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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Open Source Principles Utilized by the CERES Edition 5 Level-3 Framework

The Clouds and the Earth’s Radiant Energy System (CERES) Science Team integrates and fuses observations from six CERES instruments aboard the Terra, Aqua, S-NPP, and NOAA-20 missions with data from twenty-five geostationary imagers, in creating a nearly 25-year, ongoing record of the Earth’s radiation budget. In preparation for the next version of CERES data products, the team has been exploring software development methods leveraging open-source principles and software to streamline data product configuration and algorithm implementation. This effort will provide robust software for production while maintaining greater flexibility for the algorithm developers to explore new science.

T. Nelson Hillyer↗
NASA NTRSDate not supplied

Open Source Principles Utilized by the CERES Edition 5 Level-3 Framework

The Clouds and the Earth’s Radiant Energy System (CERES) Science Team integrates and fuses observations from six CERES instruments aboard the Terra, Aqua, S-NPP, and NOAA-20 missions with data from twenty-five geostationary imagers, in creating a nearly 25-year, ongoing record of the Earth’s radiation budget. In preparation for the next version of CERES data products, the team has been exploring software development methods leveraging open-source principles and software to streamline data product configuration and algorithm implementation. This effort will provide robust software for production while maintaining greater flexibility for the algorithm developers to explore new science.

Thomas N Hillyer↗
DOE OSTI2024

Directing Nanoparticle Organization in Response to Diverse Chemical Inputs

Signaling cascades are crucial for transducing stimuli in biological systems, enabling multiple stimuli to regulate a downstream target with precisely controlled timing and amplifying signals through a series of intermediary reactions. Developing a robust signaling system with such capabilities would be pivotal for programming complex behaviors in synthetic DNA-based molecular devices. However, although “software” such as nucleic acid circuits could potentially be harnessed to relay signals to DNA-based nanostructure hardware, such explorations have been limited. Here, in this study, we develop a platform for transducing a variety of stimuli via messenger-mediated reactions to regulate the release and reloading of gold nanoparticles (AuNPs) in a 3D DNA framework. In the first step, an in vitro transcription circuit is engineered to sense and amplify chemical stimuli, including arbitrary DNA sequences and proteins, producing RNA. In the second step, the RNA releases the DNA-coated AuNPs from the DNA framework via a strand displacement reaction. AuNP reloading is controlled by a separate step driven by degradation of the RNA. Our platform holds promise for applications requiring dynamic multiagent control over DNA-based devices, offering a versatile tool for advanced molecular device engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2024

NEAMS-Multiphysics MOOSE End Year Framework Activities FY20

The Multiphysics Object Oriented Simulation Environment (MOOSE) is a general finite element package meant for high performance solution of multiphysics problems in science and engineering. In this report, we present additions and enhancements to MOOSE funded by the Nuclear Engineering Advanced Modeling and Simulation (NEAMS) program. NEAMS-funded MOOSE framework library improvements include: expansion of support for multi-level multi-application restart; enhancement of coupling between native MOOSE applications and external libraries; addition of a sparse automatic differentiation (AD) container enabling non-local degree of freedom coupling; block-specific quadrature rules; further development of an eigenvalue executioner; faster setup of periodic boundary conditions; and creation of a mesh meta-data system streamlining simulation startup. Besides developing the framework library, NEAMS funds were used to overhaul a swath of important MOOSE infrastructure in order to substantially improve user experience. These critical infrastructure changes included adapting MOOSE to python 3, improving the test harness to catch race conditions, and most importantly transitioning MOOSE to use Conda, a globally known packaging system, that greatly eases software adoption.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1997

Why are Formal Methods Not Used More Widely?

Despite extensive development over many years and significant demonstrated benefits, formal methods remain poorly accepted by industrial practitioners. Many reasons have been suggested for this situation such as a claim that they extent the development cycle, that they require difficult mathematics, that inadequate tools exist, and that they are incompatible with other software packages. There is little empirical evidence that any of these reasons is valid. The research presented here addresses the question of why formal methods are not used more widely. The approach used was to develop a formal specification for a safety-critical application using several specification notations and assess the results in a comprehensive evaluation framework. The results of the experiment suggests that there remain many impediments to the routine use of formal methods.

