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DOE OSTI2023

Towards a Software Development Framework for Interconnected Science Ecosystems

The innovative science of the future must be multi-domain and interconnected to usher in the next generation of “self-driving” laboratories enabling consequential discoveries and transformative inventions. Such a disparate and interconnected ecosystem of scientific instruments will need to evolve using a system-of-systems (SoS) approach. The key to enabling application integration with such an SoS will be the use of Software Development Kits (SDKs). Currently, SDKs facilitate scientific research breakthroughs via algorithmic automation, databases and storage, optimization and structure, pervasive environmental monitoring, among others. However, existing SDKs lack instrument-interoperability and reusability capabilities, do not effectively work in an open federated architectural environment, and are largely isolated within silos of the respective scientific disciplines. Inspired by the scalable SoS framework, this work proposes the development of INTERSECT-SDK to provide a coherent environment for multi-domain scientific applications to benefit from the open federated architecture in an interconnected ecosystem of instruments. This approach will decompose functionality into loosely coupled software services for interoperability among several solutions that do not scale beyond a single domain and/or application. Furthermore, the proposed environment will allow operational and managerial inter-dependence while providing opportunities for the researchers to reuse software components from other domains and build universal solution libraries. We demonstrate this research for microscopy use-case, where we show how INTERSECT-SDK is developing the tools necessary to enable advanced scanning methods and accelerate scientific discovery.

Malviya, Addi Thakur↗

DOE OSTI2020

Refreshing Waste Tracking Software for the 2020's - 20059

The Waste Compliance and Tracking System (WCATS) is a software application designed to manage waste operations from cradle to grave. The system provides the support needed for characterization, generation, processing, and shipment of all waste generated or stored at Los Alamos National Laboratory (LANL). Waste is tracked with task records for containers in real-time via both desktop and mobile device applications. The software allows application administrators to configure sites with appropriate limits for Pu-239 equivalent Curies (PE-Ci), fissile gram equivalents (FGEs), volume limits, as well as custom limits for site-specific technical safety requirements (TSRs). WCATS was developed based on a need at Los Alamos National Laboratory for a modern, customizable waste tracking system that could support many different waste types. The application is built using Oracle{sup R} database and Oracle{sup R} ADF Swing application framework. The technologies and software frameworks selected for the system were finalized in 2006. Although Oracle{sup R} Database has proven to be robust, the user interface and application framework interface with the database have been deprecated and need to be replaced. The technologies selected for modernization follow the open-source model, which allows the WCATS team to more easily recruit developers, improve the speed of development, and ease the deployment and adoption of the system. The tools that support the re-engineering effort are Vue.js{sup R}, a JavaScript{sup R} framework, and Spring Boot{sup R}, an API (application programming interface) development tool written in Java{sup R}. An API allows for simplified communication from the database to the user interface of the application. In addition, legacy Crystal Reports{sup R} will be replaced with reports developed with the open source Pentaho{sup TM}f Report Designer community edition. Because the application uses HTML and JavaScript{sup R}, it builds upon tools that have been used for many years in web development. These tools have large community support and their proven track record will ensure that enhancements to WCATS can continue for years to come. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

DevOps Pragmatic Practices and Potential Perils in Scientific Software Development

The DevOps movement, which aims to accelerate the continuous delivery of high-quality software, has taken a leading role in reshaping the software industry. Likewise, there is growing interest in applying DevOps tools and practices in the domains of computational science and engineering (CSE) to meet the ever-growing demand for scalable simulation and analysis. Translating insights from industry to research computing, however, remains an ongoing challenge; DevOps for science and engineering demands adaptation and innovation in those tools and practices. There is a need to better understand the challenges faced by DevOps practitioners in CSE contexts in bridging this divide. To that end, we conducted a participatory action research study to collect and analyze the experiences of DevOps practitioners at a major US national laboratory through the use of storytelling techniques. We share lessons learned and present opportunities for future investigation into DevOps practice in the CSE domain.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

P SI4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4 's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. We announce a rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Insights From the Software Design of a Multiphysics Multicomponent Scientific Code

Using simulations for scientific discovery requires that the software used in the simulations undergoes a rigorous design and development process similar to that of the lab instruments in the experimental sciences. To devise a good design methodology, it is critical to understand the requirements, constraints, and challenges. Furthermore, this article describes insights from the long-term stewardship of a multiphysics multicomponent software, FLASH, that was designed more than 20 years ago for astrophysics, now serves multiple communities, and has been successful in adapting to the changing world of high-performance computing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Software Architecture and Hardware Organization in Mu2e Solenoid Field Mapping System

Herein, the Mu2e field mapping system is designed to produce high accuracy field maps of the detector solenoid used in the experiment. The data acquisition system is mobile and uses a self-propelled mapper with rotating arms equipped with 3D Hall probes. The measurements require not only accurate magnetic field readouts, but also accurate locations of all Hall probes while measuring data. The latter is accomplished by using the laser tracker to measure positions of several retroreflectors on the field mapper during data acquisition. The measurement process requires scanning the whole space inside the large solenoid and takes many hours to complete, which necessitates its full automation. The automation software includes control of the mapper, readout of Hall and NMR probes and control of a laser tracker, including prediction of retroreflector positions and execution of quality control checks. The software architecture and data acquisition hardware of the field mapping system are described, with special attention given to control of the laser tracker and its integration with the rest of the system.

