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Closing the Gap between FAIR Data Repositories and Hierarchical Data Formats

Many in the scientific community, particularly in publicly funded research, are pushing to adhere to more accessible data standards to maximize the findability, accessibility, interoperability, and reusability (FAIR) of scientific data, especially with the growing prevalence of machine learning augmented research. Online FAIR data repositories, such as the Open Science Framework (OSF), help facilitate the adoption of these standards by providing frameworks for storage, access, search, APIs, and other features that create organized hubs of scientific data. However, the wider acceptance of such repositories is hindered by the lack of support of hierarchical data formats, such as Technical Data Management Streaming (TDMS) and Hierarchical Data Format 5 (HDF5), that many researchers rely on to organize their datasets. Various tools and strategies should be used to allow hierarchical data formats, FAIR data repositories, and scientific organizations to work more seamlessly together. A pilot project at Los Alamos National Laboratory (LANL) addresses the disconnect between them by integrating the OSF FAIR data repository with hierarchical data renderers, extending support for additional file types in their framework. The multifaceted interactive renderer displays a tree of metadata alongside a table and plot of the data channels in the file. This allows users to quickly and efficiently load large and complex data files directly in the OSF webapp. Users who are browsing files can quickly and intuitively see the files in the way they or their colleagues structured the hierarchical form and immediately grasp their contents. This solution helps bridge the gap between hierarchical data storage techniques and FAIR data repositories, making both of them more viable options for scientific institutions like LANL which have been put off by the lack of integration between them.

97 MATHEMATICS AND COMPUTING↗

Hierarchical Data Format for Nuclear Data Sensitivities

The SCALE code system includes capabilities for sensitivity and uncertainty (S/U) analysis as part of its TSUNAMI code suite. The sensitivity of a quantity of interest (for example, an application’s $k_{eff}$) to nuclear data is stored as a profile in a text-based file, which is known as a sensitivity data file (SDF). The sensitivity profile can be used to calculate uncertainties, correlation coefficients, and similarity indices. One of the goals of the present work was to seek general performance improvements in the TSUNAMI code suite, starting with the TSUNAMI-IP code for calculating similarity indices. Through profiling, it was found that reading the text-based sensitivity files was a performance bottleneck in the TSUNAMI-IP code. In a typical TSUNAMI-IP calculation, an application might be compared to thousands of benchmarks, thus requiring the reading of thousands of SDFs. Reading of binary-based data is generally faster than reading text-based data. Hierarchical Data Format 5 (HDF5) is a binary-based format that also benefits from being portable, and it can be inspected with nonproprietary tools. This paper describes an HDF5-based file format that has been introduced for SDFs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hierarchical Data Format for Nuclear Data Sensitivities [Slides]

An HDF5-based file format was introduced for the sensitivity data calculated by TSUNAMI. The format was defined to collect the sensitivity coefficients into hyperslabs, which optimizes file reading time and therefore improves the time-to-solution for applications. In future work, this format will be extended to store sensitivity data for depletion calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fostering Geothermal Machine Learning Success: Elevating Big Data Accessibility and Automated Data Standardization in the Geothermal Data Repository

The Department of Energy's (DOE's) Geothermal Data Repository (GDR) has implemented improvements to both its data lakes and its data standards and automated data pipelines. The GDR data lakes have reduced storage and compute-related barriers to using large geothermal datasets, enabling these large datasets to be accessed by anyone with a modern computer and internet access. More recently, the GDR has been working to further reduce barriers through streamlining the data intake process, educating users on the process and requirements, and helping users access data from the data lakes. These improvements have augmented the quantity of datasets the GDR is able to accept into its data lakes and have enabled users who are new to cloud tools to access these datasets more easily, overall increasing the accessibility of big geothermal data for use in machine learning and other projects. In addition, the GDR now has built-in data standards and pipelines for drilling data, geospatial data, and distributed acoustic sensing (DAS) data. These standardization efforts aim to enhance the real-world applicability of geothermal machine learning outcomes by improving the quality of training data. Specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, thus allowing more time for actual research. By automating this process, the burden of standardization is lifted from the user, ultimately increasing the availability of standardized data. This paper provides an update on recent improvements made to the GDR's data lakes and automated data pipelines, including: (1) streamlining the data lake intake process, (2) better educating users on the process and requirements through a new data lakes page, (3) adding data lake direct access links to GDR data lake submission pages, (4) implementing a DAS data pipeline to convert DAS data uploaded in SEG-Y format to a standardized hierarchical data format v5 (HDF5), (5) extending this pipeline to encompass data in the GDR data lake, (6) adding metadata requirements for geospatial data, (7) making user interface/user experience (UX) enhancements to the data pipelines' documentation pages, and (8) improving the GDR's data standards and pipelines pages to better guide users in ensuring that their data is standardized by the GDR's automated data pipelines. 2024 Geothermal Resources Council. All rights reserved.