Knight, John C.↗
DOE OSTI2012

Consolidation and Centralization of Waste Operations Business Systems - 12319

This abstract provides a comprehensive plan supporting the continued development and integration of all waste operations and waste management business systems. These include existing systems such as ATMS (Automated Transportation Management System), RadCalc, RFITS (Radio Frequency Identification Transportation System) Programs as well as incorporating key components of existing government developed waste management systems and COTS (Computer Off The Shelf) applications in order to deliver a truly integrated waste tracking and management business system. Some of these existing systems to be integrated include IWTS at Idaho National Lab, WIMS at Sandia National Lab and others. The aggregation of data and consolidation into a single comprehensive business system delivers best practices in lifecycle waste management processes to be delivered across the Department of Energy facilities. This concept exists to reduce operational costs to the federal government by combining key business systems into a centralized enterprise application following the methodology that as contractors change, the tools they use to manage DOE's assets do not. IWITS is one efficient representation of a sound architecture currently supporting multiple DOE sites from a waste management solution. The integration of ATMS, RadCalc and RFITS and the concept like IWITS into a single solution for DOE contractors will result in significant savings and increased efficiencies for DOE. Building continuity and solving collective problems can only be achieved through mass collaboration, resulting in an online community that DOE contractors and subcontractors access common applications, allowing for the collection of business intelligence at an unprecedented level. This is a fundamental shift from a solely 'for profit' business model to a 'for purpose' business model. To the conventional-minded, putting values before profit is an unfamiliar and unnatural way for a contractor to operate - unless however; your objective is to build a strong, strategic alliance across the enterprise in order to execute an unprecedented change in waste management, transportation and logistical operations. The success of such an initiative can be achieved by creating a responsible framework by enabling key individuals to 'own' the sustainability of the program. This includes the strategic collaboration of responsible revolutionaries covering application developers, information owners and federal stakeholders to ensure compliance, security and risk management are 'baked' into the process and sustainability is fostered through continued innovation by both technology and application functionality. This ensures that working software can adapt to changing circumstances and is the principle measure of the success of the program. The consolidation of waste management business systems must be achieved in order to realize efficiencies in information technology portfolio management, data integrity, business intelligence and the lifecycle management of hazardous materials within the DOE enterprise architecture. By identifying best practices across the enterprise and aggregating computational and application development resources, you can provide a unified, holistic solution serviceable from a single location while being accessed from anywhere. The business impact of integrating and delivering a unified solution would reduce costs to the Department of Energy within the first year of deployment with increased savings annually. (author)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2020

Blackbird: Object-Oriented Planning, Simulation, and Sequencing Framework Used by Multiple Missions

Every JPL flight mission relies on activity planning and sequence generation software to perform operations. Most such tools in use at JPL and elsewhere use attribute-based schemas or domain-specific languages (DSLs) to define activities. This reliance poses user training, software maintenance, performance, and other challenges. To solve this problem for future missions, a new software called Blackbird was developed which allows engineers to specify behavior in standard Java. The new code base has over an order of magnitude fewer lines of code than other JPL planning software, since no DSL or schema interpreter is needed. The use of Java for defining activities also allows mission adapters to debug their code in an integrated development environment, seamlessly call external libraries, and set up truly multimission models. These efficiency gains have significantly reduced the amount of development effort required to support the software. This paper discusses Blackbird’s design, principles, and use cases.

Lawler, Christopher↗
NASA NTRS2017

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

easy to use and implement software tool↗
DOE OSTI2016

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinary team of engineers and computer scientists.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

MASTODON: An Open-Source Software for Seismic Analysis and Risk Assessment of Critical Infrastructure

Seismic analysis and risk assessment of safety-critical infrastructure like hospitals, nuclear power plants, dams, and facilities handling radioactive materials involve computationally intensive numerical models and coupled multiphysics scenarios. They are also performed in a strict regulatory environment that requires high software quality assurance standards, and in the case of safety-related nuclear facilities, a conformance to the American Society of Mechanical Engineers Nuclear Quality Assurance (NQA-1) standard. This paper introduces the open-source finite-element software, MASTODON (Multi-hazard Analysis of Stochastic Time-Domain Phenomena), which implements state-of-the-art seismic analysis and risk assessment tools in a quality-controlled environment. MASTODON is built on MOOSE (Multi-physics Object-Oriented Simulation Environment), which is a highly parallelizable, NQA-1 conforming, coupled multiphysics, finite-element framework developed at Idaho National Laboratory. MASTODON is capable of fault rupture and source-to-site wave propagation using the domain reduction method, nonlinear site response, and soil-structure interaction analysis, implicit and explicit time integration, automated stochastic simulations, and seismic probabilistic risk assessment. When coupled with other MOOSE applications, MASTODON can also solve strongly and weakly coupled multiphysics problems. This paper presents a summary of the capabilities of MASTODON and some demonstrative examples.