3d hall probes↗

DOE OSTI2020

Assessment of Survey Results from Advanced Reactor Industry Domain Experts on Nonlinear Soil-Structure Interaction Analysis Software Verification and Validation

The seismic load case has a significant impact on the design and cost of nuclear power plants. Given the need to substantially reduce cost, advanced reactor designers are looking to leverage numerical tools that enable seismic analysis of an integrated vessel/support/structure/soil system. Modern nonlinear analysis tools provide a solution, capturing dynamic coupling between components (including soil-structure interaction (SSI)) concurrent with nonlinear behavior in one or more parts of the system. Although these methods have a rich history of technical development and implementation, software quality assurance (SQA) following nuclear industry standards remains a significant burden for those wishing to adopt such methods for advanced reactor design and licensing. To reduce the SQA burden, this project will develop the guidance for SQA verification and validation (V&V) of coupled nonlinear SSI analysis tools, to include a test matrix of software features and test problems to support commercial grade dedication (CGD). The guidance is intended to be technology-neutral: supporting designers of all advanced reactors. To maximize the value of the project to reactor designers, the project team performed focused surveys of and interviews with advanced reactor designers. Additionally, the project surveyed members of the broader industry involved in reactor design and licensing. The aggregated industry feedback consists of written survey responses, live polling responses, focused interviews, and informal feedback provided after outreach presentations, collectively referred to as “survey results”. Herein, the survey results are reported, reviewed, and assessed to inform follow-on project activities. The survey results confirmed the familiarity of the industry with the coupled nonlinear SSI analysis. They also affirm the project need based upon the expressed intent to (1) incorporate nonlinear features and (2) pursue the coupled nonlinear SSI analysis to reduce seismic demands and construction costs. All reactor designers indicated their intent to incorporate two or more nonlinear features, and all reactor designer respondents opined that the coupled nonlinear SSI analysis would allow for the optimization of the reactor design and construction. However, the programmatic challenges, whether real or perceived, present a significant barrier to reactor designers. The barrier most commonly identified by the reactor designer population was regulatory risk, with 70% citing this as a reason not to pursue the approach. The perceived regulatory risk identified by the reactor designers underscores the importance of regulator engagement and dialogue in this project. Additionally, half of the reactor designers identified cost and lack of guidance as a deterrent. The survey results also provide insights to tailor specific aspects of the guidance document and test matrix. The project plans to prepare both a formal referenceable guidance document and a collaborative, web-based test matrix and problem set. The project will focus on more complete test problem definitions for the prioritized nonlinear features over shallower problem descriptions for a larger set of features. The nonlinearities prioritized as high based upon survey feedback include fluid-structure interaction and seismic isolation and energy dissipation devices. The nonlinearities prioritized as intermediate include nonlinear geomaterials, nonlinear concrete, nonlinear steel, and interface/contact nonlinearity. Deep embedment and the associated nonlinear phenomena are assigned the lowest priority based upon survey feedback.

42 ENGINEERING↗

DOE OSTI2024

User-Centered Software Design in the All Hazards Analysis Application

To design good software, you must always keep the end user in mind. Some benefits of incorporating the user-centered design process include saving users time and effort and helping them to utilize all capabilites of an application. In my work on the All Hazards Analysis (AHA) application, I employed principles of user-centered design to make the application easier for new users to navigate. This poster describes user-centered software design in general and showcases some of my user-centered design work on the AHA application.

58 GEOSCIENCES↗

DOE OSTI2022

A Common Tracking Software Project

Abstract The reconstruction of the trajectories of charged particles, or track reconstruction, is a key computational challenge for particle and nuclear physics experiments. While the tuning of track reconstruction algorithms can depend strongly on details of the detector geometry, the algorithms currently in use by experiments share many common features. At the same time, the intense environment of the High-Luminosity LHC accelerator and other future experiments is expected to put even greater computational stress on track reconstruction software, motivating the development of more performant algorithms. We present here A Common Tracking Software (ACTS) toolkit, which draws on the experience with track reconstruction algorithms in the ATLAS experiment and presents them in an experiment-independent and framework-independent toolkit. It provides a set of high-level track reconstruction tools which are agnostic to the details of the detection technologies and magnetic field configuration and tested for strict thread-safety to support multi-threaded event processing. We discuss the conceptual design and technical implementation of ACTS, selected applications and performance of ACTS, and the lessons learned.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Software stewardship and advancement of a high-performance computing scientific application: QMCPACK

Here, we provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions own runners, and NVIDIA and AMD GPUs used in pre-exascale systems, (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the stewardship and advancement of community HPC codes to enable scientific discovery at scale.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Robust framework and software implementation for fast speciation mapping