accessibility↗

h5bench: A unified benchmark suite for evaluating HDF5 I/O performance on pre‐exascale platforms

Summary Parallel I/O is a critical technique for moving data between compute and storage subsystems of supercomputers. With massive amounts of data produced or consumed by compute nodes, high‐performant parallel I/O is essential. I/O benchmarks play an important role in this process; however, there is a scarcity of I/O benchmarks representative of current workloads on HPC systems. Toward creating representative I/O kernels from real‐world applications, we have created h5bench , a set of I/O kernels that exercise hierarchical data format version 5 (HDF5) I/O on parallel file systems in numerous dimensions. Our focus on HDF5 is due to the parallel I/O library's heavy usage in various scientific applications running on supercomputing systems. The various tests benchmarked in the h5bench suite include I/O operations (read and write), data locality (arrays of basic data types and arrays of structures), array dimensionality (one‐dimensional arrays, two‐dimensional meshes, three‐dimensional cubes), I/O modes (synchronous and asynchronous). In this paper, we present the observed performance of h5bench executed along several of these dimensions on existing supercomputers (Cori and Summit) and pre‐exascale platforms (Perlmutter, Theta, and Polaris). h5bench measurements can be used to identify performance bottlenecks and their root causes and evaluate I/O optimizations. As the I/O patterns of h5bench are diverse and capture the I/O behaviors of various HPC applications, this study will be helpful to the broader supercomputing and I/O community.

97 MATHEMATICS AND COMPUTING↗

Model Data Archive Associated with Manuscript "Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon"

This data package supports the publication “Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon” by Li et al. (2026). The package contains processed model inputs, configuration files, restart files, simulation outputs, scripts, and visualization products used to evaluate post-fire dissolved organic carbon (DOC) dynamics in the Naches River Watershed, Washington, USA, following the 2021 Schneider Springs Fire. The modeling workflow couples ELM-BGC, the biogeochemistry-enabled Energy Exascale Earth System Model Land Model; ATS, the Advanced Terrestrial Simulator for integrated surface-subsurface hydrology; and PFLOTRAN, a reactive transport model for multicomponent aqueous geochemistry. Together, these models simulate how wildfire-induced changes in vegetation, litter, coarse woody debris, and soil organic matter influence DOC production, transport, and reaction from burned hillslopes to stream networks. The archive includes preprocessed meteorological, geospatial, hydrologic, and biogeochemical forcing data; ELM-BGC-derived DOC source terms; ATS mesh files; PFLOTRAN reactive-transport inputs; model configuration files; spin-up and transient restart files; watershed-scale diagnostic outputs; stream concentration time series; and figures or visualization files used to inspect and reproduce key results. File types include Hierarchical Data Format 5 (HDF5) files for gridded forcing and model-coupling data, model input and configuration files for ELM-BGC, ATS, and PFLOTRAN, restart and simulation-output files generated by the modeling workflow, tabular or time-series diagnostic outputs, scripts for post-processing and figure generation, and image or visualization products associated with the manuscript. Use of the package depends on the intended task. Re-running the simulations requires the relevant modeling software, including ELM-BGC, ATS, and PFLOTRAN as ATS's geochemical engine. Inspecting outputs and reproducing figures requires Python with scientific plotting libraries such as Matplotlib, and three-dimensional model outputs may be viewed with ParaView. Geographic information system files or maps may be inspected with ArcGIS Pro or comparable GIS software. The data package is intended to enable traceability, reuse, and partial reproduction of the coupled land-to-watershed hydro-biogeochemical modeling workflow used to test how wildfire disturbance affects terrestrial carbon pools and downstream DOC dynamics.