42 ENGINEERING↗
DOE OSTI2018

Tuyere: Enabling Scalable Memory Workloads for System Exploration

Memory technologies are under active development. Meanwhile, workloads on contemporary computing systems are increasing rapidly in size and diversity. Such dynamics in hardware and software further widen the gap between memory system design and performance evaluation. In this work, we propose a data-centric abstraction of high-performance computing applications for fast exploration of new memory technologies. We also provide a framework that uses a formal modeling language to describe the abstraction, automatically translates abstractions into memory traffic, and directly interfaces with cycle-accurate simulators. We evaluated the framework using 20 workloads and validated the memory traffic profile, the simulation results, and the relative memory changes of four memory technologies. Our results show that the data-centric abstraction can accurately capture application behavior adaptable to different input problems and can expedite system exploration.

Peng, Ivy Bo↗
DOE OSTI2017

Time Resolved Phonon Spectroscopy, Version 1.0

TRPS code was developed for the project "Time Resolved Phonon Spectroscopy". Routines contained in this piece of software were specially created to model phonon generation and tracking within materials that interact with ionizing radiation, particularly applicable to the modeling of cryogenic radiation detectors for dark matter and neutrino research. These routines were created to link seamlessly with the open source Geant4 framework for the modeling of radiation transport in matter, with the explicit intent of open sourcing them for eventual integration into that code base.

Goett, Johnny↗
DOE OSTI2025

SpacelyProject/spacely-docs

Spacely is an open-source framework for the post-silicon validation of analog, digital, and mixed-signal ASICs (Application-Specific Integrated Circuits) which maximizes the reuse of hardware and software, reducing the time taken to achieve meaningful test results. Spacely specifically addresses the needs of small, flexible ASIC design teams commonly found in academia or research institutions. Spacely was originally developed at Fermi National Accelerator Laboratory.

Quinn, Adam [Fermi National Accelerator Laboratory↗
DOE OSTI2016

Multigroup Radiation-Hydrodynamics with a High-Order, Low-Order Method

Recent efforts at Los Alamos National Laboratory to develop a moment-based, scale-bridging [or high-order (HO)–low-order (LO)] algorithm for solving large varieties of the transport (kinetic) systems have shown promising results. A part of our ongoing effort is incorporating this methodology into the framework of the Eulerian Applications Project to achieve algorithmic acceleration of radiationhydrodynamics simulations in production software. By starting from the thermal radiative transfer equations with a simple material-motion correction, we derive a discretely consistent energy balance equation (LO equation). We demonstrate that the corresponding LO system for the Monte Carlo HO solver is closely related to the original LO system without material-motion corrections. We test the implementation on a radiative shock problem and show consistency between the energy densities and temperatures in the HO and LO solutions as well as agreement with the semianalytic solution. We also test the approach on a more challenging two-dimensional problem and demonstrate accuracy enhancements and algorithmic speedups. This paper extends a recent conference paper by including multigroup effects.

42 ENGINEERING↗
DOE OSTI2020

Multiple social platforms reveal actionable signals for software vulnerability awareness: A study of GitHub, Twitter and Reddit

