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DTLMod: A simulation framework for in situ workflow optimization

In situ processing workflows have become essential for coping with the explosion in data volume and velocity in large-scale scientific computing, providing domain scientists with early insights at runtime. Multiple frameworks implement this paradigm through a data transport layer (DTL), offering different data access modes and deployment schemes, but researchers currently lack the appropriate tools to assess design and deployment options before committing to costly real experiments. We introduce DTLMod, an open-source simulated DTL that enables performance evaluation of in situ workflow configurations at scale. Built on SimGrid, it links into any SimGrid-based simulator and is available in C++ and Python. We evaluate DTLMod along four axes: scalability (tens of thousands of simulated processes across interconnected clusters in seconds, with linear memory scaling), versatility (three implementation variants trading fidelity for speed), accuracy (simulated times faithfully reflecting real behavior), and practical utility (two use cases demonstrating evidence-based workflow design decisions).

Suter, Fred [ORNL] (ORCID:0000000319021955)

Pypromice: A Python Package for Processing Automated Weather Station Data

The pypromice Python package is for processing and handling observation datasets from automated weather stations (AWS). It is primarily aimed at users of AWS data from the Geological Survey of Denmark and Greenland (GEUS), which collects and distributes in situ weather station observations to the cryospheric science research community. Functionality in pypromice is primarily handled using two key open-source Python packages, xarray (Hoyer & Hamman, 2017) and pandas (The pandas development team, 2020). A defined processing workflow is included in pypromice for transforming original AWS observations (Level 0, L0) to a usable, CF-convention-compliant dataset (Level 3, L3) (Figure 1). Intermediary processing levels (L1,L2) refer to key stages in the workflow, namely the conversion of variables to physical measurements and variable filtering (L1), cross-variable corrections and user-defined data flagging and fixing (L2), and derived variables (L3). Information regarding the station configuration is needed to perform the processing, such as instrument calibration coefficients and station type (one-boom tripod or two-boom mast station design, for example), which are held in a toml configuration file. Two example configuration files are provided with pypromice , which are also used in the package’s unit tests. More detailed documentation of the AWS design, instrumentation, and processing steps are described in Fausto et al. (2021).

pypromice

Pavement condition and climatic data in southeast Texas: A dataset for evaluating flood impacts on pavement performance

Effective pavement maintenance is essential for economic stability, optimal network performance, and roadway safety. Achieving this requires thorough evaluation of pavement conditions, including structural integrity, surface roughness, and distress characteristics. Pavement performance indicators play a critical role in influencing vehicle safety and ride quality. Recent advances have emphasized the use of data-driven modeling to anticipate pavement behavior, with the goal of optimizing resource allocation and refining Maintenance and Rehabilitation (M&R) strategies through accurate condition assessment. A foundational requirement for these modeling efforts is the availability of standardized, high-quality datasets that can support robust and reproducible infrastructure analysis. This data article presents a comprehensive dataset assembled to facilitate pavement performance prediction, with a geographic focus on Southeast Texas, particularly the flood-vulnerable area of Beaumont. The dataset encompasses pavement and traffic attributes, meteorological records, flood simulation outputs, ground deformation measurements, and topographic indices, enabling detailed examination of both load-associated and non-load-associated degradation mechanisms. Data preprocessing was performed using ArcGIS Pro, Microsoft Excel, and Python to ensure consistency and usability in data-driven modeling applications, including machine learning workflows. Key contributions of this dataset include its utility in analyzing the climatic and environmental factors affecting pavement conditions, identifying critical predictive features, and enabling in-depth correlation analysis across diverse variables. By filling existing gaps in input variable selection resources, this dataset supports the development of predictive tools for estimating future maintenance demand and enhancing the resilience of pavement networks in flood-impacted areas. The resource highlights the importance of standardized datasets for advancing pavement management practices and provides a robust foundation for ongoing infrastructure performance modeling.

42 ENGINEERING

pyRMG: A framework for high-throughput, large-cell DFT calculations on supercomputers

Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density functional theory (DFT) code’s grid-decomposition approach scales nearly linearly with the number of graphics processing units (GPUs), even for simulations exceeding thousands of atoms. This scalability makes RMG a compelling tool for high-throughput DFT studies of materials that would otherwise be bottlenecked in other codes (for example, by global fast Fourier transforms in plane-wave DFT). However, the limited workflow infrastructure for RMG has thus far constrained its adoption to a small user community. In this work, we present pyRMG, a Python package designed to streamline the setup and execution of RMG DFT calculations. Built on the pymatgen and ASE (Atomic Simulation Environment) computational materials science Python packages, pyRMG automates input generation and convergence checking, and it integrates with modern job schedulers (e.g., Flux) on leadership-class platforms such as Frontier and Perlmutter. Here, we demonstrate pyRMG for a high-throughput study of strain effects in 2D 2L-Bi 2 Se 3 /2L-NbSe 2 heterostructures, which offers chemical insights into this system and shows that RMG-based workflows can converge with limited user intervention.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