ATS↗

CHESS 2025: Spectrometer orthorectified at-sensor radiance from NEON AOP imaging spectroscopy surveys

This dataset provides Level 1 (L1) orthorectified at-sensor radiance derived from measurements collected by the Imaging Spectrometer-1 (NIS-1) onboard the NEON (National Ecological Observatory Network) Airborne Observation Platform (AOP) for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). NIS-1 captures light reflected from the Earth’s surface in 426 discrete wavelength bands as raw digital numbers (DNs; Level 0). These data are then calibrated to physical units (uW/cm²·sr·nm) following the processing steps described in the NEON Imaging Spectrometer Level 1B Calibrated Radiance Algorithm Theoretical Basis Document (ATBD; Gallery 2022). The data delivered here are the primary inputs for the surface reflectance product in “Custom surface reflectance, shade masks, and equivalent water thickness maps for the Colorado Headwaters Ecological Spectroscopy Study” (Carroll et al. 2026). For intertemporal comparison, the radiance data here are most directly relatable to the v2 radiance data in “NEON AOP Imaging Spectroscopy Survey of Upper East River Colorado Watersheds: Raw-Space Radiance and Observational Variable Dataset” (Goulden et al. 2018), to which the same processing methodology was applied. Together, the radiance and reflectance data enable users to exploit the unique reflection signatures of different surface objects for land cover classification, foliar trait mapping, plant vigor assessment, water content estimation, trace-element identification, and other scientific applications. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. Within each domain, data are delivered by flightline as orthorectified and calibrated hyperspectral rasters in Hierarchical Data Format version 5 (HDF5) format, with radiance values provided in uW/cm²·sr·nm on a fixed, uniform Universal Transverse Mercator (UTM) grid at 1 meter spatial resolution. The radiance rasters include all 426 NIS-1 spectral bands, along with associated quality-assurance (QA) and diagnostic and ancillary layers needed for atmospheric correction workflows. Orthorectified radiance is produced from pushbroom spectrometer observations by applying NEON’s radiometric calibration (including bad pixel masking, dark subtract, dark pedestal shift correction, electronic panel ghost correction, grating ghost correction, deblur correction and flat-fielding) and spectral calibration (using spectral response function band centers and full-width at half-maximum intensity), followed by geolocation and regridding to the fixed grid. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

VERAIO Software Management Plan

VERAIO is a set of utility codes used to provide a common set of inputs and outputs to the Virtual Environment for Reactor Applications (VERA). VERA is a collection of several different computer codes that all have a common input and output. This prevents the need to manage input and output from each individual code, allowing for ease of use and reducing errors associated with code operability. The VERAIO utilities include VERAIn, VERAView, and VERARun. Each of these utilities is described below. VERAIn is an input processor that reads an ASCII input file generated by users, parses the file, performs some error checking, and writes an XML file to be read by other VERA codes. The main purpose of VERAIn is to provide a common input to all of the VERA codes, so users only need to learn one input. VERAIn is written in Perl and uses YAML configuration files to provide flexibility. VERAView is a graphical user interface (GUI) that reads a VERA hierarchical data format (HDF) output file and allows users to visualize results. VERAView is written in Python. VERARun is a script that drives the VERA execution in a high performance computing (HPC) environment. Work performed at the code level supports the quality assurance program plan (QAPP) (VERA-QA-001) and the VERA Software Quality Assurance Plan (VERA-QA-002).

97 MATHEMATICS AND COMPUTING↗

Solar PV, Wind Generation, and Load Forecasting Dataset for ERCOT 2018: Performance-Based Energy Resource Feedback, Optimization, and Risk Management (P.E.R.F.O.R.M.)

This report describes the Advanced Research Projects Agency-Energy Performance-Based Energy Resource Feedback, Optimization, and Risk Management (PERFORM) Electric Reliability Council of Texas (ERCOT) dataset consisting of load, solar, and wind deterministic and probabilistic forecasts at three timescales. This dataset consists of 1 year of time-coincident load, wind, and solar actuals and probabilistic forecasts for a region similar to ERCOT. All the data are stored in Hierarchical Data Format 5 (HDF5) files and have been uploaded to an Amazon Web Services repository. The ERCOT data set has 2 years (2017, 2018) of actuals and 1 year (2018) of probabilistic forecasts. These data are provided at various spatial (i.e., site-level, zone-level, and system-level) and temporal scales (i.e., day-ahead, intraday, and intra-hour). Specifically, data are provided for 125 existing wind sites, 22 existing solar sites, 139 proposed wind sites, and 204 proposed solar sites.

