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LLM Benchmarking with LLaMA2: Evaluating Code Development Performance Across Multiple Programming Languages

The rapid evolution of large language models (LLMs) has opened new possibilities for automating various tasks in software development. This paper evaluates the capabilities of the LLaMA 2-70B model in automating these tasks for scientific applications written in commonly used programming languages. Using representative test problems, we assess the model's capacity to generate code, documentation, and unit tests, as well as its ability to translate existing code between commonly used programming languages. Our comprehensive analysis evaluates the compilation, runtime behavior, and correctness of the generated and translated code. Additionally, we assess the quality of automatically generated code, documentation, and unit tests. Here, our results indicate that while LLaMA 2-70B frequently generates syntactically correct and functional code for simpler numerical tasks, it encounters substantial difficulties with more complex, parallelized, or distributed computations, requiring considerable manual corrections. We identify key limitations and suggest areas for future improvements to better leverage AI-driven automation in scientific computing workflows.

97 MATHEMATICS AND COMPUTING

Recent Developments in DFTB+, a Software Package for Efficient Atomistic Quantum Mechanical Simulations

DFTB+ is a flexible, open-source software package developed by its community, designed for fast and efficient atomistic quantum mechanical simulations. It employs various methods that approximate density functional theory (DFT), such as density functional-based tight binding (DFTB) and the extended tight binding (xTB) approach allowing simulations of large systems over extended time scales with reasonable accuracy, while being significantly faster than traditional ab initio methods. In recent years, several new extensions of the DFTB method have been developed and implemented in the DFTB+ program package in order to improve the accuracy and generality of the available simulation results. In this paper, we review those enhancements, show several use case examples and discuss the strengths and limitations of its features.

36 MATERIALS SCIENCE

Simulation Process Automation for Window Attachments Rating

WINDOW (LBNL 2022) and AERCalc (LBNL 2018) software developed by Lawrence Berkely National Laboratory are needed for running the tool. The database that in installed along with WINDOW software is utilized and modified to develop database for AERCalc simulation in generic case. However, any other custom WINDOW database created by users can be utilized as well. Another requirement for use of the tool is the availability of the shading fabric in the complex glazing database (CGDB). The CGDB id of the fabric was used for database generation discussed in next section.

97 MATHEMATICS AND COMPUTING

omni-engineer-lbl (omni) v0.5

This is a fork of the omni-engineer software developed by Pietro Schirano. My collaborators and I are altering the software to work better with our LBNL infrastructure and requirements. The software is a coding agent wrapper around LLM model APIs, and can use any of the APIs provided by LBNL's CBorg service, or any service that uses an OpenAI endpoint(s).

Fong, Timothy [Lawrence Berkeley National Laborato

Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels

Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.

Kwok, Martin [Fermilab] (ORCID:0000000286936146)

Flexible Operation of Microgrids Through Operator-Configurable Microgrid Controllers

Microgrids are becoming critical assets in power distribution systems. This is partly due to the resiliency and reliability challenges faced by power distribution systems in the last decade and partly due to the increased integration of distributed energy resource assets, such as solar photovoltaic. This increased need for microgrids has created a multitude of needs for microgrid controllers. Most microgrid controllers in the past decade have been uniquely programmed or custom programmed to meet the needs of a specific microgrid. Currently, IEEE standards aim to integrate the needs and capabilities of microgrid controllers under a unified umbrella. But the standards do not recommend necessary or appropriate software development practices for microgrid controllers. In addition, the programmable nature and maintenance of controllers are also key characteristics that fall outside the coverage of the standards. In this paper, we present the best software practices that utility engineers and microgrid operators should consider in the microgrid software platform. This paper can be used as an information document for developing documentation of controller requirements and assessing microgrid controller requirements.

Banshee microgrid

RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence (University of Delaware)

This report summarizes the activities, technical accomplishments, and outcomes of the RAPIDS2 Institute project at the University of Delaware (UD). The RAPIDS2 Institute was a large multi-institution project with the objective of assisting SciDAC and Office of Science application teams in the use of DOE supercomputing resources to achieve scientific breakthroughs. The UD team contributed to this effort through work on formal software verification. This thrust aims to reduce software developer time and effort, especially regarding debugging and testing, and to increase confidence in the correctness of the results computed by the software.

97 MATHEMATICS AND COMPUTING

Numerical Modeling and Optimization of the iProTech Pitching Inertial Pump (PIP) Wave Energy Converter (WEC) (Cooperative Research and Development Final Report, CRADA Number: CRD-22-22968)

This work generated a first-of-its-kind automated workflow to couple time-domain simulations of wave energy converters written in one software language with a set of design generation and evaluation scripts written in another software language. This automated workflow used an existing optimization package to analyze the sensitivity of different design parameters on the power output of a specific WEC, iProTech’s Pitching Inertial Pump (PIP). Geometric, inertial, and power take-off variables were all varied and optimized to find values that produced the highest amount of power generated over varying wave conditions. The findings on these parameter sensitivity studies are used to inform future design iterations of the PIP WEC. Including more design variables in the optimizations will only increase computational run time and further software development is needed to analyze a larger optimization.

