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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Open Source Platform for Live Processing of High Data Rate Electron Microscopy (SBIR Phase I Award Topic 15, Subtopic B, Final Scientific / Technical Report)

4D scanning transmission electron microscopy (STEM) is experiencing a revolution both in terms of data size, and data veracity, as are many other areas of experimental data acquisition. This presents enormous opportunities to make new scientific discoveries, but is also hamstrung by aging software that is no longer fit for purpose. Experimental data acquisition platforms must make the same investments in software infrastructure that the simulation community made decades ago to take advantage of high-performance computing (HPC) if they hope to realize the full potential of the latest advances made in detector technology. This requires rethinking the design and deployment of hardware, moving away from small, fixed commodity computing capabilities with closed interfaces to open, modular, scalable systems designed for parallelism and throughput. The technical approach will leverage best-in-class open source technologies, and develop new approaches strategically to build an open source platform for experimental data acquisition targeting high data rate electron microscopy. The project will develop a software platform that uses the power and performance of modern HPC resources to ingest the large volume of data produced by electron microscopes using direct electron detectors. A set of configurable pipelines will be used to enable the processing to be tailored to the problem being investigated with builtin visualization of data at interactive rates. This project will leverage investments made by the DOE and other agencies to provide a powerful software platform for the experimental data community working with most powerful electron microscopes, such as 4D STEM detectors. It will create a platform that serves as a reference for the community. Permissive open source licensing will make the platform available to all, with a simple deployment strategy offering the ability to keep data close to where it is generated. This advanced software platform will require customization for each deployment, creating opportunities for software services that are typically offered to extend open source software platforms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

TACPLUS-DO-AUTH

SF-23-084 This software provides enhanced authorization and access control support to be used in tandem with the open source Terminal Access Controller Access Control System (TACACS+) software tac_plus; providing Authentication, Authorization and Auditing (AAA) capabilities for networking devices.

WEST, GABRIALA↗
DOE OSTI2026

BASIN-3D Data Integration for Selected ARM Data Field Campaign Report

The purpose of this data services request was to demonstrate integration of the Atmospheric Radiation Measurement (ARM) User Facility’s “met” datastreams with time series data from other earth science data sources using the BASIN-3D data synthesis software tool. BASIN-3D is an open-source Python library that enables researchers to integrate data across configured public and private data sources. It provides a common query language for researchers to request measurement locations and time series data based on specified locations, variables, time period, statistics, aggregation, and data quality. BASIN-3D acquires the data that match the query from each configured data source and translates the results into harmonized vocabularies, thus reducing researchers' data-wrangling effort. In addition, because the queries are executed on demand, researchers can easily regenerate their synthesized data sets as new data and/or data updates become available, eliminating one-off data products. BASIN-3D can output data using a variety of different data structures for end-user applications including Python pandas data frames and hdf5 output formats.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A Survey of Multizone Airflow Simulation Software