End-to-End Workflow for Machine-Learning-Based Qubit Readout With QICK and hls4ml

In this article, we present an end-to-end workflow for superconducting qubit readout that embeds codesigned neural networks into the quantum instrumentation control kit (QICK). Capitalizing on the custom firmware and software of the QICK platform, which is built on Xilinx radiofrequency system-on-chip field-programmable gate arrays (FPGAs), we aim to leverage machine learning (ML) to address critical challenges in qubit readout accuracy and scalability. The workflow utilizes the hls4ml package and employs quantization-aware training to translate ML models into hardware-efficient FPGA implementations via user-friendly Python application programming interfaces. We experimentally demonstrate the design, optimization, and integration of an ML algorithm for single transmon qubit readout, achieving 96% single-shot fidelity with a latency of 32.25 ns and less than 16% FPGA lookup table resource utilization. Our results offer the community an accessible workflow to advance ML-driven readout and adaptive control in quantum information processing applications.

42 ENGINEERING

LLM Information Extraction Toolkit

A modular Python framework for information extraction using large language models with support for multiple backends and optional verification workflows.

Yoon, Hong-Jun [Oak Ridge National Laboratory (ORN

geoPFA: A Python-Based Open-Source Software for 3D Geothermal PFA

This work presents a novel Python-based framework, geoPFA, for conducting 3D play fairway analysis (PFA) tailored to superhot geothermal systems. The workflow has been applied to the Nesjavellir field in Iceland, a candidate site for the third Iceland Deep Drilling Project's superhot production scenarios. This application demonstrates the value of modular, transparent, and extensible workflows for integrating geological, geophysical, and simulation-derived datasets in high-enthalpy environments. Preliminary results indicate favorable zones consistent with known hydrothermal activity. The geoPFA library will soon be publicly available, offering a scalable and reproducible approach to geothermal exploration across varied geological contexts.

15 GEOTHERMAL ENERGY

The SunPy Project: An Interoperable Ecosystem for Solar Data Analysis

The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package provides general purpose tools to access data from different providers, read image and time series data, and transform between commonly used coordinate systems. Affiliated packages perform more specialized tasks that do not fall within the more general scope of the sunpy core package. In this article, we give a high-level overview of the SunPy Project, how it is broader than the sunpy core package, and how the project curates and fosters the affiliated package system. We demonstrate how components of the SunPy ecosystem, including sunpy and several affiliated packages, work together to enable multi-instrument data analysis workflows. We also describe members of the SunPy Project and how the project interacts with the wider solar physics and scientific Python communities. Finally, we discuss the future direction and priorities of the SunPy Project.

Solar physics

Machine Learning-Based Anomaly Detection for PMT Data Quality Monitoring in the SBN and DUNE

Maintaining high-quality detector data is essential for achieving the scientific objectives of the Short-Baseline Neutrino (SBN) Program at Fermilab. Current data quality monitoring (DQM) procedures rely primarily on threshold-based metrics and manual inspection of detector monitoring plots, making the detection of subtle or gradually developing anomalies both time-consuming and dependent on expert interpretation. This project developed and evaluated a machine-learning workflow for automatically identifying anomalous photomultiplier tube (PMT) channels in the Short-Baseline Near Detector (SBND) using optical-hit amplitude data. A Python-based analysis program was developed to process ROOT files, extract statistical features describing individual PMT amplitude distributions, and generate feature vectors for anomaly detection. These features were used to train an Isolation Forest model using data representing normal detector operation. The trained model was subsequently applied to independent detector runs to identify channels exhibiting statistically unusual behavior relative to the learned reference response. To support expert interpretation, the workflow generated complementary diagnostic products, including anomaly score distributions, normalized amplitude comparisons, decision-tree visualizations, and principal component analysis (PCA) projections. This project demonstrated the feasibility of integrating unsupervised machine learning into detector data-quality monitoring and developed a complete workflow for automated PMT performance assessment to aid expert-driven review. Beyond its technical contributions, the VFP appointment fostered a research collaboration between Aurora University and Fermilab and provided direct workforce development benefits by training the visiting faculty member in detector-scale machine-learning methods that are now being incorporated into undergraduate coursework and research. The methodology developed here provides a foundation for future applications to ProtoDUNE and other liquid argon time projection chamber (LArTPC) detectors, contributing to ongoing efforts to improve detector reliability, reduce manual monitoring requirements, and enable scalable data quality monitoring for future large-scale neutrino experiments, including the Deep Underground Neutrino Experiment (DUNE).

