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DOE OSTI2024

HAPPA: A Modular Platform for HPC Application Resilience Analysis with LLMs Embedded

High-performance computing (HPC) systems are increasingly vulnerable to soft errors, which pose significant challenges in maintaining computational accuracy and reliability. Predicting the resilience of HPC applications to these errors is crucial for robust code protection and detailed resilience analysis. In this study, we present HAppA, a modular platform designed for HPC Application Resilience Analysis. Embedding Large Language Models (LLMs), HAppA addresses understanding the context information of long code sequences typical in HPC applications. HAppA implements a novel code representation module that chunks the code into fixed-size segments and aggregates the embeddings of these segments. Three aggregation methods have been explored: MeanPooling, MaxPooling, and LSTM-based techniques. We built a DAtaset for REsilience analysis using Fault Injection (FI), named DARE. Using our DARE dataset, HAppA is trained for regression prediction tasks. Our evaluation results demonstrate the predictive accuracy of HAppA compared to other models, particularly noting that the LSTM-based aggregation method -- HAppA-LSTM -- achieves a mean squared error (MSE) of 0.078 for SDC prediction, surpassing the existing state-of-the-art PARIS model, which recorded an MSE of 0.1172. Additionally, HAppA with the KeyBERT model extracts a list of keywords representing the source code. A comprehensive importance analysis of these keywords further elucidates the code patterns contributing to the error rate. These findings highlight the effectiveness of HAppA in analyzing the resilience of HPC applications and establish a new benchmark for predictive accuracy in resilience.

Jiang, Hailong [Kent State University]↗

DOE OSTI2024

Collection And Analysis Of Telemetry For The Cyote Heuristic

CATCH CLI focuses on gathering telemetry data, storing it in the Neo4j database, querying for Mitre ATT&CK patterns, and creating STIX 2.1 reports. Key Components: Analysis Modules: Analyze data to detect attack patterns. GoSTOTS Collection Engines: Collect telemetry data. These tools can be used together or individually. Analysis modules rely on data from specific engines to identify attack patterns. Source Code Organization: Engines: CATCH/catch/cmd/collection Modules: CATCH/catch/cmd/analysis CGUI Overview CATCH Graphical User Interface (CGUI) offers a graphical shell to execute CATCH CLI, allowing easy editing of: Analysis Modules Database configurations Profiles (collection and device settings) Neo4j Overview Neo4j is a graph database using the Cypher query language, storing data in JSON. It seamlessly integrates with STIX 2.1 data for: Data Submission: CATCH Collection Engines Data Querying: Analysis Modules CATCH modifies STIX 2.1 data for Neo4j submission and reverts it back during querying. STIG Overview Structured Threat Intelligence Graph (STIG) is a tool for creating, editing, querying, analyzing, and visualizing threat intelligence using STIX 2.1 and storing data in Neo4j. Usage Tools can be run: Manually (CLI): Refer to CATCH documentation User Interface: Run ./cgui/CGUI or go run ./cgui/ Additional Information Logging System: Detailed in the config documentation Further Documentation: Available for CATCH and CGUI

Madsen, MichaelJ. [Idaho National Laboratory (INL)↗

DOE OSTI2024

Demonstration and Automation of Reflected Target Optical Measurement for Heliostats

Accurate optical surfaces are a primary driver of concentrated solar power plant performance. Errors in pointing and tracking mirrors, the canting of individual mirror facets, and the surface slope of the mirror itself can be caused by errors during assembly, transportation, wind loading, gravity, and many other sources. The tools that exist to measure these error sources today largely rely on fringe deflectometry (SOFAST, QDec, others), or photogrammetry with targets attached to the mirror surface. Since 2022, NREL has been developing a measurement method called the Reflected Target Non-intrusive Assessment (ReTNA) system. This system differs from most established methods in that we perform deflectometry with a pattern of coded targets, identified in space with photogrammetry. Reflected target systems have several advantages over traditional fringe deflectometry systems. Firstly, they can be operated in bright or ambient lighting, a challenge for fringe systems that use a projector and screen. Reflected target systems also can use a much lighter and less expensive target than projector-based systems. Lastly, 2D slope measurement can be solved from a single image, which leads to several advantages for accommodating faster measurements and smaller sized targets. These advantages make ReTNA particularly well-suited for applications where there are space or lighting constraints, like performing heliostat quality assurance on an assembly line. It's also useful when a lightweight, flexible system is needed, like for heliostat developers to quickly measure a new heliostat design at different orientations, to observe gravitational effects on the mirror surface shape. In the last year, significant improvements were made to this tool to make it more useful for these applications. These improvements were focused around validation of the ReTNA measurement system, and automation of the setup and measurement process. First, we present an improved ReTNA layout, for use on the heliostat assembly line. Next, we detail the various changes to the ReTNA software and computer vision methods to automate data collection in this new setup, and lessons learned from this process. The goal with this new setup is to perform a full heliostat surface characterization without removing the mirror from the assembly line. Lastly, we share results from several ReTNA validation studies undertaken over the last year. These include repeated ReTNA measurement on demonstration mirror facets, comparisons with other optical measurement tools, and some studies aimed at quantifying the uncertainty of ReTNA measurement under various constraints (mirror-target spacing, camera resolution, etc.). These results are compared with 2024 HelioCon performance targets, and our planned next steps for the ReTNA measurement system are presented.