H-Canyon simulates the building and process ventilation to ensure positive contamination control for any modifications as well as evaluating off-normal conditions. Simulations can also be used to identify air quality of personnel occupied areas. The models can be classified into two groups, single and multi-zone models. As the name states, a single zone model assumes that the building can be described by a single, well-mixed zone. Whereas large buildings have structures that must be described as multizone. Multizone airflow models deal with the difficulty of flows in a building by distinguishing the effects of internal flow restrictions. Several models have been developed that take internal partitions into account. CONTAM (currently used) is a multizone airflow program created by NIST to determine airflows including infiltration, exfiltration, wind pressures acting outside the building, buoyancy effects caused by the indoor and outdoor air temperature difference. COMIS is a multizone air infiltration, ventilation, and contaminant transport model that was developed at Lawrence Berkeley National Laboratory. COMIS deals with applied pressure distribution, airflow components, HVAC systems, schedules, and contaminant transport. EnergyPlus is designed by DOE. It supports flexible component level configuration of HVAC models and simulates sub-hourly time steps to control fast dynamic systems. The program features include providing accurate environmental performance data including energy consumption and carbon emissions, and reporting solar gains on surfaces. Heavent is used to model industrial ventilation systems to control airborne contaminants. It's designed based on the American Conference of Governmental Industrial Hygienists (ACGIH) Ventilation manual. DesignBuilder is the most recognized and advanced user interface to EnergyPlus. It gives access to all of the most frequently required simulation capabilities covering building fabric, thermal mass, glazing, shading renewables, and HVAC analysis. The objective of this study is to identify all relevant software available including commercially licensed, freely licensed, and open source, that can be used to simulate large, complex process facility ventilation systems. All discovered software tools are evaluated for salient features and compared to the software tool currently used to simulate the H-Canyon ventilation system. The design criteria of a ventilation system has two basic requirements: Supplying fresh air for the occupants and changing the air in the room sufficiently; therefore, the smells, fumes, and contaminants will be removed. In this study, first, whether the software simulates airflow (infiltration, natural ventilation, and interzonal) or considers them to be inputs is discussed. Second, if indoor contaminant levels are considered; and finally suggestions on how airflow analysis can be more appropriately accounted for when performing airflow simulation of a building. All of the airflow software reviewed for this study can account for constant infiltration and natural ventilation rates that are not affected by changes in indoor and outdoor conditions. Modelling infiltration in EnergyPlus or DesignBuilder are applicable for small buildings and not appropriate for larger buildings like the H-Canyon. The effect of wind on external pressures, infiltration, and natural and mechanical ventilation, can also be calculated using all of these software. These programs have control options to switch between natural to mechanical ventilation modes or both (hybrid). Interzonal airflow can be applied which means one zone can be specified to receive a fixed amount of air from another zone. The following ventilation modeling software is recommended for further testing: CONTAM, COMIS, Heavent. The next step in evaluating the software will consist of creating test facility simulations using evaluation copies of the software.

42 ENGINEERING↗
DOE OSTI2018

The TENNLab Exploratory Neuromorphic Computing Framework

Spiking, neuromorphic computing systems are in a period of active exploration by the computing community. While they feature computational expressiveness beyond both von Neumann computing models and feed-forward neural networks, they are also challenging to design and program. The TENNLab exploratory neuromorphic computing framework is a software infrastructure, soon to be open-source, whose goal is to enable potential users of spiking, neuromorphic computing systems to develop applications and evaluate computing architectures, and for architecture researchers to develop and evaluate their architectures with a variety of applications. In this letter, we present the software architecture of the TENNLab framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Framework for Analysis and Visualization of Simulation Data (VizAly)

As supercomputing resources increase, cosmological scientists are able to run more detailed and larger simulations generating massive amounts of data. Analyzing these simulations with an available open-source toolkit is important for collaborative Department of Energy scientific discovery across labs, universities, and other partners. Developed software as a part of this collection include: comparing data with other existing simulations, verifying and validating results with observation databases, new halo finder algorithms, and using analytical tools to get insights into the physics of the cosmological universe. The goal of this software project is to provide a set of open-source libraries, tools, and packages for large-scale cosmology that allows scientists to visualize, analyze, and compare large-scale simulation and observational data sets. Developed software will provide a variety of methods for processing, visualization, and analysis of astronomical observation and cosmological simulation data. These tools are intended for deployment on multiple scientific computing platforms, including but not limited to personal computers, cloud computing, experimental sites (telescopes) and high performance supercomputers.