14 SOLAR ENERGY↗

Counter Unmanned Aircraft System Metrics Tool

SAND2023-05387O The Counter Unmanned Aircraft System (CUAS) Metrics Tool consists of three applications: • The Data Collection Tool is designed to be used during testing and captures details that can be imported into the Figure Creator application. • The Unmanned Aircraft System (UAS) Log Converter converts different UAS logs into a standardized hierarchical data format with a timeline of geospatial data. • The Figure Creator develops relevant images for the test event. The application includes logic to ingest and correlate data from the Data Collection Tool and the UAS Log Converter to produce the chosen figures. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Mayle, Ashley↗

Coincident Capture through Post-processing PTRAC [Slides]

This presentation discusses the new PTRAC capabilities and workflows. The PTRAC capability in MCNP6.3 has seen a massive overhaul since MCNP6.2. The new HDF5 file format allows for both MPI- and thread-based parallelism. MCNPTools has been updated to handle the new HDF5 PTRAC format and is now open sourced on GitHub. Built-in capabilities, such as the pulse-height tally coincident capture special treatment, can largely be replicated through separate postprocessing scripts that leverage both PTRAC and MCNPTools. This allows for greater flexibility in user-specified and controlled detector response functionality, ultimately using the MCNP code for what it is best at (i.e., particle transport).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

HDF5 in the exascale era: Delivering efficient and scalable parallel I/O for exascale applications

Accurately modeling real-world systems requires scientific applications at exascale to generate massive amounts of data and manage data storage efficiently. However, parallel input and output (I/O) faces challenges due to new application workflows and the state-of-the-art memory, interconnect, and storage architectures considered in exascale designs. The storage hierarchy has expanded with node-local persistent memory, solid-state storage, and traditional disk and tape-based storage, thus requiring efficiency at each layer and much more efficient data movement among these layers. This paper discusses how the ExaHDF5 project improved the I/O performance and data management for exascale architectures by enhancing HDF5, a widely used parallel I/O library. The team developed an Asynchronous I/O Virtual Object Layer (VOL) connector that allowed overlapping I/O with computation. They also created a Cache VOL to complement asynchronous I/O by incorporating fast storage layers, such as burst buffer and node-local storage, into the parallel I/O workflow through caching and staging data. Additionally, the team enabled data aggregation and I/O at the node level by using a Subfiling Virtual File Driver (VFD). To demonstrate superior I/O performance with HDF5 at exascale, the ExaHDF5 team collaborated with several exascale applications. In this paper, we show I/O performance improvements for three applications: Cabana (a particle-based simulation library), EQSIM (a regional earthquake simulation software), and E3SM (a climate system modeling library).

Asynchronous I/Ol↗

Recent MCNP6 ® Code Developments and Improvements for Nuclear Engineering Applications [Slides]

The Los Alamos MCNP Monte Carlo radiation transport code has been the international gold standard for particle transport applications for over three decades. Many developments to the code have taken place with several significant new feature additions, major improvements, and enhancements to existing features. With significant institutional and programmatic investment in the code since the time of the last public release in 2018, important code development and infrastructure modernization has taken place and remains a high priority for all ongoing efforts across the code development team.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Enabling event-by-event precision in γ-ray cascades for neutron-induced reactions

Neutron-induced γ-ray spectra provide key inputs for modern active interrogation applications. A precise modeling of the nuclear reaction and subsequent emission of γ rays is challenging and often impossible due to limitations on evaluated data file formats and nuclear transport simulation codes. We present a framework that addresses these challenges by combining experimental data and reaction-model calculation outputs into an extended candidate version of the Generalized Nuclear Data Structure (GNDS) file, the successor format for the legacy Evaluated Nuclear Data File (ENDF-6). This proposed GNDS hierarchical format contains all the necessary ingredients for inline γ-ray cascade reproduction with event-by-event precision, including continuum–continuum and continuum–discrete transitions following neutron-capture and inelastic neutron scattering reactions. Cascade-event generation based on our approach demonstrates improved energy conservation on an event-by-event basis and permits the use of γ-γ coincidences in applications. This work offers, for the first time, a method to generate neutron-capture and inelastic neutron-scattering γ-ray cascades where energy conservation, correlations, and experimental primaries are fully accounted for.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Accelerating Random Forest Classification on GPU and FPGA