16 TIDAL AND WAVE POWER

Neutrino interaction vertex reconstruction in DUNE with Pandora deep learning

The Pandora Software Development Kit and algorithm libraries perform reconstruction of neutrino interactions in liquid argon time projection chamber detectors. Pandora is the primary event reconstruction software used at the Deep Underground Neutrino Experiment, which will operate four large-scale liquid argon time projection chambers at the far detector site in South Dakota, producing high-resolution images of charged particles emerging from neutrino interactions. While these high-resolution images provide excellent opportunities for physics, the complex topologies require sophisticated pattern recognition capabilities to interpret signals from the detectors as physically meaningful objects that form the inputs to physics analyses. A critical component is the identification of the neutrino interaction vertex. Subsequent reconstruction algorithms use this location to identify the individual primary particles and ensure they each result in a separate reconstructed particle. A new vertex-finding procedure described in this article integrates a U-ResNet neural network performing hit-level classification into the multi-algorithm approach used by Pandora to identify the neutrino interaction vertex. The machine learning solution is seamlessly integrated into a chain of pattern-recognition algorithms. The technique substantially outperforms the previous BDT-based solution, with a more than 20% increase in the efficiency of sub-1 cm vertex reconstruction across all neutrino flavours.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Practical Insights on Applying Simulation-Based Control Methods in Experimental Studies

Advanced nuclear reactors are crucial to the future of energy both in the United States and around the globe. In contrast to the current operating fleet, they are characterized as being deployable in remote locations and able to operate in semi-autonomous or autonomous fashion. This leap forward necessitates a new reactor control paradigm. Because advanced nuclear reactors are still under development in the United States, the creation of new control methods to achieve autonomous operations has been based on systems modeling and simulation. However, an important factor in successfully deploying these new control methods is the ability to seamlessly transition from simulation environments to real-world settings. Control methods tested in both simulation and experimental settings need to be investigated in the context of advanced reactor applications. This work developed a series of simple controllers for Idaho National Laboratory (INL)’s Microreactor Applications Research Validation and Evaluation (MARVEL) microreactor operating in load-following scenarios. These controllers were tested in both simulation and experimental settings, and a comparative performance analysis was performed. The simulation tests leveraged the Control and Optimization Modular Modeling Application for Nuclear Deployment (COMMAND) software developed in a previous stage of the current effort, along with the MARVEL Reactor Excursion and Leak Analysis Program (RELAP5-3D) and Monte Carlo N-Particle (MCNP) models. The experimental tests leveraged the COMMAND software, MARVEL models, and the U.S. Department of Energy Microreactor Program’s Microreactor Automated Control System (MACS). MACS was developed to serve as a control method testbed. It was customized to mirror the MARVEL microreactor, and COMMAND enabled MACS to emulate the physics of MARVEL. The load-following controller was developed using the simulation platform, with efforts to emulate real systems by introducing actuator saturation and noise. These factors were incrementally accounted for in the controller design. After finalizing the controller design, it was implemented with the experimental setup. The experimental conditions tested included an initial test under conditions similar to the final simulation test, and two additional scenarios. The first scenario introduced additional actuator saturation to account for equipment aging over time, which was unknown to the controller. The second scenario introduced sensor delay, a phenomenon anticipated with the use of remote operations or wireless communication in advanced reactors. These tests revealed several notable differences. While the controller performed well in simulation, it exhibited several limitations when transitioning to hardware. The main challenges involved maintaining the steady-state target power, as evidenced by larger error values between the true reactor power and setpoint power, as well as persistent oscillations in controlled reactor power. These issues could lead to unacceptable transient conditions in real reactor testing. Introducing actuator aging and stochastic delays in the experimental setup significantly impacted controller performance, resulting in increased overshoot and undershoot, and exacerbated error and oscillations previously mentioned. These findings underscore the importance of experimental testbeds for testing and validating control methods, as controllers developed using only theory and/or simulation may perform unexpectedly when applied to actual hardware. This research emphasizes the need for an experimental testbed for achieving such validation.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN

Intelligent Experiments through Real-Time AI: Fast Data Processing and Autonomous Detector Control for High-Energy Nuclear Experiments

