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DOE OSTI2023

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↗

DOE OSTI2021

TINES - Time Integration, Newton and Eigen Solver v. 1.0

SAND2021-1505 O. TINES is an open source software providing math infrastructure for solving many stiff time ordinary differential equations (ODEs) and/or differential algebraic equations (DAEs) using a batch hierarchical parallelism. The code is written using a parallel programming model (i.e., Kokkos) to future-proof the next generation parallel computing platforms such as GPU accelerators. This code is developed to support Exascale Catalytic Chemistry (ECC) Project. The code provides fundamental math helpers that can aid other research projects. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Kim, Kyungjoo↗

DOE OSTI2017

Wayne—A Simulator for HST WFC3 IR Grism Spectroscopy

Wayne is an algorithm that simulates Hubble Space Telescope Wide Field Camera 3 (WFC3) grism spectroscopic frames, including sources of noise and systematics. It can simulate both staring and spatial scan modes, and observations such as the transit and the eclipse of an exoplanet. Unlike many other instrument simulators, the focus of Wayne is on creating frames with realistic systematics in order to test the effectiveness of different data analysis methods in a variety of different scenarios. This approach is critical for method validation and optimizing observing strategies. In this paper we describe the implementation of Wayne for WFC3 in the near-infrared channel with the G102 and G141 grisms. We compare the simulations to real data obtained for the exoplanet HD 209458b, to verify the accuracy of the simulation. The software is now available as open source at https://github.com/ucl-exoplanets/wayne.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

SCEPTRE 2.3 Quick Start Guide

This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general- purpose C++ code for solving the linear Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates (Sn) and spherical harmonics (Pn). Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Party Libraries (TPL) to be available, and example scripts for building these TPL are provided. The TPL needed by SCEPTRE are Trilinos, Boost, and Netcdf. SCEPTRE uses an autotools build system, and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

SCEPTRE 2.0 Quick Start Guide

This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general purpose C++ code for solving the Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates and spherical harmonics. Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Party Libraries (TPL) to be available, and example scripts for building these TPL's are provided. The TPL's needed by SCEPTRE are Trilinos, boost, and netcdf. SCEPTRE uses an autoconf build system, and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2016

SCEPTRE 1.7 Quick Start Guide

This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general purpose C++ code for solving the Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates and spherical harmonics. Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Party Libraries (TPL) to be available, and example scripts for building these TPL's are provided. The TPL's needed by SCEPTRE are Trilinos, boost, and netcdf. SCEPTRE uses an autoconf build system, and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

SCEPTRE 2.1 Quick Start Guide

This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general purpose C++ code for solving the Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates and spherical harmonics. Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Party Libraries (TPL) to be available, and example scripts for building these TPL's are provided. The TPL's needed by SCEPTRE are Trilinos, boost, and netcdf. SCEPTRE uses an autoconf build system, and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

SCEPTRE 2.2 Quick Start Guide

This report provides a summary of notes for building and running the Sandia Computational Engine for Particle Transport for Radiation Effects (SCEPTRE) code. SCEPTRE is a general- purpose C++ code for solving the li near Boltzmann transport equation in serial or parallel using unstructured spatial finite elements, multigroup energy treatment, and a variety of angular treatments including discrete ordinates and spherical harmonics. Either the first-order form of the Boltzmann equation or one of the second-order forms may be solved. SCEPTRE requires a small number of open-source Third Part y Libraries (TPL) to be available, and example scripts for building these TPLs are provided. The TPLs needed by SCEPTRE are Trilinos, boost, and netcdf. SCEPTRE uses an autotools build system , and a sample configure script is provided. Running the SCEPTRE code requires that the user provide a spatial finite-elements mesh in Exodus format and a cross section library in a format that will be described. SCEPTRE uses an xml-based input, and several examples will be provided.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2024