Random Forests (RFs) are a commonly used machine learning method for classification and regression tasks spanning a variety of application domains, including bioinformatics, business analytics, and software optimization. While prior work has focused primarily on improving performance of the training of RFs, many applications, such as malware identification, cancer prediction, and banking fraud detection, require fast RF classification. In this work, we accelerate RF classification on GPU and FPGA. In order to provide efficient support for large datasets, we propose a hierarchical memory layout suitable to the GPU/FPGA memory hierarchy. We design three RF classification code variants based on that layout, and we investigate GPU- and FPGA-specific considerations for these kernels. Our experimental evaluation, performed on an Nvidia Xp GPU and on a Xilinx Alveo U250 FPGA accelerator card using publicly available datasets on the scale of millions of samples and tens of features, covers various aspects. First, we evaluate the performance benefits of our hierarchical data structure over the standard compressed sparse row (CSR) format. Second, we compare our GPU implementation with cuML, a machine learning library targeting Nvidia GPUs. Third, we explore the performance/accuracy tradeoff resulting from the use of different tree depths in the RF. Finally, we perform a comparative performance analysis of our GPU and FPGA implementations. Our evaluation shows that for high accuracy targets, our GPU implementation yields 5-9x speedup over CSR, and up to a 2x speedup over cuML.

FPGA, Xilinx FPGA, GPU, Random Forest classificati↗

TRACE Input Modernization

This work presents a Tom’s Obvious Minimal Language (TOML)-based representation of input for the US Nuclear Regulatory Commission’s TRAC/RELAP Advanced Computational Engine (TRACE) thermal hydraulics code. Implemented using the Workbench Analysis Sequence Processor (WASP), the approach maps traditional TRACE input structures to a hierarchical format composed of named parameters, typed values, and native data collections. The resulting representation preserves TRACE’s existing modeling capabilities while providing a modern, structured interface for model development and management. WASP further extends TOML through a file import directive that supports modular model composition and reusable input organization. In addition, WASP provides extended array data entry convenience with various data repeat and interpolation capabilities. Examples of the new TOML syntax are provided for major TRACE input categories, including hydraulic components, heat structures, control systems, and trip logic. The TOML representation establishes a foundation for improved validation, tooling, automation, and model maintainability while remaining compatible with existing TRACE workflows. To facilitate migration to the TOML-based input format, the TRACE executable now supports conversion of native TRACE input into an intermediate JSON representation. A Python utility subsequently transforms the JSON data into an equivalent TOML model. Lastly, the TRACE executable now supports execution using TOML-formatted input.

Lefebvre, Robert A. [Oak Ridge National Laboratory↗

Galaxy zoo builder: Morphological dependence of spiral galaxy pitch angle

ABSTRACT Spiral structure is ubiquitous in the Universe, and the pitch angle of arms in spiral galaxies provide an important observable in efforts to discriminate between different mechanisms of spiral arm formation and evolution. In this paper, we present a hierarchical Bayesian approach to galaxy pitch angle determination, using spiral arm data obtained through the Galaxy Builder citizen science project. We present a new approach to deal with the large variations in pitch angle between different arms in a single galaxy, which obtains full posterior distributions on parameters. We make use of our pitch angles to examine previously reported links between bulge and bar strength and pitch angle, finding no correlation in our data (with a caveat that we use observational proxies for both bulge size and bar strength which differ from other work). We test a recent model for spiral arm winding, which predicts uniformity of the cotangent of pitch angle between some unknown upper and lower limits, finding our observations are consistent with this model of transient and recurrent spiral pitch angle as long as the pitch angle at which most winding spirals dissipate or disappear is larger than 10°.

Lingard, Timothy↗

Reverse-mode differentiation in arbitrary tensor network format: with application to supervised learning.

This paper describes an efficient reverse-mode differentiation algorithm for contraction operations of tensor networks that may have arbitrary and unconventional network topologies. The approach leverages the tensor contraction tree of Evenbly and Pfeifer (2014), which provides an instruction set for the contraction sequence of a network. We show that this tree can be efficiently leveraged for differentiation of a full tensor network contraction using a recursive scheme that exploits (1) the bilinear property of contraction and (2) the property that trees have single path from root to leaves. While differentiation of tensor-tensor contraction is already possible in most automatic differentiation packages, we show that exploiting these two additional properties in the specific context of contraction sequences can improve efficiency. Following a description of the algorithm and computational complexity analysis, we investigate its utility for gradient-based supervised learning for low-rank function recovery and for fitting real-world unstructured datasets. We demonstrate improved performance over alternating least-squares optimization approaches and the capability to handle heterogeneous and arbitrary tensor network formats. When compared to alternating minimization algorithms, we find that the gradient-based approach requires a smaller oversampling ratio (number of samples compared to number model parameters) for recovery. This increased efficiency extends to fitting unstructured data of varying dimensionality and when employing a variety of tensor network formats. Here, we show improved learning using the hierarchical Tucker method over the tensor-train in high-dimensional settings on a number of benchmark problems.

97 MATHEMATICS AND COMPUTING↗