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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2021

AlphaBuilding ResCommunity: A multi-agent virtual testbed for community-level load coordination

Training and validating algorithms in a simulation testbed can accelerate research and applications of optimal control of residential loads to improve energy flexibility and grid resilience. We developed an open-source simulation environment, AlphaBuilding ResCommunity, that can be used to train and validate algorithms to control a single thermostatically controlled load (TCL) or coordinate a group of TCLs. We used reduced-order models to simulate the thermodynamics of TCLs, and the parameter values were determined from the connected smart thermostat data of real households. The environment was built upon the standardized OpenAI Gym interface. Ancillary functions, such as retrieving the parameters and weather forecasts, are provided to facilitate control strategies that require predictive information. Compared with existing efforts, AlphaBuilding ResCommunity has three advantages: (1) more realistic model settings because the parameter values are identified from actual household operating data, and modelling and measurement uncertainty are considered; (2) passive thermal storage control; and (3) ease of use due to a simple software dependency and standardized interface. We demonstrated the applications of the environment by implementing a Kalman Filter and Model Predictive Control on a single TCL and a Priority-Stack-Based Control and Alternating Direction Method of Multipliers to coordinate multiple TCLs for load tracking.

Wang, Z↗

DOE OSTI2023

Standards, dissemination, and best practices in systems biology

In this study, the reproducibility of scientific research is crucial to the success of the scientific method. Here, we review the current best practices when publishing mechanistic models in systems biology. We recommend, where possible, to use software engineering strategies such as testing, verification, validation, documentation, versioning, iterative development, and continuous integration. In addition, adhering to the Findable, Accessible, Interoperable, and Reusable modeling principles allows other scientists to collaborate and build off of each other’s work. Existing standards such as Systems Biology Markup Language, CellML, or Simulation Experiment Description Markup Language can greatly improve the likelihood that a published model is reproducible, especially if such models are deposited in well-established model repositories. Where models are published in executable programming languages, the source code and their data should be published as open-source in public code repositories together with any documentation and testing code. For complex models, we recommend container-based solutions where any software dependencies and the run-time context can be easily replicated.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Reproducibility in materials informatics: lessons from ‘A general-purpose machine learning framework for predicting properties of inorganic materials’

The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open data and open-source tools to propel the field. Despite the increasing usefulness and capabilities of these tools, developers neglecting to follow reproducible practices presents a significant barrier for other researchers looking to use or build upon their work. In this study, we investigate the challenges encountered while attempting to reproduce a section of the results presented in “A general-purpose machine learning framework for predicting properties of inorganic materials.” Our analysis identifies four major categories of challenges: (1) reporting software dependencies, (2) recording and sharing version logs, (3) sequential code organization, and (4) clarifying code references within the manuscript. The result is a proposed set of tangible action items for those aiming to make material informatics tools accessible to, and useful for the community.

36 MATERIALS SCIENCE↗

DOE OSTI2019

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences

Background: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community. Findings: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation–supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP). Conclusions: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

Abstract Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’s primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Scoreboard

Emerging HPC machines have given rise to enhanced compute power that far outstrips the machine's ability to save large scale results for post-processing. To combat this, in situ data analysis techniques are slowly being adopted. With in situ data management favoring workflows composed of multiple simulations and analyses connected in transit on heterogeneous machines, scientists and engineers need a tool that enables them to create data extracts, visualizations, and interactively monitor and steer their simulations. Scoreboard Phase II is a next generation analysis software that supports composite in transit workflows on heterogeneous architectures and restores interactivity to in situ data analysis through simulation monitoring and computational steering. Scoreboard provides a simulation dashboard with graphs of metrics over time, controls for setting custom simulation steering parameters, controls for managing the set of data extracts being produced in the simulation, as well as the ability to explore data extracts, all from a web browser. Realizing the vision outlined in this project required research into making a system that integrates end to end from simulations all the way to the user. In situ tools generally suffer from complexity and excessive software dependencies. Scoreboard, by contrast, is easy to build and integrate into simulation codes and it provides first class FORTRAN support. The Scoreboard library is capable of in situ and in transit data analysis that can produce data extracts commonly needed for Computational Fluid Dynamics (CFD) analysis. Simulations can transparently stage data in transit to a Scoreboard Endpoint program, which can accept their data and produce the requested data extracts. This lets simulations return to their work while the Endpoint works on the analysis. Efficiently staging the data at scale was a topic of this research. Scoreboard provides the means to let the user manage data extracts and monitor/steer many simulations from a web browser. This area of the research focused on discovery of in transit network components to expose and control their steering parameters within an interactive browser-based user interface that includes: system topology, gathered metrics, notifications, dynamically-generated steering controls, and exploration of visualization data products.

