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Best practices for documenting a scientific Python project

Documentation is a crucial component of software development that helps users with installation and usage of the software. Documentation also helps onboard new developers to a software project with contributing guidelines and API information. The INTERSECT project is an open federated hardware/software library to facilitate the development of au- tonomous laboratories. A documentation strategy using Sphinx has been utilized to help developers contribute to source code and to help users understand the INTERSECT Python interface. Docstrings as well as reStructuredText files are used by Sphinx to automatically compile HTML and PDF files which can be hosted online as API documentation and user guides. The resulting documentation website is automatically built and deployed using GitLab runners to create Docker containers with NGINX servers. The approach discussed in this paper to automatically deploy documentation for a Python project can improve the user and developer experience for many scientific projects.

Wiggins, Gavin↗

Speeding up software with VecCore

Portable and efficient vectorization is a significant challenge in large software projects such as GeantV, ROOT, and experiments’ frameworks. Nevertheless, fully exploiting SIMD parallelism will be a required step in order to bridge the widening gap between the needs and availability of computing resouces for data analysis and processing in particle physics. Although there are SIMD libraries that wrap compiler intrinsics into a convenient interface, they do not always support all available architectures, or they only perform well in some of them. The VecCore library was created to address some of these performance and portability issues by providing a unified abstraction layer on top of existing libraries, such as Vc or UME::SIMD. In this article, we discuss VecCore’s programming model for SIMD code and some use cases in HEP software packages such as VecGeom and GeantV.

Amadio, G.↗

Applications of square-root information filtering and smoothing in spacecraft orbit determination

The JPL (Jet Propulsion Laboratory) Orbit Determination Software System is a set of computer programs developed for the primary purpose of determining the flight path of deep-space mission spacecraft in NASA's Planetary Program and highly elliptical orbiting spacecraft in Earth orbit. The filtering processes available within the JPL Orbit Determination Software are discussed, and several examples are presented. In particular, solutions obtained by the Square Root Information Filter (SRIF) using Bierman's Estimation Subroutine Library (ESL) are discussed and compared with the solutions obtained by the singular value decomposition (SVD) technique. It is concluded that the SRIF filtering and smoothing algorithms are efficient and numerically stable for well-conditioned systems. The use of Bierman's ESL simplifies the task of maintaining the orbit determination software by providing efficient, tested filtering tools. For solving a large well-conditioned system (rank higher than 120), SRIF is approximately four times faster than SVD; however, for solving an ill-conditioned system, SVD is recommended.

Wang, Tseng-Chan↗

Earthbound applications for NASA's physician workstation

The dream of a space probe to Mars or an astronaut colony on the moon persists. Despite years of setbacks and delays, NASA continues to lay the foundation for a new frontier in space. The necessity of a self contained health maintenance facility is an integral part of this stellar venture. As a subsystem of this health maintenance facility, the physician or astronaut workstation was envisioned as the vehicle of interface between the computer resources of the space station and the care provider. Our efforts to define and build this interface have resulted in a series of programs which can now be tested and refined using earth-based applications. The modules which have dual-use application from the NASA workstation include: patient scheduling and master patient index, pharmacy, laboratory, medical library, problem list/progress notes, and digital medical records. Our current plan is to develop these tools as objects that can be assembled in a variety of configurations. This will allow the technology to be used by the private sector where each doctor can select the starting point of his outpatient office system and add modules as he makes progress in system integration and training.

NASA Discipline Number 70-30↗

Development of nuclear data processing code FRENDY version 2

Nuclear data processing is an important interface between an evaluated nuclear data library and neutronics calculation codes. JAEA has been developed the new nuclear data processing code FRENDY from 2013. FRENDY version 1 generates the ACE files used for the continuous-energy Monte Carlo codes including PHITS, Solomon, Serpent,and MCNP and it was released as the open-source software under the 2-clause BSD license in 2019.After we released FRENDY version 1, many functions, e.g., the multi-group neutron cross-section library generation, the statistical uncertainty quantification of the probability tables for unresolved resonance cross-section, the 'perturbation' of the ACE file for uncertainty quantification, and the modification of the ENDF-6 formatted nuclear data file, have been developed. We released FRENDY version 2 including these functions. The present paper gives an overview of FRENDY and presents features of new functions implemented in FRENDY version 2. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Software product description

An overview of the MultiNet system is presented. Services, supported configurations, remote printer services, netstat, netcontrol, DECnet interoperability services, and programming libraries are briefly described.