Colón Santana, Juan A. [Unlisted, US, IL]

Boride-based Ceramic Super-high Temperature Thermocouples in Harsh Environments (Final Scientific/Technical Report)

An electromotive force (emf) can be generated along a temperature gradient between the cold end and hot end of a thermoelectric material, termed the Seebeck effect. Based on the Seebeck effect, metallic alloys have been extensively employed to detect temperatures for centuries, named thermocouples. However, commercially available thermocouple alloys suffer from limitations, such as oxidation, chemical degradation, and poor long-term stability under high-temperature harsh environments. This DOE-funded project aimed to develop high-temperature, chemically tolerant thermocouples suitable for operation in extreme environments relevant to semiconducting thermoelectric materials. The research focused on boride-based semiconducting thermoelectric compounds as candidates for next-generation thermocouples with enhanced oxidation resistance, chemical stability, and thermal robustness under conditions representative of charcoal-fired electricity facilities. During the funded years, boride materials were synthesized using an arc-plasma technique under ambient air and argon atmospheres, enabling scalable and cost-effective production compared with conventional boride fabrication methods. The synthesized borides were processed into nanostructured powders, followed by consolidation into dense bulk materials using a spark plasma sintering (SPS) bottom-up approach. Comprehensive characterization was performed, including microstructural analysis, electrical transport measurements, and optical and thermal property evaluation. Both p-type and n-type boride electric legs were fabricated and integrated into boride-based thermocouples. The thermal and irradiation stabilities of the boride nanomaterials and bulk thermoelectric materials were systematically evaluated to assess suitability for long-term operation in harsh environments. Additionally, 12 students were broadly hands-on trained spanning the full research workflow, including word processing and technical editing (e.g., LATEX for manuscript and poster preparation), data collection and analysis (using Python and related libraries and hardware interfaces), sample preparation (including arc-plasma synthesis and spark plasma sintering), and advanced characterization techniques (such as X-ray diffraction, UV–vis spectroscopy, electron microscopy, differential thermal analysis (DTA), and Seebeck coefficient measurements, etc). Overall, this project demonstrated the feasibility of boride-based thermoelectric materials as durable high-temperature thermocouples, providing a promising pathway toward robust temperature sensing technologies aligned with DOE energy infrastructure and extreme-environment monitoring needs.

20 FOSSIL-FUELED POWER PLANTS

PyLRO: A Python calculator for analyzing long-range structural order

We present PyLRO, an open-source Python calculator designed to detect, quantify, and display long-range order in periodic structures. The program’s design methodology, workflow, and approach to order quantification are described and demonstrated using a simple toy model. Additionally, we apply PyLRO to a series of metastable AlPO 4 structural intermediates from a prior high-pressure study, demonstrating how to compute and visualize structural order in all directions on a Miller sphere. We further highlight the program’s capabilities through a high-throughput analysis of structural patterns in the pressure-induced amorphization of AlPO 4 , revealing atomistic insights into specific energy regions of massive amorphous structures. These results suggest that PyLRO can be a valuable tool for investigating crystal–amorphous transition in materials research.

36 MATERIALS SCIENCE

SM25C-2002: Kamodo’s Satellite Constellation Mission Planning Tool

Kamodo provides a functional model-agnostic interface to a growing collection of Heliophysics model outputs. The CCMC, in collaboration with the Geospace Dynamics Constellation Science Team, has recently developed Kamodo’s satellite constellation mission planning tool to perform reconstructions in any pair of dimensions, including time. The ‘reconstruction’ tool enables users to fly any 4-dimensional grid of satellites through a given model data set, reconstructing what the given constellation would observe during the mission. This capability facilitates determination of what satellite configuration is best for a given science question, even allowing comparison across multiple models. This tool, written in Python, is built upon Kamodo’s flythrough tool, which in turn depends on a growing network of model-specific interfaces. Since each model interface is designed with model-agnostic syntax, the flythrough tool and the satellite constellation mission planning tool also feature model-agnostic syntax. In this work, we will describe the basic analysis choices available in the tool and provide a variety of sample workflows. The tool is freely available at https://github.com/nasa/Kamodo for the public. We invite the community to use the reconstruction tool and adapt the provided workflows for their mission planning, and to contribute their own workflows to share with others.

