation. In this paper we present the first of its kind GPU-Accelerated implementation of the local assembly approach that is an integral part of a widely used large-scale metagenome assembler, MetaHipMer. Local assembly uses algorithms that induce random memory accesses and non-deterministic workloads, which make GPU offloading a challenging task. Our GPU implementation outperforms the CPU version by about 7x and boosts the performance of MetaHipMer by 42% when running on 64 Summit nodes.

Awan, Muaaz Gul↗
DOE OSTI2022

FPGA-based computing system for processing data in size, weight, and power constrained environments

Technologies that are well-suited for use in size, weight, and power (SWAP)-constrained environments are described herein. A host controller dispatches data processing instructions to hardware acceleration engines (HAEs) of one or more field programmable gate arrays (FPGAs) and further dispatches data transfer instructions to a memory controller, such that the HAEs perform processing operations on data stored in local memory devices of the HAEs in parallel with other data being transferred from external memory devices coupled to the FPGA(s) to the local memory devices.

Napier, Matthew↗
DOE OSTI2021

The PetscSF Scalable Communication Layer

PetscSF, the communication component of the Portable, Extensible Toolkit for Scientific Computation (PETSc), is designed to provide PETSc's communication infrastructure suitable for exascale computers that utilize GPUs and other accelerators. PetscSF provides a simple application programming interface (API) for managing common communication patterns in scientific computations by using a star-forest graph representation. PetscSF supports several implementations based on MPI and NVSHMEM, whose selection is based on the characteristics of the application or the target architecture. An efficient and portable model for network and intra-node communication is essential for implementing large-scale applications. The Message Passing Interface, which has been the de facto standard for distributed memory systems, has developed into a large complex API that does not yet provide high performance on the emerging heterogeneous CPU-GPU-based exascale systems. Here, we discuss the design of PetscSF, how it can overcome some difficulties of working directly with MPI on GPUs, and we demonstrate its performance, scalability, and novel features.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Operando characterization of conductive filaments during resistive switching in Mott VO 2

Significance To perform hardware-based neuromorphic computing, novel materials exhibiting a wide variety of electronic properties are currently being explored. VO 2 is well known to exhibit an insulator-to-metal transition as well as volatile resistive switching. Many questions regarding the basic mechanism of the nonvolatile switching in this material are unanswered. In this work, the formation and relaxation of conductive filaments through nonvolatile resistive switching in VO 2 devices have been realized. The V 5 O 9 Magnéli phase conductive filament has been identified. Our results demonstrate that both resistive switching behaviors can be achieved in a single material, crucial for future technology like resistive switching memories or neuromorphic logic.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Pre-training Vision Models for the Classification of Alerts from Wide-field Time-domain Surveys

Modern wide-field time-domain surveys facilitate the study of transient, variable and moving phenomena by conducting image differencing and relaying alerts to their communities. Machine learning tools have been used on data from these surveys and their precursors for more than a decade, and convolutional neural networks (CNNs), which make predictions directly from input images, saw particularly broad adoption through the 2010s. Since then, continually rapid advances in computer vision have transformed the standard practices around using such models. It is now commonplace to use standardized architectures pre-trained on large corpora of everyday images (e.g., ImageNet). In contrast, time-domain astronomy studies still typically design custom CNN architectures and train them from scratch. Here, we explore the effects of adopting various pre-training regimens and standardized model architectures on the performance of alert classification. We find that the resulting models match or outperform a custom, specialized CNN like what is typically used for filtering alerts. Moreover, our results show that pre-training on galaxy images from Galaxy Zoo tends to yield better performance than pre-training on ImageNet or training from scratch. We observe that the design of standardized architectures are much better optimized than the custom CNN baseline, requiring significantly less time and memory for inference despite having more trainable parameters. On the eve of the Legacy Survey of Space and Time and other image-differencing surveys, these findings advocate for a paradigm shift in the creation of vision models for alerts, demonstrating that greater performance and efficiency, in time and in data, can be achieved by adopting the latest practices from the computer vision field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