CSP↗

DOE OSTI2026

QPatLib v1.0 — Measurement-based quantum simulation Pauli string unitary pattern collections

This Zenodo record accompanies the paper “Scalable Measurement-Based Quantum Simulation Patterns for Benchmarking” arXiv.2605.12502 and provides QPatLib v1.0 measurement-pattern datasets in human-readable JSONL together with a ZIP archive of OpenQASM 3.0 circuits used for validation and reproducibility. The patterns and circuits implement Pauli string unitaries for benchmark cases. Cases include all possible string combinations for less than 6 qubits and strings used in Hamiltonians for certain diatomic molecules for 6 or more qubits. Format: Each pattern_*.jsonl file is containins measurement patterns for all subsets for a given model/instance and subset strategy: it begins with a preamble containing model metadata, subset definitions, provenance, and (when feasible) full-pattern test results, followed by one pattern entry per subset. Each subset entry includes a required pattern_ascii field storing the measurement pattern in the measurement-calculus/Graphix standard with signal shifting, written left-to-right in the canonical order nodes → edges → measurements (with signal dependencies) → byproduct corrections (X/Z). The circuits are included as circuit_files.zip. Patterns in this record were validated against the corresponding circuits and checked for causal flow. Codes for generating these patterns can be found at QPatLib repository on Github

Graphix↗

DOE OSTI2026

Dual Context: Leveraging Structured Application Context for Code Generation and Runtime Feature Activation via Chat Interfaces

Integrating artificial intelligence (AI) capabilities into software applications typically involves two common paths. For developers, AI assists in generating and documenting source code and other related software engineering efforts. For users, AI assists them through question-and-answer exchanges via chatbots. Both approaches have their value, but neither effectively leverages the modularity of component-based architectures that modern web application frameworks offer. We implement a proof of concept within a centralized suite of applications used for the Atmospheric Radiation Measurement (ARM) Data Center Operational Tools, where we introduce a third integration path through the ARM Context Engine (ACE). ACE is a context driven system that uses structured contextual specifications to enable Large Language Models (LLMs) to render interactive and feature-rich user interface (UI) components directly within chat responses, alongside or in place of conventional text outputs. These specifications serve two important purposes across what we call code context and UI context. Code context provides AI-assisted development tools with structured application knowledge beyond raw code, including component relationships, architectural patterns and schematic information, enabling the generation of consistent, well-structured code. UI context defines the rules for enabling and rendering component features at runtime based on the user's natural language input, allowing end users to activate capabilities such as data export, filtering, and pagination within chat responses, without requiring code changes or redeployment. We demonstrate, through a comparative evaluation against general-purpose AI chatbots, that context-driven component rendering provides interactive capabilities that text-based responses cannot replicate, including deterministic component behavior, application-consistent design language, and on-demand feature activation. A development effort comparison further shows that features that traditionally require multi-step development cycles can be activated with a single naturallanguage request. In this ongoing work, we present ACE as an emerging approach to AI integration that positions modular, well-documented software architecture as the foundation for AI-ready applications. ACE treats context as a shared resource across both development and user-facing AI, bringing cohesion to conventionally disconnected efforts, bridging developer tooling and end-user capabilities within a single framework.