Software vulnerabilities are flaws in computer systems that leave users open to attack. In many cases, these vulnerabilities go unnoticed and remain unresolved in codebases. Thus, awareness of software vulnerabilities among the public is crucial to ensure effective cybersecurity practices, the development of high quality software, and ultimately national security. This awareness can be better understood by studying the spread and evolution of software vulnerability discussions in online communities. This work is the first to evaluate and contrast how discussions about software vulnerabilities spread on three social platforms -- Twitter, GitHub, and Reddit. To lay the groundwork, we showcase a novel fundamental framework for measuring information spread that identifies the spread mechanisms and observables across platforms, the units of information, and the groups of measurements that can be applied to focus on a specific phenomena e.g., information cascades. We then analyze and contrast social network topologies for three example social networks and measure the scale and speed of the spread of discussion of specific vulnerabilities to understand how far and how widely they spread, how many users participate in discussions, and the duration of their spread. To demonstrate the awareness of more impactful software vulnerabilities, a subset of our analysis focuses on vulnerabilities targeted during recent major cyber attacks as well as vulnerabilities exploited by advanced persistent threat groups. We discover that usually, vulnerability discussions start on GitHub, before occurring on Twitter and Reddit. While studying how some user-level and content-level characteristics influence vulnerability spread, we observe that Twitter discussions started by users predicted to be humans have larger size, breadth, depth, adoption rate, lifetime, and structural virality compared to those started by users predicted to be bots. On Reddit, we contrast the differences in thread structure that originate from posts with positive, negative and neutral polarity. We find that posts that are positive have larger, deeper and wider discussions compared to negative and neutral posts. We anticipate the results of our analysis to not only increase the understanding of software vulnerability awareness but also inform models for simulating information spread across multiple social environments online.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1994

The design of a petabyte archive and distribution system for the NASA ECS project

The NASA EOS Data and Information System (EOSDIS) Core System (ECS) will contain one of the largest data management systems ever built - the ECS Science and Data Processing System (SDPS). SDPS is designed to support long term Global Change Research by acquiring, producing, and storing earth science data, and by providing efficient means for accessing and manipulating that data. The first two releases of SDPS, Release A and Release B, will be operational in 1997 and 1998, respectively. Release B will be deployed at eight Distributed Active Archiving Centers (DAAC's). Individual DAAC's will archive different collections of earth science data, and will vary in archive capacity. The storage and management of these data collections is the responsibility of the SDPS Data Server subsystem. It is anticipated that by the year 2001, the Data Server subsystem at the Goddard DAAC must support a near-line data storage capacity of one petabyte. The development of SDPS is a system integration effort in which COTS products will be used in favor of custom components in very possible way. Some software and hardware capabilities required to meet ECS data volume and storage management requirements beyond 1999 are not yet supported by available COTS products. The ECS project will not undertake major custom development efforts to provide these capabilities. Instead, SDPS and its Data Server subsystem are designed to support initial implementations with current products, and provide an evolutionary framework that facilitates the introduction of advanced COTS products as they become available. This paper provides a high-level description of the Data Server subsystem design from a COTS integration standpoint, and discussed some of the major issues driving the design. The paper focuses on features of the design that will make the system scalable and adaptable to changing technologies.

Caulk, Parris M.↗
DOE OSTI2016

Time Resolved Phonon Spectroscopy, Version 1.0

TRPS code was developed for the project "Time Resolved Phonon Spectroscopy". Routines contained in this piece of software were specially created to model phonon generation and tracking within materials that interact with ionizing radiation, particularly applicable to the modeling of cryogenic radiation detectors for dark matter and neutrino research. These routines were created to link seamlessly with the open source Geant4 framework for the modeling of radiation transport in matter, with the explicit intent of open sourcing them for eventual integration into that code base.

Goett, Johnny↗
DOE OSTI2020

Towards Acceptance Testing at the Exascale Frontier

At the 2007 Cray User Group meeting, the Oak Ridge Leadership Computing Facility (OLCF) introduced the OLCF Test Harness (OTH), a framework[1] used for acceptance testing of the Jaguar supercomputer[2]. Since then, the OTH framework has evolved to version 2.0 which adds new features and streamlines usability. The OTH is the key piece of software used to orchestrate acceptance testing for all OLCF computational resources before they are deployed for production use, including our leadership class high performance computing (HPC) systems. The OTH framework is written in Python and is publicly available[3].In this paper, we first describe the requirements, design, and structure of the OTH. Then, we present specific improvements developed to support acceptance testing of the OLCF’s Summit system[4]. We will also showcase new OTH features that have been added to streamline the acceptance test process as well as the motivation behind those changes. As part of this work, we also evaluated different workflow tools in order to determine whether these tools could complement the OTH in two key areas: automation and reporting. The advantages and disadvantages identified with each tool will be discussed. Lastly, we summarize the challenges and lessons learned collected from using the OTH for the acceptance of the last three flagship systems at the OLCF. These may be useful for other HPC centers developing their own testing frameworks or those interested in using the OTH.

Melesse Vergara, Veronica↗