In-situ TEM EELS analysis of memristive thin films for neuromorphic computing

Neuromorphic computing stands as a promising frontier for advancing AI algorithms and applications like ChatGBT, offering significant energy efficiency gains. This paper delves into the hardware design intricacies of memristive thin films and their elementary switching mechanisms, including anion migration, electron migration, and phase transitions. Through comprehensive analysis of electron energy loss spectroscopy (EELS) data via in-situ transmission electron microscopy (TEM), we will deduce the primary memristive switching mechanisms vital for optimizing thin film fabrication parameters and achieving desired film thickness, conductivity, and memory retention. A single crystal ptype Si substrate was used with TiN as the bottom metal electrode, TiO x as the insulating dielectric layer, and Pt as the top metal electrode. In-situ TEM was able to tell us the thin film didn’t behave like a filamentary or phase transition material. EELS data deduced that electron trapping/detrapping was one of the primary switching mechanisms. By shedding light on these elementary mechanisms, our study aims to catalyze the development of more 2 efficient and effective neuromorphic computing systems to be deployed into mainstream technologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

An Adaptive-Mesh-Refinement Based Computational Tool for Simulating Catalysis at Mesoscale

In this work, we present a computational tool for mesoscale applications using open-source exascale- computing compatible adaptive-mesh-refinement (AMR) library, AMReX [2]. AMReX is software library that enables development of application solvers with block-structured Cartesian AMR. Our tool has capabilities to include realistic geometry representation, chemical species transport, reactions and thermodynamics that are critical for capturing mesoscale physics. A significant achievement is the ability of our solver to automatically import electron microscopy data in the form of a stereolithography (STL) or pixelated file format (mrc, tiff) without undergoing the tedious task of unstructured mesh generation. This feature allows for rapid simulation of catalyst particles with complex morphologies using an immersed-boundary formulation. The use of AMR allows for higher resolutions at catalyst surface interfaces, which in turn provides an accurate description of surface reactions and transport. Our solver uses a hybrid distributed and shared memory parallelism (OpenMP/GPU-based) with which strong scaling up to 10,000 processors for realistic catalyst particle simulations have been demonstrated.

BIOMASS FUELS,MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Scalable self attraction and loading calculations for unstructured ocean tide models

Self attraction and earth-loading effects are important for accurately modeling global tides. A common approach of handling this forcing is to expand mass anomalies into spherical harmonics, which are scaled by load Love numbers to account for elastic earth deformation. We investigate two different approaches to perform these calculations for ocean models that employ unstructured meshes and distributed memory parallelization. The first approach leverages a highly efficient spherical harmonics library, but requires all-to-one and one-to-all communications and interpolation operations between the unstructured and a structured mesh. This approach is compared to a parallel algorithm that computes the spherical harmonic transformations directly on the unstructured mesh with an all-reduce communication. Here, our results show that although the unstructured mesh calculations are more expensive, the scalability of the unstructured mesh approach allows for more efficient spherical harmonics transforms for high-resolution meshes and large processor counts. This methodology enables the efficient inclusion of tidal dynamics large-scale Earth system model simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Evaluating the Performance of Integer Sum Reduction in SYCL on GPUs

SYCL is a promising programming model for heterogeneous computing—allowing a single-source code to target devices from multiple vendors. One significant task performed on these accelerators is a primitive operation for integer sum reduction. This paper presents several SYCL implementations of integer sum reduction—using atomic functions, shared local memory, vectorized memory accesses and parameterized workload sizes—to compare the performance and maturity of SYCL against open-source vendor-specific implementations of the same reduction. For a sufficiently large number of integers, tuning the parameters of our SYCL implementations achieves 1.4X speedup over the open-source implementations on an Intel UHD630 integrated GPU. The SYCL reduction is 3% faster than the templated reduction in Thrust, and 0.3% faster than the device reduction in CUB on an Nvidia P100 GPU. The SYCL reduction is 1.9% faster than the templated reduction in Thrust, and 0.4% faster than the device reduction in CUB on an Nvidia V100 GPU.