Tadimeti, Vijay [ORNL]↗

DOE OSTI2024

Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body

The arthropod mushroom body is well-studied as an expansion layer representing olfactory stimuli and linking them to contingent events. However, 8% of mushroom body Kenyon cells in Drosophila melanogaster receive predominantly visual input, and their function remains unclear. Here, we identify inputs to visual Kenyon cells using the FlyWire adult whole-brain connectome. Input repertoires are similar across hemispheres and connectomes with certain inputs highly overrepresented. Many visual neurons presynaptic to Kenyon cells have large receptive fields, while interneuron inputs receive spatially restricted signals that may be tuned to specific visual features. Individual visual Kenyon cells randomly sample sparse inputs from combinations of visual channels, including multiple optic lobe neuropils. These connectivity patterns suggest that visual coding in the mushroom body, like olfactory coding, is sparse, distributed, and combinatorial. However, the specific input repertoire to the smaller population of visual Kenyon cells suggests a constrained encoding of visual stimuli.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Serpentine Magnet Designs for the Interaction Region of the Electron-Ion Collider (EIC)

The Electron-Ion Collider (EIC), hosted by Brookhaven National Laboratory, is designed to deliver a peak luminosity of 1 × 10 34 cm −2 sec −1 . The interaction region (IR) of the EIC imposes several constraints in terms of field quality, aperture, and spatial layout, which necessitates the development of several unique superconducting serpentine direct wind magnets. These magnets are constructed using either a single strand or a small-diameter 6-around-1 NbTi cable, presenting unique challenges for design and optimization. This paper introduces a new computational code specifically developed to streamline and integrate the design process for these magnets, enabling faster design iterations while addressing their complex requirements. Here, in this paper, we first introduce the code, which builds on established electromagnetic fundamentals. The code incorporates tools for optimizing winding patterns and for correcting magnetic multipoles; additionally, it interfaces with established magnet design software. We also present the design of several serpentine magnets for the EIC IR, demonstrating the code’s capability to deliver precise and efficient solutions. These designs highlight the code’s ability to accelerate the development cycle, ensuring the serpentine magnets meet the demanding specifications of the EIC project.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Power and Limitations of Linear Programming Decoder for Quantum LDPC Codes

Decoding quantum error-correcting codes is a key challenge in enabling fault-tolerant quantum computation. In the classical setting, linear programming (LP) decoders offer provable performance guarantees and can leverage fast practical optimization algorithms. Although LP decoders have been proposed for quantum codes, their performance and limitations remain relatively underexplored. In this work, we uncover a key limitation of LP decoding for quantum low-density parity-check (LDPC) codes: certain constant-weight error patterns lead to ambiguous fractional solutions that cannot be resolved through independent rounding. To address this issue, we incorporate a post-processing technique known as ordered statistics decoding (OSD), which significantly enhances LP decoding performance in practice. Our results show that LP decoding, when augmented with OSD, can outperform belief propagation with the same post-processing for intermediate code sizes of up to hundreds of qubits. These findings suggest that LP-based decoders, equipped with effective post-processing, offer a promising approach for decoding near-term quantum LDPC codes.

Gu, Shouzhen [Yale U.]↗

DOE OSTI2025

Power and Limitations of Linear Programming Decoder for Quantum LDPC Codes

Gu, Shouzhen [Yale U.]↗

DOE OSTI2025

Power and Limitations of Linear Programming Decoder for Quantum LDPC Codes

Gu, Shouzhen [Yale U.]↗

DOE OSTI2026

High-speed quantitative X-ray multi-contrast imaging with deep learning based modulated pattern analysis

The advent of X-ray multi-contrast imaging methods, providing absorption, phase, and dark-field images, holds tremendous promise for complementary and non-destructive visualization of inner structures within materials and bio-samples. However, the low efficiency in measuring and analyzing X-ray modulated patterns has hindered their application in high-resolution in situ imaging. In this work, the Enhanced Scanning Pattern-based Imaging Neural Network (ESPINNet) is introduced as a powerful tool for achieving high-speed, high-resolution quantitative imaging. ESPINNet is faster than correlation-based speckle tracking methods such as XSVT and UMPA, and provides a balanced performance in terms of resolution and speed for data collection by using fewer scanning images. In comparison with our previously developed neural network, ESPINNet introduces the capability to generate dark-field images, further enhancing its versatility. By leveraging scanning patterns, ESPINNet significantly improves resolution and measurement precision. Furthermore, its adaptability to various modulation patterns, including those produced by sandpaper, coded masks, or gratings, ensures broad applicability. These features enable real-time 2D and 3D multi-contrast imaging, positioning ESPINNet as a transformative solution for applications in materials science and biomedical research, particularly for high-speed and in situ measurements.