Source record↗

EDXplorer: A Utility for APA Analysis

The automated particle analysis (APA) method of scanning electron microscopy (SEM) energy dispersive X-ray spectroscopy (EDS/EDX) is a useful tool for analyzing the elemental and morphological data of particulate samples. Often, such datasets have many thousands of particles, and it can be difficult to sift through the data to find meaningful trends. EDXplorer is a software utility for processing APA data. They enable the user to easily load data and determine the important components and aspects of the datasets using a powerful and versatile library of data plotting functions, mainly centered around scatter plots and histograms. These programs are intended to fill a void in the data processing of data from certain instruments, where often the user must rely on their own code or other software that is not user-friendly. EDXplorer is intended as a general plotting utility for browsing through data and discovering data trends.

Moseley, Duncan [ORNL] (ORCID:0000000343518347)↗

Automated Strain Construction for Biosynthetic Pathway Screening in Yeast

Automation accelerates the Design-Build-Test-Learn (DBTL) cycle for synthetic biology; however, most strain construction pipelines lack robotic integration. Here, in this study, we present the workflow design and source code for a modular, integrated protocol that automates the Build step in Saccharomyces cerevisiae. We programmed the Hamilton Microlab VANTAGE to integrate off-deck hardware via its central robotic arm, enabling automated steps that increased throughput to 2,000 transformations per week. We developed a user interface with the Hamilton VENUS software to support on-demand parameter customization. As a proof of concept, we screened a gene library in an engineered yeast strain producing verazine, a key intermediate in the biosynthesis of steroidal alkaloids. Our pipeline rapidly identified pathway bottlenecks and genes that enhanced verazine production by 2.0- to 5-fold. This technical note provides resources for synthetic biologists designing yeast workflows for biofoundries to screen libraries for pathway discovery/optimization, combinatorial biosynthesis, and protein engineering.

automation↗

Using OpenMP for HEP framework algorithm scheduling

The OpenMP standard is the primary mechanism used at high performance computing facilities to allow intra-process parallelization. In contrast, many HEP specific software packages (such as CMSSW, GaudiHive, and ROOT) make use of Intel’s Threading Building Blocks (TBB) library to accomplish the same goal. In these proceedings we will discuss our work to compare TBB and OpenMP when used for scheduling algorithms to be run by a HEP style data processing framework. This includes both scheduling of different interdependent algorithms to be run concurrently as well as scheduling concurrent work within one algorithm. As part of the discussion we present an overview of the OpenMP threading model. We also explain how we used OpenMP when creating a simplified HEP-like processing framework. Using that simplified framework, and a similar one written using TBB, we will present performance comparisons between TBB and different compiler versions of OpenMP.

97 MATHEMATICS AND COMPUTING↗

COUPLING OF RELAP5-SCDAP MOD4.0 AND NEUTRONIC CODES

High-fidelity and accurate nuclear system codes play a key role in the design and analysis of complex nuclear power plants, which consist of multiple subsystems, such as the reactor core (and its fuel, burnable poisons, control elements, etc.), the reactor internal structures, the vessel, and the energy conversion subsystem and beyond to grid demand. Most commonly the interplay between these various subsystems is modeled using coupled codes, each of which represents one of the subsystems. And the most common direct coupling is that of thermal-hydraulics and neutronics codes. The subject of this paper is the coupling of codes that model not only thermal-hydraulics and neutronics, but also structural components damage. Furthermore, the neutronic component is not limited to the sole core solver. The coupled code system encompasses thermal-hydraulics, material performance of the fuel, neutronic solver, and neutronic data preparation. Thus, this paper presents a framework for coupling RELAP5/SCDAPSIM/MOD4.0 with a suite of neutron kinetics codes that includes NESTLE, DRAGON and a version of the ENDF library. The version of the RELAP5/SCDAPSIM/MOD4.0 code used in this work is one developed by Innovate System Software (ISS) as part of the international SCDAP Development and Training Program (SDTP) for best-estimate analysis to model reactor transients including severe accident phenomena. This RELAP5/SCDAPSIM/MOD4.0 code version is also capable of predicting nuclear fuel performance. It uses nodal power distributions to calculate mechanical and thermal parameters such as heat-up, oxidation and meltdown of fuel rods and control rods, the ballooning and rupture of fuel rod cladding, the release of fission products from fuel rods, and the disintegration of fuel rods into porous debris and molten material. On the neutronics side, this work uses the NESTLE and DRAGON codes. NESTLE is a multi-dimensional static and kinetic neutronic code developed at North Carolina State University. It solves up to four energy groups neutron diffusion equations utilizing the Nodal Expansion Method (NEM) in Cartesian or hexagonal geometry. The DRAGON code, developed at Ecole Polytechnique de Montreal, performs lattice physics calculations based on the neutron transport equation and is capable of using very fine energy group structures. In this work, we have developed a coupling approach to exchange data among the various modules. In the coupling process, the generated nuclear data (in fine multigroup energy structure) are collapsed down into two- or four-group energy structures for use in NESTLE. The neutron kinetics and thermal-hydraulics modules are coupled at each time step by using the cross-section data. The power distribution results of the neutronic calculations are transmitted to the thermal-hydraulics code. The spatial distribution of coolant density and the fuel-moderator temperature, which result from the thermal-hydraulic calculations, are transmitted back to the neutron kinetics codes and then the loop is closed using new neutronics results. Details of the actual data transfers will be described in the full length paper.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