Making Uintah Performance Portable for Department of Energy Exascale Testbeds

To help ease ports to forthcoming Department of Energy (DOE) exascale systems, testbeds have been made available to select users. These testbeds are helpful for preparing codes to run on the same hardware and similar software as in their respective exascale systems. This paper describes how the Uintah Computational Framework, an open-source asynchronous many-task (AMT) runtime system, has been modified to be performance portable across the DOE Crusher, DOE Polaris, and DOE Sunspot testbeds in preparation for portable simulations across the exascale DOE Frontier and DOE Aurora systems. The Crusher, Polaris, and Sunspot testbeds feature the AMD MI250X, NVIDIA A100, and Intel PVC GPUs, respectively. This performance portability has been made possible by extending Uintah’s intermediate portability layer [18] to additionally support the Kokkos::HIP, Kokkos::OpenMPTarget, and Kokkos::SYCL back-ends. This paper also describes notable updates to Uintah’s support for Kokkos, which were required to make this extension possible. Results are shown for a challenging radiative heat transfer calculation, central to the University of Utah’s predictive boiler simulations. These results demonstrate single-source portability across AMD-, NVIDIA-, and Intel-based GPUs using various Kokkos back-ends.

Holmen, John↗

DOE OSTI2024

MITgcm-AD v2: Open source tangent linear and adjoint modeling framework for the oceans and atmosphere enabled by the Automatic Differentiation tool Tapenade

The Massachusetts Institute of Technology General Circulation Model (MITgcm) is widely used by the climate science community to simulate planetary atmosphere and ocean circulations. A defining feature of the MITgcm is that it has been developed to be compatible with an algorithmic differentiation (AD) tool, TAF, enabling the generation of tangent-linear and adjoint models. These provide gradient information which enables dynamics-based sensitivity and attribution studies, state and parameter estimation, and rigorous uncertainty quantification. Importantly, gradient information is essential for computing comprehensive sensitivities and performing efficient large-scale data assimilation, ensuring that observations collected from satellites and in-situ measuring instruments can be effectively used to optimize a large uncertain control space. As a result, the MITgcm forms the dynamical core of a key data assimilation product employed by the physical oceanography research community: Estimating the Circulation and Climate of the Ocean (ECCO) state estimate. Although MITgcm and ECCO are used extensively within the research community, the AD tool TAF is proprietary and hence inaccessible to a large proportion of these users. The new version 2 (MITgcm-AD v2) framework introduced here is based on the source-to-source AD tool Tapenade, which has recently been open-sourced. Another feature of Tapenade is that it stores required variables by default (instead of recomputing them) which simplifies the implementation of efficient, AD-compatible code. The framework has been integrated with the MITgcm model’s main branch and is now freely available.

Adjoints↗

DOE OSTI2024

Polyglot Framework

Polyglot utilizes a combination of custom and open source tools and libraries to provide developers with a consistent environment for building tools, etc. for a wide variety of targets with minimal changes to the code being built. It supports a variety of architectures and operating systems/firmware in as target-agnostic way as possible. This allows for developers to minimize the amount of time/effort required to port tools—in particular, forensic tools—to a wide variety of targets. The project is comprised of two main components: a frontend toolchain that understands how to utilize other tools in order to build code for a specific target, and a minimalistic C library specific to Polyglot. These collectively provide the method to build code for a specific target, and the capability for code to interact with the underlying operating system when run on the target. Both components are written in a way to minimize the amount of target-specific knowledge required to both develop and utilize the project.

Huddleston, TimothyA.↗

DOE OSTI2024

Polyglot C Library

The C library component of Polyglot. Polyglot utilizes a combination of custom and open source tools and libraries to provide developers with a consistent environment for building tools, etc. for a wide variety of targets with minimal changes to the code being built. It supports a variety of architectures and operating systems/firmware in as target-agnostic way as possible. This allows for developers to minimize the amount of time/effort required to port tools-in particular, forensic tools-to a wide variety of targets. The project is comprised of two main components: a frontend toolchain that understands how to utilize other tools in order to build code for a specific target, and a minimalistic C library specific to Polyglot. These collectively provide the method to build code for a specific target, and the capability for code to interact with the underlying operating system when run on the target. Both components are written in a way to minimize the amount of target-specific knowledge required to both develop and utilize the project.