Wendelberger, Joanne↗
DOE OSTI2018

Alternative Database Designs for the Distribution Common Information Model

The distribution Common Information Model (CIM) offers a means for interoperable distribution system applications. Adoption has been slow in part because of the steep learning curve, and the mismatch between CIM’s object-oriented schema and widely-used relational database schemas. We evaluated alternative database technologies, and tested a triple-store database with SPARQL queries on a set of IEEE distribution test feeders. These alternative queries were much simpler to design and use, so they should help lower one of the important barriers to CIM adoption. An open-source platform has been provided for other developers to work with CIM in this way. One use case is to more rapidly develop interoperable ADMS and DERMS applications. Another use case is to convert feeder models between commercial CIM-compliant products and research software like GridLAB-D and OpenDSS.

lenses, computational modeling, relational databas↗
DOE OSTI2023

PyFLEXTRKR: a flexible feature tracking Python software for convective cloud analysis

Abstract. This paper describes the new open-source framework PyFLEXTRKR (Python FLEXible object TRacKeR), a flexible atmospheric feature tracking software package with specific capabilities to track convective clouds from a variety of observations and model simulations. This software can track any atmospheric 2D objects and handle merging and splitting explicitly. The package has a collection of multi-object identification algorithms, scalable parallelization options, and has been optimized for large datasets including global high-resolution data. We demonstrate applications of PyFLEXTRKR on tracking individual deep convective cells and mesoscale convective systems from observations and model simulations ranging from large-eddy resolving (∼100s m) to mesoscale (∼10s km) resolutions. Visualization, post-processing, and statistical analysis tools are included in the package. New Lagrangian analyses of convective clouds produced by PyFLEXTRKR applicable to a wide range of datasets and scales facilitate advanced model evaluation and development efforts as well as scientific discovery.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Continuous integration for concurrent MOOSE framework and application development on GitHub

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Several specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A reusable neural network pipeline for unidirectional fiber segmentation

Abstract Fiber-reinforced ceramic-matrix composites are advanced, temperature resistant materials with applications in aerospace engineering. Their analysis involves the detection and separation of fibers, embedded in a fiber bed, from an imaged sample. Currently, this is mostly done using semi-supervised techniques. Here, we present an open, automated computational pipeline to detect fibers from a tomographically reconstructed X-ray volume. We apply our pipeline to a non-trivial dataset by Larson et al . To separate the fibers in these samples, we tested four different architectures of convolutional neural networks. When comparing our neural network approach to a semi-supervised one, we obtained Dice and Matthews coefficients reaching up to 98%, showing that these automated approaches can match human-supervised methods, in some cases separating fibers that human-curated algorithms could not find. The software written for this project is open source, released under a permissive license, and can be freely adapted and re-used in other domains.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Data systems for the Linac coherent light source

Abstract The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

COMPOSE-HPC: Software Composition for Extreme Scale Computational Science and Engineering

Software composition is an important aspect of computational science software engineering due to large scale production science codes involving multiple programming languages, execution and concurrency models. To date, programmers must manage the complexity of building and maintaining such systems largely by hand with minimal (if any) automated assistance. As such, a great deal of programmer time is spent generating and maintaining code which leads to a high maintenance and development cost, as well as an increased risk of errors being introduced by hand than would be expected in an automated system. COMPOSE-HPC was a multi-institutional effort, with the Galois contribution focused on a specific area of code analysis and software infrastructure. Specifically, Galois led the design and implementation for the Parser for Annotations in a User-specified Language (PAUL), as well as collaborating with SNL and LLNL on the Retargetable Open Transformation Engine (ROTE). Both components were built on top of the ROSE compiler infrastructure from LLNL. All artifacts developed under the COMPOSE-HPC program are available on the github.com and sourceforge.net open source hosting sites under permissive BSD3 software licenses.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Bridging Python to Silicon: The SODA Toolchain

Systems performing scientific computing, data analysis, and machine learning tasks have a growing demand for application-specific accelerators that can provide high computational performance while meeting strict size and power requirements. However, the algorithms and applications that need to be accelerated are evolving at a rate that is incompatible with manual design processes based on hardware description languages. Agile hardware design tools based on compiler techniques can help by quickly producing an application-specific integrated circuit (ASIC) accelerator starting from a high-level algorithmic description. Here, we present the software-defined accelerator (SODA) synthesizer, a modular and open-source hardware compiler that provides automated end-to-end synthesis from high-level software frameworks to ASIC implementation, relying on multilevel representations to progressively lower and optimize the input code. Our approach does not require the application developer to write any register-transfer level code, and it is able to reach up to 364 giga floating point operations per second (GFLOPS)/W efficiency (32-bit precision) on typical convolutional neural network operators.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Real-time Distribution Simulation and Application Development for Power Systems Education