Jin, Zheming↗
DOE OSTI2020

Consistent Space Runtime (CSPACER) v1.0

This software provides a runtime for communication-bound applications, especially with irregular communication patterns. The target programming abstraction for the runtime is the space consistency model, which defines consistency guarantees at the granularity of memory spaces. This model has relaxed consistency semantics that enables a wide range of runtime optimizations. The runtime leverages threading to accelerate communication primitives, especially collective operations. It also allows efficient pipelining of communication operations and enable constructing a consistent state of multiple unordered communication activities targeting a memory space. The runtime uses a reduced API design that decomposes complex communication primitives in traditional general-purpose runtime into a sequence of simpler steps. To improve the productivity of using this runtime, we provide communication patterns commonly used for regular scientific computing applications and irregular data analytics. These communication patterns offer skeletons for the integration with application computation to allow efficient overlap.

Ibrahim, Khaled↗
DOE OSTI2022

3D spherical functional expansion tallies in Serpent 2 Monte Carlo code

This work extends the application of functional expansion tallies to 3D spherical geometries. The 3D Zernike polynomials are set as an orthonormal polynomials basis for the functional reconstruction. The study describes the construction of the complete set of polynomials, a natural expansion of the spherical harmonics polynomials where 3D Zernike moments can be evaluated as a linear combination of the geometrical moments. The 3D Zernike polynomials formulation and the computational approach implemented in Serpent 2 are presented and tested through the Godiva model from the ICSBEP criticality benchmark test cases. The implementation results are in agreement with a reference solution described in a fine-resolution mesh, enhancing also the performance and memory demand. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Scalable line and plane relaxation in a parallel structured multigrid solver

The efficient solution of sparse, linear systems that arise through the discretization of partial differential equations remains a key challenge for a range of high performance scientific simulations. One approach for reducing data movement and improving performance is by exposing and exploiting structure in a problem through the use of robust structured multilevel solvers. By choosing coarsening that preserves the structure of the problem, these methods maintain efficient structured computation and communication throughout the multigrid hierarchy. However, when coarsening is not permitted to be dependent on the operator, anisotropy must be addressed by the smoother — producing error compatible for coarse-grid correction with structured coarsening. Here, the components required in a scalable parallel structured solver are described with a focus on memory and communication efficiency of robust smoothers. While the implementation of communication and memory reduction techniques in smoothers integrated in a complete 3D solver present a significant engineering challenge, a novel approach is proposed that addresses these challenges systematically through a change to the solver’s execution model. Enabled by user-level threading paired with a set of data and communication abstractions, this approach permits seamless aggregation of communication in plane smoothers — directly reusing code for a 2D distributed multilevel cycle. Results show an effective reduction in communication costs for coarse-grid problems, and result in a speedup of 8.7x in smoothing routines shown in Fig. 12 using this approach. This produces a significant improvement to strong scalability while maintaining favorable weak scaling behavior. Finally, a parallel scaling study using a series of refined meshes is included that demonstrates the effectiveness of this approach in an application of interest.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Evaluating the Potential and Challenges of an Uncertainty Quantification Method for Long Short–Term Memory Models for Soil Moisture Predictions

Recently, recurrent deep networks have shown promise to harness newly available satellite–sensed data for long–term soil moisture projections. However, to be useful in forecasting, deep networks must also provide uncertainty estimates. Here we evaluated Monte Carlo dropout with an input–dependent data noise term (MCD+N), an efficient uncertainty estimation framework originally developed in computer vision, for hydrologic time series predictions. MCD+N simultaneously estimates a heteroscedastic input–dependent data noise term (a trained error model attributable to observational noise) and a network weight uncertainty term (attributable to insufficiently constrained model parameters). Although MCD+N has appealing features, many heuristic approximations were employed during its derivation, and rigorous evaluations and evidence of its asserted capability to detect dissimilarity were lacking. To address this, we provided an in–depth evaluation of the scheme's potential and limitations. We showed that for reproducing soil moisture dynamics recorded by the Soil Moisture Active Passive (SMAP) mission, MCD+N indeed gave a good estimate of predictive error, provided that we tuned a hyperparameter and used a representative training data set. The input–dependent term responded strongly to observational noise, while the model term clearly acted as a detector for physiographic dissimilarity from the training data, behaving as intended. However, when the training and test data were characteristically different, the input–dependent term could be misled, undermining its reliability. Additionally, due to the data–driven nature of the model, data noise also influences network weight uncertainty, and therefore the two uncertainty terms are correlated. Altogether, this approach has promise, but care is needed to interpret the results.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