Whitlock, BradJoseph [Intelligent Light] (00000001↗

DOE OSTI2020

Python Robust Phase Estimation (PyRPE)

Robust Phase Estimation (RPE) is a quantum algorithm to determine the relative phases of eigenstates of a unitary operator. This code implements the classical portion of the RPE algorithm, useful both in simulation (e.g., Sandia's pyGSTi or IBM's Qiskit simulators) and on actual quantum hardware (e.g., IBM's Qiskit Quantum Experience). It additionally implements improvements in these dependent software packages, for both required core function of the RPE and improved usability. SAND2020-12547 M 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.

Russo, Antonio↗

DOE OSTI2019

Build Guide for the Geophysical Monitoring System (GMS) Common Source Code 2019 Release

This document provides a "Build Guide" for a Generic Runnable System (GRS) of the Geophysical Monitoring Systems (GMS) common source code. This guide includes a list of software dependencies and licenses, hardware specifications, and instructions for how to build the system from the source code. The document is written for individuals who are experienced as administrators of Linux systems.

58 GEOSCIENCES↗

DOE OSTI2019

Preliminary Build Guide for the Geophysical Monitoring Systems Common Source Code. 2019 Release

The purpose of this document to provide an advance copy of a "Build Guide" for a Generic Runnable System (GRS) of the Geophysical Monitoring Systems' (GMS) common source code. This guide includes a list of software dependencies and licenses, hardware specifications, and related instructions for how to build the system from the source code. The document is written for individuals who are experienced as administrators of Linux systems. The intention is to support preparation activities prior to the open source release so that dependencies may be in place to build and run the system. This document will be updated and provided with the open source release on GitHub, accompanied by a "Run Guide" for the system. An additional "Configuration Guide" will also be provided after the open source release so that users may explore system configuration options.

58 GEOSCIENCES↗

DOE OSTI2021

VC3: Virtual Clusters for Community Computation (Final Technical Report)

A traditional HPC computing facility provides a large amount of computing power but has a fixed environment designed to satisfy local needs. This makes it very challenging for users to deploy complex applications that span multiple sites and require specific application software, scheduling middleware, or sharing policies. This project addressed many of these challenges by making it possible for researchers to easily aggregate and share resources, install custom software environments, and deploy clustering frameworks across multiple HPC facilities through the concept of “virtual clusters”. We designed and implemented a prototype virtual cluster facility that enabled unprivileged users to create dynamic aggregations of computing power across multiple sites, deployed with custom middleware and complex software dependencies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

External Release of Organic Scintillator DRiFT Software - Technology Evaluation and Demonstration Project Accomplishments [Slides]

Overview and Objectives: DRiFT post processes radiation transport output from MCNP, and generates realistic nuclear instrumentation response; Organic scintillator response has been developed, tested, and validated with measurements, these instruments are widely used in nuclear safeguards. At the beginning of this project, DRiFT was only available to LANL employees with access to yellow High Performance Computing clusters. Additionally, there are many complicated external software dependencies. Our TED project request proposed using funds to: Comment and clean up code, friendly testing, generating test suites and examples; Expansion of scintillator types natively supported by DRiFT; External release of DRiFT accompanied by documentation. We accomplished all objectives (and many others), they are highlighted in these slides.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

VC3: Virtual Clusters for Community Computation

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1983

Transient upset models in computer systems

Essential factors for the design of transient upset monitors for computers are discussed. The upset is a system level event that is software dependent. It can occur in the program flow, the opcode set, the opcode address domain, the read address domain, and the write address domain. Most upsets are in the program flow. It is shown that simple, external monitors functioning transparently relative to the system operations can be built if a detailed accounting is made of the characteristics of the faults that can happen. Sample applications are provided for different states of the Z-80 and 8085 based system.

Mason, G. M.↗

NASA NTRS1989

Laboratory test methodology for evaluating the effects of electromagnetic disturbances on fault-tolerant control systems

Control systems for advanced aircraft, especially those with relaxed static stability, will be critical to flight and will, therefore, have very high reliability specifications which must be met for adverse as well as nominal operating conditions. Adverse conditions can result from electromagnetic disturbances caused by lightning, high energy radio frequency transmitters, and nuclear electromagnetic pulses. Tools and techniques must be developed to verify the integrity of the control system in adverse operating conditions. The most difficult and illusive perturbations to computer based control systems caused by an electromagnetic environment (EME) are functional error modes that involve no component damage. These error modes are collectively known as upset, can occur simultaneously in all of the channels of a redundant control system, and are software dependent. A methodology is presented for performing upset tests on a multichannel control system and considerations are discussed for the design of upset tests to be conducted in the lab on fault tolerant control systems operating in a closed loop with a simulated plant.