The aim of this project is to develop software and hardware for fast real-time data processing and autonomous detector control and calibration for the sPHENIX and the future EIC experiments. Below summarizes Georgia Tech team efforts in the past year: 1. We developed a real-time clustering algorithm and FPGA-based pipeline architecture for processing fired pixel data from ALPIDE sensors in sPHENIX experiments. Our Columnar Clustering Co-Design introduces a hardware-aware, stream-friendly approach that segments pixel data by column pairs using a Column Pair Clustering (CPC) strategy, followed by Cluster Stitching to merge adjacent subclusters. Implemented in Vitis HLS, the pipeline comprises five stages—read-in, subclustering, stitching, analysis, and write-out—connected by tagged HLS streams with custom end-of-event signaling for robust synchronization. We designed a pipelined dataflow model optimized for throughput, low latency, and minimal buffering, enabling scalable clustering across events of arbitrary size. Our system maintains spatial precision via center-of-mass and shape key extraction and efficiently handles edge cases such as fragmented or nested clusters. Compared against DBSCAN in both software and hardware, our approach demonstrates competitive performance under FPGA constraints. 2. We also conducted a comprehensive algorithm-to-hardware co-design of connected component analysis tailored for sPHENIX experiments, focusing on real-time, low-latency processing using FPGAs and High-Level Synthesis (HLS). Starting from a Python-based particle tracking pipeline, the team translated the core logic—graph traversal via DFS and Union-Find—into an HLS-compatible C++ model, replacing dynamic memory and recursion with static arrays and pipelined control flow. The final design includes a fully streamed and dataflow-compatible Union-Find kernel optimized across five iterations, incorporating loop pipelining, array partitioning, AXI/FIFO interface tuning, and function flattening. Experimental results show up to 14.8× speedup over the CPU baseline, reducing per-graph latency to 1.58 μs and demonstrating strong resource efficiency with only ~7k LUTs and zero BRAM usage. The design maintains functional correctness against the Python reference using a Python-based C-simulation framework and Mean Squared Error metrics. This work validates the potential of HLS-driven FPGA designs for edge-level HEP data acquisition, laying a scalable foundation for future integration with real-time detector pipelines and multi-graph processing systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Machine learning models for segmentation and classification of cyanobacterial cells

Abstract Timelapse microscopy has recently been employed to study the metabolism and physiology of cyanobacteria at the single-cell level. However, the identification of individual cells in brightfield images remains a significant challenge. Traditional intensity-based segmentation algorithms perform poorly when identifying individual cells in dense colonies due to a lack of contrast between neighboring cells. Here, we describe a newly developed software package called Cypose which uses machine learning (ML) models to solve two specific tasks: segmentation of individual cyanobacterial cells, and classification of cellular phenotypes. The segmentation models are based on the Cellpose framework, while classification is performed using a convolutional neural network named Cyclass. To our knowledge, these are the first developed ML-based models for cyanobacteria segmentation and classification. When compared to other methods, our segmentation models showed improved performance and were able to segment cells with varied morphological phenotypes, as well as differentiate between live and lysed cells. We also found that our models were robust to imaging artifacts, such as dust and cell debris. Additionally, the classification model was able to identify different cellular phenotypes using only images as input. Together, these models improve cell segmentation accuracy and enable high-throughput analysis of dense cyanobacterial colonies and filamentous cyanobacteria.

Huffine, Clair A.

A Microservices Architecture Toolkit for Interconnected Science Ecosystems

Microservices architecture is a promising approach for developing reusable scientific workflow capabilities for inte- grating diverse resources, such as experimental and observational instruments and advanced computational and data management systems, across many distributed organizations and facilities. In this paper, we describe how the INTERSECT Open Architec- ture leverages federated systems of microservices to construct interconnected science ecosystems, review how the INTERSECT software development kit eases microservice capability develop- ment, and demonstrate the use of such capabilities for deploying an example multi-facility INTERSECT ecosystem.

Brim, Michael

HP-FLEX MPC v0.1.0

HP-FLEX MPC is control software developed by Lawrence Berkeley National Laboratory with support from the California Energy Commission (CEC) through EPIC-19-301. HP-FLEX aims to provide load flexibility for heat pumps (HPs) in response to dynamic grid signals (including Time-of-Use, Dynamic Pricing, and Critical Peak Pricing) while maintaining thermostat temperatures within user-specified bounds. The software includes a system-identification module, which models the dynamics of the building envelope with thermostat data, and a control module based on a model predictive controller (MPC) to make optimal decisions. HP-FLEX receives forecasts of outdoor air temperature, solar irradiation, and internal gain (if available), as well as trajectories of energy price, temperature lower and upper bounds over a prediction horizon. It then optimizes heating and cooling capacities to minimize energy cost and peak power (with a user-defined weight on peak power) over the prediction horizon, while maintaining room air temperature within the temperature constraints, and outputs the optimal thermostat setpoints.