X-ray at-wavelength metrology↗

DOE OSTI2026

ChatMPI: LLM-Driven MPI Code Generation for HPC Workloads

The Message Passing Interface (MPI) standard plays a crucial role in enabling scientific applications for parallel computing and is an essential component in high-performance computing (HPC). However, implementing MPI code manually—especially applying a proper domain decomposition and communication pattern—is a challenging and error-prone task. We present ChatMPI, an AI assistant for MPI parallelization of sequential C codes. In our analysis, we focus on testing six essential HPC workloads, which are based on Basic Linear Algebra Subprograms levels 1, 2, and 3 as well as sparse, stencil, and iterative operations. We analyze the process of creating ChatMPI by using the ChatHPC library. This lightweight large language model (LLM)–based infrastructure enables HPC experts to efficiently create and supervise trustworthy AI capabilities for critical HPC software tasks. We study the data required for training (fine-tuning) ChatMPI to generate parallel codes that not only use MPI syntax correctly but also apply HPC techniques to reduce memory communication and maximize performance by using proper work decomposition. With a relatively small training dataset composed of a few dozen prompts and fewer than 15 minutes of fine-tuning on one node equipped with two NVIDIA H100 GPUs, ChatMPI elevates trustworthiness for MPI code generation of current LLMs (e.g., Code Llama, ChatGPT-4o and ChatGPT 5). Additionally, we evaluate the performance of the MPI codes generated by ChatMPI in comparison with the ones generated by ChatGPT-4o and ChatGPT-5. The codes generated by ChatMPI provide up to a 4 × boost in performance by using better problem decomposition, communication patterns, and HPC techniques (e.g., communication avoiding).

Valero Lara, Pedro [ORNL] (ORCID:0000000214794310)↗

DOE OSTI2026

WFSUITE: A PYTHON SOFTWARE SUITE FOR X-RAY WAVEFRONT SENDING AND AT-WAVELENGTH METROLOGY

SF-26-025 WFSuite is a graphical and command-line toolkit for coded-mask-based X-ray wavefront sensing and phase reconstruction at synchrotron beamlines. It integrates analysis tools for both relative and absolute speckle-based measurements. In the relative metrology module, WFSuite implements Wavelet-transform-based X-ray Speckle Tracking (WXST) and Wavelet-transform-based Speckle Vector Tracking (WSVT) methods to retrieve differential phase and wavefront distortions by comparing speckle patterns recorded with and without the test sample. In the absolute phase module, WFSuite uses coded-mask speckle patterns and replaces the measured reference with a numerically simulated one, enablingsingle-shot wavefront reconstruction using either WXST or a neural-network-based method (SPINNet).

Rebuffi, Luca [Argonne National Laboratory (ANL), ↗

DOE OSTI2024

Refactoring the elastic–viscous–plastic solver from the sea ice model CICE v6.5.1 for improved performance

This study focuses on the performance of the elastic–viscous–plastic (EVP) dynamical solver within the sea ice model, CICE v6.5.1. The study has been conducted in two steps. First, the standard EVP solver was extracted from CICE for experiments with refactored versions, which are used for performance testing. Second, one refactored version was integrated and tested in the full CICE model to demonstrate that the new algorithms do not significantly impact the physical results. The study reveals two dominant bottlenecks, namely (1) the number of Message Parsing Interface (MPI) and Open Multi-Processing (OpenMP) synchronization points required for halo exchanges during each time step combined with the irregular domain of active sea ice points and (2) the lack of single-instruction, multiple-data (SIMD) code generation. The standard EVP solver has been refactored based on two generic patterns. The first pattern exposes how general finite differences on masked multi-dimensional arrays can be expressed in order to produce significantly better code generation by changing the memory access pattern from random access to direct access. The second pattern takes an alternative approach to handle static grid properties. The measured single-core performance improvement is more than a factor of 5 compared to the standard implementation. The refactored implementation of strong scales on the Intel® Xeon® Scalable Processors series node until the available bandwidth of the node is used. For the Intel® Xeon® CPU Max series, there is sufficient bandwidth to allow the strong scaling to continue for all the cores on the node, resulting in a single-node improvement factor of 35 over the standard implementation. This study also demonstrates improved performance on GPU processors.