Belcastro, Celeste M.↗

NASA NTRS1989

Real-time closed-loop simulation and upset evaluation of control systems in harsh electromagnetic environments

Digital control systems for applications such as aircraft avionics and multibody systems must maintain adequate control integrity in adverse as well as nominal operating conditions. For example, control systems for advanced aircraft, and especially those with relaxed static stability, will be critical to flight and will, therefore, have very high reliability specifications which must be met regardless of operating conditions. In addition, multibody systems such as robotic manipulators performing critical functions must have control systems capable of robust performance in any operating environment in order to complete the assigned task reliably. Severe operating conditions for electronic control systems can result from electromagnetic disturbances caused by lightning, high energy radio frequency (HERF) transmitters, and nuclear electromagnetic pulses (NEMP). For this reason, techniques must be developed to evaluate the integrity of the control system in adverse operating environments. The most difficult and illusive perturbations to computer-based control systems that can be caused by an electromagnetic environment (EME) are functional error modes that involve no component damage. These error modes are collectively known as upset, can occur simultaneously in all of the channels of a redundant control system, and are software dependent. Upset studies performed to date have not addressed the assessment of fault tolerant systems and do not involve the evaluation of a control system operating in a closed-loop with the plant. A methodology for performing a real-time simulation of the closed-loop dynamics of a fault tolerant control system with a simulated plant operating in an electromagnetically harsh environment is presented. In particular, considerations for performing upset tests on the controller are discussed. Some of these considerations are the generation and coupling of analog signals representative of electromagnetic disturbances to a control system under test, analog data acquisition, and digital data acquisition from fault tolerant systems. In addition, a case study of an upset test methodology for a fault tolerant electromagnetic aircraft engine control system is presented.

Belcastro, Celeste M.↗

NASA NTRS1991

The Land Analysis System (LAS)

The Land Analysis System (LAS) is an interactive software system, available in the public domain, for the analysis, display, and management of multispectral and other digital image data. The system was developed to support earth sciences research and development activities. LAS provides over 240 applications functions and utilities, a flexible user interface, complete on-line and hardcopy documentation, extensive image data file management, reformatting, and conversion utilities, and high level device independent access to image display hardware. The capabilities are summarized of the latest release of the system (version 5). Emphasis is given to the system portability and the isolation of hardware and software dependencies in this release.

Lu, Yun-Chi↗

NASA NTRS1991

Technology readiness assessment of advanced space engine integrated controls and health monitoring

An evaluation is given for an integrated control and health-monitoring (ICHM) system that is designed to be used with hydrogen-oxygen rocket engines. The minimum required ICHM functions, system elements, technology readiness, and system cost are assessed for a system which permits the operation of H-O engines that are space-based, reusable, and descent-throttleable. Only the advanced sensors and some engine-dependent software are not found to be ready for applications to laboratory demonstration. Other systems related to the minimum functions are more developed, bringing the total system readiness to the conceptual design stage. Based on the evaluation of the H-O ICHM, it is estimated that the minimum system requirements for demonstration on an engine system testbed will require an investment of 30-45 million dollars over 6 years.

Millis, Marc G.↗

NASA NTRS1991

Formulation of a strategy for monitoring control integrity in critical digital control systems

Advanced aircraft will require flight critical computer systems for stability augmentation as well as guidance and control that must perform reliably in adverse, as well as nominal, operating environments. Digital system upset is a functional error mode that can occur in electromagnetically harsh environments, involves no component damage, can occur simultaneously in all channels of a redundant control computer, and is software dependent. A strategy is presented for dynamic upset detection to be used in the evaluation of critical digital controllers during the design and/or validation phases of development. Critical controllers must be able to be used in adverse environments that result from disturbances caused by an electromagnetic source such as lightning, high intensity radiated field (HIRF), and nuclear electromagnetic pulses (NEMP). The upset detection strategy presented provides dynamic monitoring of a given control computer for degraded functional integrity that can result from redundancy management errors and control command calculation error that could occur in an electromagnetically harsh operating environment. The use is discussed of Kalman filtering, data fusion, and decision theory in monitoring a given digital controller for control calculation errors, redundancy management errors, and control effectiveness.

Belcastro, Celeste M.↗