User-Defined Types as Task Parameters and Arguments in FleCSI

FleCSI is a C++ framework for writing multi-physics simulations. FleCSI abstracts away complicated backends, enabling high performance while eliminating the need for users to directly manage memory and execution. This is done via FleCSI’s data and execution model.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Machine Learning Assisted Safety Modeling and Analysis of Advanced Reactors

With the advances in computational power and numerical methods, analysts can now rely on first-principle simulations to predict ultra-fine details in a variety of applications. Advances in machine learning (ML) have produced algorithms that can now learn high-level abstractions via hierarchical models. This project aims to leverage advances in ML techniques and the available high-resolution simulation data to develop a novel modeling and simulation (M\&S) methodology for reactor safety analysis. While application-agnostic ML techniques are available, complex physics constraints need to be incorporated into ML techniques to build ML-based closures for computationally efficient predictive simulations. This project intends to develop a physics-guided data-driven multi-scale methodology for M\&S of advanced reactors. The project focuses on thermal fluid (T/F) phenomena, which play major roles in advanced reactor safety. Specifically, we propose a data-driven coarse-mesh turbulence model based on local flow features for the transient analysis of thermal mixing and stratification in a sodium-cooled fast reactor (SFR). The model has a coarse-mesh setup to ensure computational efficiency, while it is trained by fine-mesh computational fluid dynamics (CFD) data with Reynolds-averaged Navier-Stokes (RANS) turbulence model to ensure accuracy. Three different neural networks are developed and tested for loss-of-flow transients in the hot pool of SFR, i.e. the densely connected convolutional neural network (DCNN), long-short-term-memory network based on proper orthogonal decomposition (POD-LSTM), and the DCNN informed by LSTM (DCNN-LSTM). The performances of these three neural networks are evaluated based on baseline models. The DCNN-LSTM model has been chosen for further hyperparameter optimization. Furthermore, based on a simplified two-dimensional case, uncertainty quantification (UQ) of the developed ML-based closure are investigated with three methods, i.e. Monte Carlo dropout, deep ensemble, and Bayesian neural network. The developed ML-based turbulent viscosity closure relation based on deep ensemble is then integrated into the system analysis module SAM and serves as a term in the conservation equations. Such a SAM-ML based procedure guarantees that the obtained results are consistent with the physical constraints of the thermal-fluid system. The SAM-ML simulation on the same loss-of-flow transient showed comparable accuracy with the CFD simulation but with a much coarser mesh setup. Last but not least, the ML-based closure improvement with the support of higher-fidelity data from large eddy simulation (LES) is discussed. As a first step towards this direction, a baseline LES simulation is performed to obtain comparable data with RANS results. Based on the early results, future investigation on further improving the ML-based closure is discussed. We believe the developed approach that combines scientific machine learning with nuclear system analysis code can benefit the advanced reactor community as more accurate safety analyses will better characterize reactor safety margins and reduce licensing efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A comparison of machine learning surrogate models of street-scale flooding in Norfolk, Virginia

Low-lying coastal cities, exemplified by Norfolk, Virginia, face the challenge of street flooding caused by rainfall and tides, which strain transportation and sewer systems and can lead to personal and property damage. While high-fidelity, physics-based simulations provide accurate predictions of urban pluvial flooding, their computational complexity renders them unsuitable for real-time applications. Using data from Norfolk rainfall events between 2016 and 2018, this study compares the performance of a previous surrogate model based on a random forest algorithm with two deep learning models: Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU). The comparison of deep learning to the random forest algorithm is motivated by the desire to utilize a machine learning architecture that allows for the future inclusion of common uncertainty quantification techniques and the effective integration of relevant, multi-modal features.

54 ENVIRONMENTAL SCIENCES↗