Huddleston, TimothyA.↗

DOE OSTI2022

Common Information Model for Electromagnetic Transients (CIM for EMT): CRADA 533 [Abstract only}

The control and protection functions of inverter-based resources (IBR) have raised concerns with bulk system reliability. Most of the current interest lies with solar photovoltaic generation but increasing amounts of storage would pose the same risks. Newer North American Electric Reliability Corporation (NERC) guidelines call for electromagnetic transient (EMT) studies of IBR and recommend that transmission operators collect distributed energy resource (DER) data to support such modeling. IEEE Standard P2800.1 is defining tests for model parameterization, so good model data should become available from inverter vendors. (EMT studies also apply to large power transformer reliability, and transformer vendors can provide EMT models.) Utilities don’t currently have the rest of the bulk system represented for EMT studies at large scale. An International Electrotechnical Commission (IEC) standard Common Information Model (CIM) provides a way of supporting these detailed models from physical asset data, e.g., conductors, towers, transformer data sheets, control block diagrams, while avoiding software vendor lock-in. CIM-for-EMT, with proposed schema extensions and open-source converters, provides a way to exchange EMT data between organizations and tools. This project leverages Office of Electricity (OE) funding of CIM-for-EMT code base through the GridAPPS-DTM project, and of GridPACKTM (parallelized transmission solver), for interoperability testing in CIM-for-EMT. The project also leverages partner PGSTech investments in EMTP® interoperability with CIM.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Development of a MOOSE thermal model of the MPC-32 canister and HI-STORM overpack

Nuclear power is a significant source of electricity in the United States, but the average age of nuclear power plants is around 40 years old. Safe management of spent nuclear fuel (SNF) is a key aspect of the back end of the nuclear fuel cycle, and SNF dry storage systems are becoming a popular, effective solution in this area, given the absence of a final disposal system. The spent fuel cask system (dry cask method) provides a feasible solution for maintaining SNF (~60 years) prior to final disposal. This project aims to develop a thermal model of the MPC-32 canister and HI-STORM overpack, using the Multiphysics Object-Oriented Simulation Environment (MOOSE). MOOSE is an open-source framework developed by Idaho National Laboratory (INL) for multiscale, multiphysics simulations. This study will investigate and demonstrate the thermal-hydraulics capabilities of the MOOSE framework, including natural circulation, heat transfer, porous flows, etc. The ultimate goal of the project is to verify whether MOOSE tools (including Pronghorn) can be used to study the thermal performance of the SNF dry cask storage system. This study provides reliable and inclusive solving strategy for dry cask problems. The detailed information about the solving scheme and the governing equations related to the physics of the system is provided in the report. The results for thermal-hydraulic analysis of the HI-STORM system is produced with using open source modules of the MOOSE framework. This results highlights the flexibility and modularity of the MOOSE which makes it a unique candidate for the frameworks and code packages. Therefore, integration of the MOOSE to UNF ST&DARDS will improve the thermal-hydraulic capability of the system while providing distinctive features to users.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Metabolomics (PB-DP5)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Culture samples were collected at 0, 0.5, 1, 2, 4, 6, and 8 hours for extracellular sucrose analysis. Circadian metabolomics data was acquired using a Agilent single quadrupole gas chromatography-mass spectrometer and processed using Agilent Mass Hunter for targeted sucrose quantification. Metabolomic analysis of PCC 7942 light-dark cycle cultures transitioned to constant light revealed distinct temporal patterns in sucrose production. Processed metabolomic datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed GC-MS results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. Processed RNA-Seq datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed RNA-seq results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Sirepo - Warp

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure and widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.

Nagler, Robert↗

DOE OSTI2016

Sirepo - Warp

Nagler, Robert↗