python

PvaPy streaming framework for real-time data processing

User facility upgrades, new measurement techniques, advances in data analysis algorithms as well as advances in detector capabilities result in an increasing amount of data collected at X-ray beamlines. Some of these data must be analyzed and reconstructed on demand to help execute experiments dynamically and modify them in real time. In turn, this requires a computing framework for real-time processing capable of moving data quickly from the detector to local or remote computing resources, processing data, and returning results to users. In this paper, we discuss the streaming framework built on top of PvaPy, a Python API for the EPICS pvAccess protocol. We describe the framework architecture and capabilities, and discuss scientific use cases and applications that benefit from streaming workflows implemented on top of this framework. We also illustrate the framework's performance in terms of achievable data-processing rates for various detector image sizes.

EPICS pvAccess

Kamodo’s Satellite Constellation Mission Planning Tool

Kamodo provides a functional model-agnostic interface to a growing collection of Heliophysics model outputs. The CCMC, in collaboration with the Geospace Dynamics Constellation Science Team, has recently developed Kamodo’s satellite constellation mission planning tool to perform reconstructions in any pair of dimensions, including time. The ‘reconstruction’ tool enables users to fly any 4-dimensional grid of satellites through a given model data set, reconstructing what the given constellation would observe during the mission. This capability facilitates determination of what satellite configuration is best for a given science question, even allowing comparison across multiple models. This tool, written in Python, is built upon Kamodo’s flythrough tool, which in turn depends on a growing network of model-specific interfaces. Since each model interface is designed with model-agnostic syntax, the flythrough tool and the satellite constellation mission planning tool also feature model-agnostic syntax. In this work, we will describe the basic analysis choices available in the tool and provide a variety of sample workflows. The tool is freely available at https://github.com/nasa/Kamodo for the public. We invite the community to use the reconstruction tool and adapt the provided workflows for their mission planning, and to contribute their own workflows to share with others.

software

PyHydroGeophysX: An extensible open-source platform for integrating hydrological models with geophysical measurements

Hydrological models and geophysical measurements are widely used tools for understanding subsurface hydrological processes relevant to water resource management, yet they typically remain disconnected due to technical barriers. We present PyHydroGeophysX, an open-source Python platform bridging this gap by providing standardized interfaces between hydrological modeling software (MODFLOW, ParFlow) and geophysical simulation tools (PyGIMLi, SimPEG). The platform implements bidirectional workflows: translating hydrological outputs into simulated geophysical responses through petrophysical models, and extracting hydrological information from geophysical inversions. Key features include bidirectional workflow modules, configurable petrophysical models, time-lapse inversion with temporal regularization, parallel computing, and mesh utilities for property transfer between geophysical and hydrological grids. The modular architecture of PyHydroGeophysX enables researchers to incorporate additional models and methods, fostering broader adoption of integrated hydrogeophysical approaches. The software is freely available on GitHub and is intended for researchers and practitioners working at the intersection of hydrology and geophysics.

Hydrogeophysics

A bespoke model of Arctic river basins based on hillslope delineation: Model Archive