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. In this work, several authors have used different multivariate data processing strategies to establish speciation maps. Furthermore, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. Additionally, the algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Implementing a Hardware Testbed Using 3-Level ANPC Software Defined Inverters for Fault Analysis of a Transmission Network

In this paper, we propose the implementation of a hardware testbed using 3-level active neutral point clamped (ANPC) software-defined inverters for fault analysis. A test case transmission network equipped with two grid forming (GFM) inverters and four resistive loads is considered in this research. Firstly, grid forming control laws including PI feedback control and droop control are implemented to operate the inverters in parallel. Then, we implement a fault ride-through (FRT) logic and perform a simulation of the test system by applying a three-phase fault. Simulation results show the effectiveness of the fault recovery algorithm upon clearance of the fault. Finally, a 3-level ANPC software-defined inverter is programmed with required control laws and characterized through various lab experiments.

3-level ANPC inverter↗

DOE OSTI2026

DISARM: Target Electronic Device Informed Mitigation of Software Runtime Side-Channel Vulnerabilities

Program runtime/timing attacks exploit variations in a program’s execution times to extract sensitive information from the program (e.g. encryption keys, sensitive variable data, intellectual property). State-of-the-art solutions to runtime side-channel attacks attempt to balance the execution time of the sensitive code for different control flow paths to eliminate the timing leakage. However, during the mitigation process, most techniques do not consider the underlying hardware/device on which the target program is supposed to run on. This can lead to over-fixing (unnecessary extra operations), under-fixing (not solving the imbalance properly), and even failures. Here, we propose DISARM, a joint hardware-software methodology (unlike any existing solution) for mitigating runtime side-channel vulnerabilities that utilizes timing values from real embedded devices to generate targeted software fixes. We implement DISARM to support C/C++/Java source codes and validate it across 22 standard benchmarks. DISARM outperforms state-of-the-art solutions such as PENDULUM and DifFuzzaR in terms of execution time overhead, code size overhead, and correctness on five different embedded/edge devices.

Timing/runtime side-channel↗

DOE OSTI2022

RUScal : Software for the analysis of resonant ultrasound spectroscopy measurements

Resonant ultrasound spectroscopy is used to nondestructively measure the elastic resonances of small solids to elucidate the material's elastic properties or other qualities like size, shape, or composition. In this work, we introduce the software RUScal for the purpose of determining elastic properties by analyzing the eigenfrequencies of solid specimens with common shapes, such as rectangular parallelepipeds, cylinders (solid and hollow tube), ellipsoids, and octahedrons, as well as irregularly shaped ellipsoids that can be described analytically. All symmetry classes are supported, from isotropic to triclinic, along with the option to add or remove up to three orthogonal mirror planes as well as the ability to reorient the crystal axes with respect the sample edges via Euler angles. Additional features include tools to help find initial sets of elastic constants, including grid exploration and Monte Carlo methods, a tool to analyze frequencies as a function of sample length or crystal orientation, an error analysis tool to assess fit quality, and formatting of the input and output files for batch fitting, e.g., as a function of temperature. This software was validated with published resonant ultrasound spectroscopy data for various materials, shapes, and symmetries with noted improvements in calculation time compared to finite element methods.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Using Neural Architecture Search for Improving Software Flaw Detection in Multimodal Deep Learning Models

Software flaw detection using multimodal deep learning models has been demonstrated as a very competitive approach on benchmark problems. In this work, we demonstrate that even better performance can be achieved using neural architecture search (NAS) combined with multimodal learning models. We adapt a NAS framework aimed at investigating image classification to the problem of software flaw detection and demonstrate improved results on the Juliet Test Suite, a popular benchmarking data set for measuring performance of machine learning models in this problem domain.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Software-defined Networking for Energy Delivery Systems (SDN4EDS): An Architectural Blueprint (Final Report)

This is the initial version of a reference for suppliers and energy companies of all sizes to deploy networks based on software-defined networking technology (SDN) to improve reliability, reduce cyber security attack surface, and facilitate mitigation of adversarial behavior. It is a living document and will progress over the life cycle of the Software-Defined Networking for Energy Delivery Systems (SDN4EDS) project. Version 2 of this report provides information on the Red Team tabletop assessment performed against the initial reference architecture. Version 3 of this report updates the reference architecture with lessons learned from the Red Team tabletop assessment, as well as provides additional details for the use cases. It also provides information on the decision process that could be used by an organization when considering deploying SDN in their environment. The final version of this report consolidates all the interim reports generated by the project into a final report. It also draws from PNNL’s experience in deploying SDN to make recommendations on how SDN could be deployed in a utility environment, and provides rationale for those decisions allowing individual utilities to make risk-based and knowledge-based decisions on how to best deploy SDN in their own environment

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Software-defined Networking for Energy Delivery Systems (SDN4EDS): An Architectural Blueprint (Final Summary Report)

97 MATHEMATICS AND COMPUTING↗