pnnl/projection_ntk

This is a repository for work conducted in our research paper we would like to make open source. The main features are that we forked another open source library and added functionality that enabled us to compute neural-kernel objects using random vector projection software for both computer vision and large language text models. The new features are specifically code that enables the calculation of objects we define and refer to as the projection pseudo neural tangent kernel and the projection trace neural tangent kernel; both of which are approximations of the empirical neural tangent kernel. The software that computes the projections themselves are not part of the invention, but are necessarily tied to our software and licensed via MIT license, and BSD 2 license.

Georgiev, Kristian↗

Scientific Core Library Stack (SCLS) v2026

SCLS (Scientific Core Library Stack) is an opinionated build and packaging system for scientific computing libraries developed at Lawrence Berkeley National Laboratory. It produces a coherent, reproducible stack of numerical libraries — including BLAS/LAPACK, MPI, sparse direct and iterative solvers, graph partitioners, and parallel I/O libraries (e.g., PETSc, SLEPc, HDF5, NetCDF, MUMPS, OpenBLAS) — that work together without manual repair by downstream scientific software. From a single recipe-and-flavor model, SCLS produces native RPM packages for RHEL-family Linux, DEB packages for Debian/Ubuntu, direct Unix-style prefix installs for HPC and locked-down environments, and native macOS builds. Multiple build "flavors" (e.g., GCC+OpenBLAS, GCC+MKL, Intel+MKL, debug) coexist in distinct prefixes on the same host. Compared to general-purpose meta-build frameworks, SCLS is deliberately curated rather than infinitely configurable. It enforces deterministic, audit-friendly behavior: explicit build dependencies, no silent feature autodetection, a clear open-source license policy, and rpath-based runtime linkage so installs integrate cleanly with standard package-manager workflows.

Messe, Christian [Lawrence Berkeley National Labor↗

A computer program for processing impedance cardiographic data: Improving accuracy through user-interactive software

This report contains the source code and documentation for a computer program used to process impedance cardiography data. The cardiodynamic measures derived from impedance cardiography are ventricular stroke column, cardiac output, cardiac index and Heather index. The program digitizes data collected from the Minnesota Impedance Cardiograph, Electrocardiography (ECG), and respiratory cycles and then stores these data on hard disk. It computes the cardiodynamic functions using interactive graphics and stores the means and standard deviations of each 15-sec data epoch on floppy disk. This software was designed on a Digital PRO380 microcomputer and used version 2.0 of P/OS, with (minimally) a 4-channel 16-bit analog/digital (A/D) converter. Applications software is written in FORTRAN 77, and uses Digital's Pro-Tool Kit Real Time Interface Library, CORE Graphic Library, and laboratory routines. Source code can be readily modified to accommodate alternative detection, A/D conversion and interactive graphics. The object code utilizing overlays and multitasking has a maximum of 50 Kbytes.

Cowings, Patricia S.↗

An interactive environment for the analysis of large Earth observation and model data sets

We propose to develop an interactive environment for the analysis of large Earth science observation and model data sets. We will use a standard scientific data storage format and a large capacity (greater than 20 GB) optical disk system for data management; develop libraries for coordinate transformation and regridding of data sets; modify the NCSA X Image and X DataSlice software for typical Earth observation data sets by including map transformations and missing data handling; develop analysis tools for common mathematical and statistical operations; integrate the components described above into a system for the analysis and comparison of observations and model results; and distribute software and documentation to the scientific community.