This dataset is a model archive of the paper A bespoke model of Arctic river basins based on hillslope delineation (in prep), which introduces a watershed decomposition and parameterization method for large scale permafrost hydrology simulation. With this dataset, this study aims to address the research question: whether a computationally efficient hillslope-based modeling framework can reliably simulate discharge at Arctic river-basin scales. This dataset contains model input and output data for five modeling scenarios at a study site located in the Sagavanirktok River basin. The five modeling scenarios include three modeling cases under temperate conditions using full 3D, decomposed 3D, and decomposed 2D modeling strategies; and two modeling cases under actual Arctic conditions with permafrost using full 3D and decomposed 2D modeling strategies. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.6 for three temperate scenarios and v1.5 for two Arctic scenarios), a physics-rich integrated surface–subsurface hydrologic model with cryo-hydrology features. For the three temperate models, simulations were conducted for the period of 10/01/1993 - 09/30/2002; and for the two Arctic models, simulations were conducted for the period of 01/01/1994 - 12/31/2002. To facilitate reproducibility of simulations, all datasets are organized hierarchically. The dataset contains: (1) Mesh files (.exo) for full 3D model, decomposed 3D models, and decomposed 2D models, located in huc/190604020802_gauge15906000/mesh/. Mesh files can be visualized through Paraview or read by Python. (2) Climate forcings (.h5) for full 3D model and decomposed 3D/2D models are located in huc/190604020802_gauge15906000/daymet_onePiece/, and huc/190604020802_gauge15906000/vp_pr_revised_daymet_1980_2006_with_wind/ separately. Accessible by Python. (3) Raw measured gage discharge (.csv) from USGS, located in huc/190604020802_gauge15906000/gaged_basin15906000_discharge_usgs/. Accessible by Python. (4) Delineated subdomain raster (.tif) and shape files (.shp), and the final parameterized results (.npy) for decomposed models, located in huc/190604020802_gauge15906000/data_preprocessed-meshing. Accessible by Python. (5) Temperate models are located in nonpermaf_huc190604020802_gauge15906000/, which includes three cases: decomposed 2D models (inside model_0*-hillslope_*), decomposed 3D models (inside model_1*-subcatchment_*), and full 3D model (inside model_2*-onepiece_*). Two step spin-up results (checkpoint_final.h5) are located in model_*1-*_spinup_steadystate and model_*2-*_spinup_cycle, separately, which are used to initialize real transient models. The input files (.xml) and output results (.dat) of the real transient models are located in model_*3-*_transient/. Especially, for two example hillslope models (ID=-11 and 11), additional h5py files are included in model_03-hillslope_transient/hillslope-11/, model_03-hillslope_transient/hillslope11, model_13-subcatchment_transient/subcatchment-11/, model_13-subcatchment_transient/subcatchment/11, respectively, which are used to plot the saturation figure (Figure 5) in the manuscript. Accessible by Python. (6) Arctic models are located in huc190604020802_gauge15906000/, which includes two cases: decomposed 2D models (inside model_04-hillslope_transient), and full 3D model (inside model_05-onepiece_transient_mannp1_ra). Three step spin-up results (checkpoint_final.h5) are located in model_01-column_freezeup/, model_02-column_spinup/, model_03-hillslope_spinup/, respectively, which are used to initialize real 2D transient hillslope models. The input files (.xml) and output results (.dat) of transient 2D hillslope models are located in model_04-hillslope_transient/. The input files (.xml) and output results (.dat) of the full 3D transient model is located in model_05-onepiece_transient_mannp1_ra/. The full 3D transient model is initialized by model_02-column_spinup/. Accessible by Python. (7) The MOSART routed discharge results (.csv) under Arctic conditions is located in huc190604020802_gauge15906000/MOSART/. Accessible by Python. (8) All Python codes (.py) used to parameterize full 3D model to decomposed 2D models are located in script/. These codes fit with watershed workflow (a watershed delineation tool) v1.4 under the branch gaob/v1.4 from https://github.com/gaobhub/watershed-workflow.git.

EARTH SCIENCE > CRYOSPHERE

FAIRmaterials: Ontology Tools with Data FAIRification in Development

The bilingual FAIRmaterials package simplifies the creation and visualization of materials and data science ontologies. FAIRmaterials, available in the Python and R languages, addresses the complexities associated with traditional ontology editors based on manual user input such as Protege with an intuitive workflow and easy-to-use templates, making it accessible to users both experienced and inexperienced with ontologies. The FAIRmaterials package is its ability to programatically convert simple and structured CSV inputs into rich, well-defined ontologies. This capability is designed to support the findability, accessibility, interoperability, and reusability (FAIR) of research data and serve as a tool in the process of data FAIRification. Its additional features, such as automated ontology merging, static visualizations, and comprehensive documentation for outputs extend its utility, making it a valuable tool for any researcher engaged in knowledge management.

Bradley, Alexander Harding [Case Western Reserve U

Visualizing UPSP Data with Python

The Unsteady Pressure-Sensitive Paint (uPSP) projects uses Pressure-Sensitive paint applied over aerospace models during wind tunnel testing to collect pressure data with high spatial and temporal resolution in order to inform unsteady aerodynamics studies. For each of the 800+ experimental runs, four cameras generate up to 50 GB of video data, which must then be processed, analyzed, and visualized on the NASA Advanced Supercomputing system (NAS) to assess the result. One of the final data analysis products is the dynamic modal decomposition (DMD) results, which decomposes the pressure reading signals by their frequency component. The goal of this project is to visualize the DMD results over a 3D rendering of the model, using efficient and parallelized python routines. The software uses the pytecplot library, a high-level API that connects python scripting to a Tecplot 360 engine. Tecplot is an industry standard high-performance visualization tool that can handle large datasets and workflow. Various animation, rendering, and image-combination techniques were investigated to generate the final videos using OpenCV on the NAS. The final result is a software tool that takes in data products from the uPSP processing chain and generates high resolution visualization videos in parallel for every data file, allowing researchers to view their results efficiently and at an unprecedentedly detailed level.

Emma Dolores McMillian