To help bridge the gap between traditional power system engineering instruction and emerging industry needs, a new set of classroom and research tools are needed. Real-time simulation tools emulating power system control room software present an opportunity to introduce students to the array of operational considerations, technical challenges, and decision-making associated with power system operations. The GridAPPS-D platform is proposed to support coursework and academic research as it provides an open-source platform for simulation, application development, and software integration. The GridAPPS-D platform, simulation capabilities, development environment, and interactive training are discussed in the context of lessons-learned from implementation for undergraduate and graduate students in the US and India. A series of potential GridAPPS-D supported academic capabilities are introduced.

Active distribution networks, open educational res↗
DOE OSTI2014

FOX: A Fault Oblivious Extreme-Scale Execution Environment

The FOX project, funded under the ASCR X-stack I program, developed systems software and runtime libraries for a new approach to the data and work distribution for massively parallel, fault oblivious application execution. Our work was motivated by the premise that exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today’s machines. To deliver the capability of exascale hardware, the systems software must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massive data analysis in a highly unreliable hardware environment with billions of threads of execution. Our OS research has prototyped new methods to provide efficient resource sharing, synchronization, and protection in a many-core compute node. We have experimented with alternative task/dataflow programming models and shown scalability in some cases to hundreds of thousands of cores. Much of our software is in active development through open source projects. Concepts from FOX are being pursued in next generation exascale operating systems. Our OS work focused on adaptive, application tailored OS services optimized for multi → many core processors. We developed a new operating system NIX that supports role-based allocation of cores to processes which was released to open source. We contributed to the IBM FusedOS project, which promoted the concept of latency-optimized and throughput-optimized cores. We built a task queue library based on distributed, fault tolerant key-value store and identified scaling issues. A second fault tolerant task parallel library was developed, based on the Linda tuple space model, that used low level interconnect primitives for optimized communication. We designed fault tolerance mechanisms for task parallel computations employing work stealing for load balancing that scaled to the largest existing supercomputers. Finally, we implemented the Elastic Building Blocks runtime, a library to manage object-oriented distributed software components. To support the research, we won two INCITE awards for time on Intrepid (BG/P) and Mira (BG/Q). Much of our work has had impact in the OS and runtime community through the ASCR Exascale OS/R workshop and report, leading to the research agenda of the Exascale OS/R program. Our project was, however, also affected by attrition of multiple PIs. While the PIs continued to participate and offer guidance as time permitted, losing these key individuals was unfortunate both for the project and for the DOE HPC community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

OpenPET Hardware, Firmware, Software, and Board Design Files

OpenPET is an open source, flexible, high-performance, and modular data acquisition system for a variety of applications. The OpenPET electronics are capable of reading analog voltage or current signals from a wide variety of sensors. The electronics boards make extensive use of field programmable gate arrays (FPGAs) to provide flexibility and scalability. Firmware and software for the FPGAs and computer are used to control and acquire data from the system. The command and control flow is similar to the data flow, however, the commands are initiated from the computer similar to a tree topology (i.e., from top-to-bottom). Each node in the tree discovers its parent and children, and all addresses are configured accordingly. A user (or a script) initiates a command from the computer. This command will be translated and encoded to the corresponding child (e.g., SB, MB, DB, etc.). Consecutively, each node will pass the command to its corresponding child(ren) by looking at the destination address. Finally, once the command reaches its desired destination(s) the corresponding node(s) execute(s) the command and send(s) a reply, if required. All the firmware, software, and the electronics board design files are distributed through the OpenPET website (http://openpet.lbl.gov).

Abu-Nimeh, Faisal↗