Bowman, Kenneth P.↗

Noise Exposure Maps of Urban Air Mobility

A noise exposure map is “a scaled geographic depiction of an airport, its noise exposure contours, noise-sensitive facilities, and land uses in the airport surrounding area” developed in accordance with the FAA’s 14 Code of Federal Regulation Part 150. This paper is the first to explore the applicability of airport noise exposure maps to Urban Air Mobility (UAM). The FAA’s airport noise compatibility planning program is first described. Then the applicability of the noise exposure map to Urban Air Mobility (UAM) is explored. Finally, new airspace infrastructure, including vertiport locations and UAM routes from NASA’s UAM engineering simulations, and local noise-sensitive facility locations and land use information were collected and processed to develop the noise exposure maps of UAM near the Dallas-Fort Worth area. The DNL noise contours resulting from a six-passenger electric quadrotor prototype vehicle are predicted using NASA’s AIRNOISEUAM software. The noise exposure maps of UAM are generated automatically using Python’s data analysis and visualization libraries. The results have applications for UAM’s noise compatibility planning, noise-reducing route planning, and vertiport location selection

Urban Air Mobility↗

Noise Exposure Map of Urban Air Mobility

A noise exposure map is “a scaled geographic depiction of an airport, its noise exposure contours, noise-sensitive facilities, and land uses in the airport surrounding area” developed in accordance with the FAA’s 14 Code of Federal Regulation Part 150. This paper is the first to explore the applicability of airport noise exposure maps to Urban Air Mobility (UAM). The FAA’s airport noise compatibility planning program is first described. Then the applicability of the noise exposure map to Urban Air Mobility (UAM) is explored. Finally, new airspace infrastructure, including vertiport locations and UAM routes from NASA’s UAM engineering simulations, and local noise-sensitive facility locations and land use information were collected and processed to develop the noise exposure maps of UAM near the Dallas-Fort Worth area. The DNL noise contours resulting from a six-passenger electric quadrotor prototype vehicle are predicted using NASA’s AIRNOISEUAM software. The noise exposure maps of UAM are generated automatically using Python’s data analysis and visualization libraries. The results have applications for UAM’s noise compatibility planning, noise-reducing route planning, and vertiport location selection. (To hear the voice please utilize the video uploaded to the record)

Urban Air Mobility↗

Current and Future Performance of the CMS Simulation

The CMS full simulation using Geant4 has delivered billions of simulated events for analysis during Runs 1 and 2 of the LHC. However, the HL-LHC dataset will be an order of magnitude larger, with a similar increase in occupancy per event. In addition, the upgraded CMS detector will be considerably more complex, with an extended silicon tracker and a high granularity calorimeter in the endcap region. Increases in conventional computing resources are subject to both technological and budgetary limitations, so novel approaches are needed to improve software efficiency and to take advantage of new architectures and heterogeneous resources. Several projects are in development to address these needs, including the vectorized geometry library Vec-Geom and the GeantV transport engine, which uses track-level parallelization. The current computing performance of the CMS simulation will be presented as a baseline, along with an overview of the various optimizations already available for Geant4. Finally, the progress and outlook for integrating VecGeom and GeantV in the CMS software framework will be discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

HamLib: A Library of Hamiltonians for Benchmarking Quantum Algorithms and Hardware

For a considerable time, large datasets containing problem instances have proven valuable for analyzing computer hardware, software, and algorithms. One notable example of the value of large datasets is ImageNet [1], a vast repository of images that has been instrumental in testing numerous deep learning packages. Similarly, in the domain of computational chemistry and materials science, the availability of extensive datasets such as the Protein Data Bank [2], the Materials Project [3], and QM9 [4] has greatly facilitated the evaluation of new algorithms and software approaches, while also promoting standardization within the field. These well-defined datasets and problem instances, in turn, serve as the foundation for creating benchmarking suites like MLPerf [5] and LINPACK [6], [7]. These suites enable fair and rigorous comparisons of different methodologies and solutions, fostering continuous advancements in various areas of computer science and beyond.

Sawaya, Nicolas PD↗