Kim, Donghun

CI-MOR Final Report: Analysis and Validation of Critical Infrastructure Models using Model Order Reduction

This report summarizes the research and capabilities developed as part of the project “Analysis and Validation of Critical Infrastructure Models using Model Order Reduction” (CI-MOR) LDRD project. CI-MOR research enables the solution of large, complex optimization models that naturally arise in national security challenges involving critical infrastructures. Specifically, CI-MOR researchers developed methods to (1) rigorously approximate complex, nonlinear optimization formulations, (2) identify alternative near-optimal solutions, (3) accelerate optimization workflows used for complex applications, and (4) rigorously integrate domain knowledge in stochastic-process models. This report provides an overview of the research done in CI-MOR, and we describe application exemplars used to illustrate CI-MOR capabilities. Furthermore, we describe the software developed by CI-MOR that researchers can leverage to analyze new applications.

97 MATHEMATICS AND COMPUTING

Development of POTATO for 2S Module Grading for the CMS Phase-2 Outer Tracker Upgrade

Due to the High Luminosity-Large Hadron Collider (HL-LHC) upgrade, several detectors of the Compact Muon Solenoid (CMS) will need to be upgraded, specifically the new Outer Tracker detector that will be composed of 13,200 silicon modules. The Outer Tracker features two types of modules; the PS (pixel-strip) and the 2S (strip-strip) modules. With a large influx of production of modules, extensive testing is required to ensure they fulfill the performance requirements. This research introduces POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a specialized software developed in C++ to analyze, grade, and store results in a centralized database since module data will be collected from various international production facilities. The implementation of POTATO will facilitate the selection of the best performing modules for the Outer Tracker upgrade. This paper is focused on the implementation of the analysis of 2S Module results within POTATO.

43 PARTICLE ACCELERATORS

Digitizing Today’s Buildings in the Real World: Lessons from Field Demonstrations

Digital twins, created by generating a virtual replica of a building, enable safe evaluation of operational scenarios and applications like fault detection and diagnosis and advanced controls. However, a prerequisite is the creation of a machine-readable digital representation of a building, currently hindered by fragmented information scattered across mechanical drawings, point lists, and natural language sequences. As a result, digital twin development remains labor-intensive, error-prone, and difficult to validate. To address these challenges, two efforts from ASHRAE aim to support the digitalization of buildings. ASHRAE s223 establishes a semantic model of buildings, representing system components, configuration, and data sources. ASHRAE s231 defines a vendor-neutral programming language for expressing their control logic. As the industry evaluates implementing them in their products, understanding the challenges that vendors and implementers may face is crucial. In this paper, we present findings and lessons learned from field demonstrations in five buildings that implemented control applications using ASHRAE s223 and s231. The demonstrations highlight how semantic modeling and formalized control descriptions can significantly reduce software development time, manual point mapping, and hard-coding. Beyond time efficiency, they enable reliable automation by minimizing human interpretation and providing a means for consistency across projects. We describe the processes and best practices for model creation and model usage, from translating heterogeneous building documentation into semantic representations to implementing control logic in real-world systems. Finally, we discuss the challenges that persist, including integration with legacy software environments, gaps in interoperability, and the level of expertise still required to effectively leverage semantic models.

Prakash, Anand Krishnan

Graph-Based Modeling for the Detection and Tracking of Sarin-Surrogate-Induced Neurotoxicity Using a Human-Relevant, In-Vitro Brain Model

Organophosphorus (OP) nerve agents are a chemical threat to the United States, to the civilian population (e.g., pesticides) and historically weaponized (e.g., sarin) as chemical warfare agents. The unprecedented, accelerated process from “bench-to-bedside” during the SARSCov2 pandemic has made it clear that technology and tools need to be readily available for immediate response. Advances in human organ tissue mimetic systems are a promising technology to evaluate the human-relevant response in vitro for basic and applied research and drug screening. In particular, current brain microphysiological systems (MPS) have the capability to monitor and detect changes in engineered human neural circuit activity. However, current data analytics approaches for these systems lack the granularity to functionally detect and distinguish the different mechanisms that occur in the brain following neurotoxicity, injury, and disease. The goal of this project was to advance the computational analytical capabilities of the brain MPS to detect functional changes in neural circuit structure at different stages of Sarin surrogate-induced neurotoxicity. We developed graph-based models to (1) identify the composition of the neural circuit structure; (2) detect and monitor how this structure changes following sarin-induced neurotoxicity; and (3) evaluate the analytical pipeline using known/promising oxime reactivators. Through experiments on the bMPS where in vitro neuronal cultures were exposed to a sarin surrogate, we demonstrated the capabilities of our computational pipeline to identify different responses in the functional networks of brain cells exposed to low and high concentrations of the nerve agent. We identified a biphasic response of human neural network activity following exposure to a sarin-surrogate that had not been reported in the literature before. The graph-based models and software developed in this project can be used for future studies that leverage the brain MPS technology, such as treatment efficacy assessment.

59 BASIC BIOLOGICAL SCIENCES