58 GEOSCIENCES↗

DOE OSTI2026

LaueMatching: an approach for rapid and robust indexing of Laue diffraction patterns

Traditional Laue diffraction pattern indexing often struggles with noisy data, weak signals, peak overlap and missing reflections, particularly from complex or deformed microstructures. Here, we introduce LaueMatching, a high-throughput indexing algorithm designed to overcome these limitations. LaueMatching utilizes a fundamentally different approach based on direct pattern correlation: experimentally pre-processed images are compared against a comprehensive pre-computed library of simulated diffraction patterns corresponding to a dense grid of possible orientations. This approach bypasses the need for explicit peak identification and fitting, steps that are often a failure point for traditional methods. The algorithm rapidly and robustly indexes multiple crystallographic orientations and crystal systems simultaneously, even from challenging patterns. LaueMatching's effectiveness and accuracy have been rigorously tested and validated on diverse experimental (Ni, Al, EuAl 2 O 4 ) and simulated diffraction patterns, demonstrating high-fidelity orientation refinement. Code to implement this approach on both CPU and GPU resources can be downloaded from https://github.com/AdvancedPhotonSource/LaueMatching.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Dataset for "Climatic and socioeconomic drivers of water use and their spatio-temporal patterns for small and mid-sized cities in the Contiguous United States"

This dataset contains all code for calibrating and analyzing machine learning models for "Climatic and socioeconomic drivers of water use and their spatio-temporal patterns for small and mid-sized cities in the Contiguous United States". Please unzip the folders and follow the instructions from 'README.txt'. Required python modulessklearn=1.2.2numpy=1.23.3xgboost=2.0.2joblib=1.2.0 Required R libraryshapFlex:devtools::install_github("nredell/shapFlex")library(shapFlex)

Dave, Hari [Civil and Environmental Engineering De↗

DOE OSTI2026

Exploring Sustainability in Scientific Software through Code Quality & Test Coverage Metrics

Context: Scientific open-source software (SciOSS) plays a foundational role in research and engineering, yet its long-term sustainability has often been overlooked and remains a significant concern. Objective: This study investigates the long-term sustainability of SciOSS through code and test quality metrics. Method: We analyze CASS Software Portfolio projects, classifying them by sustainability and comparing their code structure, test coverage, and links between code quality and testing across the dataset. Results: Sustainable projects show higher, more consistent test coverage and clearer code-test correlations, while unsustainable ones show weaker patterns. Overall, test coverage is low in scientific software, and high complexity and coupling reduce testability. Conclusion: In this study, we present a practical, data-driven approach for assessing sustainability in scientific software, offering a foundation for evaluating long-term software health and supporting future efforts in quality assurance and sustainability monitoring.

Md mushfiqur rahman, Sheikh [University of Tenness↗

DOE OSTI2025

Enhancing chemical bioproduction with rational control of bacterial post-translational modifications

Efficient conversion of inexpensive feedstocks to valuable chemicals by microbes is critical for a robust bioeconomy, but the ability to rationally design bacteria is hampered by insufficient knowledge of how post translational modifications (PTMs) control bacterial protein function and thus bioproduction phenotypes. Our study will focus on the lysine acetylation, a ubiquitous bacterial PTM that can affect the function of enzymes in central metabolism that are often critical for bioproduction processes, disrupt transcriptional regulation, and reduce translation. However, most lysine acetylation data is observational, which means that we do not know when, how, and what specific acetylated residues affect protein function and bacterial physiology. For our model host, we will use a Pseudomonas putida strain that we previously engineered to convert lignocellulosic feedstocks into chemicals such as itaconic acid (ITA). With this strain, we use a dynamic two-stage bioproduction process in which ITA is produced during a non-growth associated production phase. Production is highest during growth stages when lysine acetylation is low in other organisms (early stationary phase) and stalls in conditions where acetylation is highest (late stationary phase). The switch from high to stalled ITA production is also correlated with an unexpected increase in acetate levels – the precursor to non-enzymatic lysine acetylation. As such, we predict that lysine acetylation plays a substantial role in regulating the metabolic pathways required for ITA production. We will develop a generalizable approach that combines high-throughput genetic screens and cutting-edge genome engineering with state-of-the-art proteomics, metabolomics, and genetic code expansion methods to identify and modulate lysine acetylation patterns in bacteria. Ultimately, these strategies aim to manipulate protein expression and acetylation patterns to enhance bioproduction phenotypes (e.g., sustained ITA production in late stationary phase).

60 APPLIED LIFE SCIENCES↗