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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

FrESCO

The National Cancer Institute (NCI) monitors population level cancer trends as part of its Surveillance, Epidemiology, and End Results (SEER) program. This program consists of state or regional level cancer registries which collect, analyze, and annotate cancer pathology reports. From these annotated pathology reports, each individual registry aggregates cancer phenotype information and summary statistics about cancer prevalence to facilitate population level monitoring of cancer incidence. Extracting cancer phenotype from these reports is a labor intensive task, requiring specialized knowledge about the reports and cancer. Automating this information extraction process from cancer pathology reports has the potential to improve not only the quality of the data by extracting information in a consistent manner across registries, but to improve the quality of patient outcomes by reducing the time to assimilate new data and enabling time-sensitive applications such as precision medicine. Here we present FrESCO: Framework for Exploring Scalable Computational Oncology, a modular deep-learning natural language processing (NLP) library for extracting pathology information from clinical text documents.

Spannaus, Adam [Oak Ridge National Lab. (ORNL), Oa↗
DOE OSTI2021

Geospatial Data from the Alpine Treeline Warming Experiment (ATWE) on Niwot Ridge, Colorado, USA

This is a collection of all GPS- and computer-generated geospatial data specific to the Alpine Treeline Warming Experiment (ATWE), located on Niwot Ridge, Colorado, USA. The experiment ran between 2008 and 2016, and consisted of three sites spread across an elevation gradient. Geospatial data for all three experimental sites and cone/seed collection locations are included in this package. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––Geospatial files include cone collection, experimental site, seed trap, and other GPS location/terrain data. File types include ESRI shapefiles, ESRI grid files or Arc/Info binary grids, TIFFs (.tif), and keyhole markup language (.kml) files. Trimble-imported data include plain text files (.txt), Trimble COR (CorelDRAW) files, and Trimble SSF (Standard Storage Format) files. Microsoft Excel (.xlsx) and comma-separated values (.csv) files corresponding to the attribute tables of many files within this package are also included. A complete list of files can be found in this document in the “Data File Organization” section in the included Data User's Guide. Maps are also included in this data package for reference and use. These maps are separated into two categories, 2021 maps and legacy maps, which were made in 2010. Each 2021 map has one copy in portable network graphics (.png) format, and the other in .pdf format. All legacy maps are in .pdf format. .png image files can be opened with any compatible programs, such as Preview (Mac OS) and Photos (Windows). All GIS files were imported into geopackages (.gpkg) using QGIS, and double-checked for compatibility and data/attribute integrity using ESRI ArcGIS Pro. Note that files packaged within geopackages will open in ArcGIS Pro with “main.” preceding each file name, and an extra column named “geom” defining geometry type in the attribute table. The contents of each geospatial file remain intact, unless otherwise stated in “niwot_geospatial_data_list_07012021.pdf/.xlsx”. This list of files can be found as an .xlsx and a .pdf in this archive.As an open-source file format, files within gpkgs (TIFF, shapefiles, ESRI grid or “Arc/Info Binary”) can be read using both QGIS and ArcGIS Pro, and any other geospatial softwares. Text and .csv files can be read using TextEdit/Notepad/any simple text-editing software; .csv’s can also be opened using Microsoft Excel and R. .kml files can be opened using Google Maps or Google Earth, and Trimble files are most compatible with Trimble’s GPS Pathfinder Office software. .xlsx files can be opened using Microsoft Excel. PDFs can be opened using Adobe Acrobat Reader, and any other compatible programs. A selection of original shapefiles within this archive were generated using ArcMap with associated FGDC-standardized metadata (xml file format). We are including these original files because they contain metadata only accessible using ESRI programs at this time, and so that the relationship between shapefiles and xml files is maintained. Individual xml files can be opened (without a GIS-specific program) using TextEdit or Notepad. Since ESRI’s compatibility with FGDC metadata has changed since the generation of these files, many shapefiles will require upgrading to be compatible with ESRI’s latest versions of geospatial software. These details are also noted in the “niwot_geospatial_data_list_07012021” file.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Occupant Behavior XML Schema

This software implements the DNAS framework into an XML (eXtensible Markup Language) schema, titled "occupant behavior XML" (obXML). The obXML schema is used for the practical implementation of the DNAS framework into building simulation tools. The topology of the DNAS framework implemented in the obXML schema has a main root element OccupantBehavior, linking three main elements representing Buildings, Occupants and Behaviors. Using the schema structure, the actions of turning on an air conditioner and closing blinds provide two examples of how the schema standardizes these actions using XML. The obXML schema has inherent flexibility to represent numerous, diverse and complex types of occupant behaviors in buildings, and it can also be expanded to encompass new types of behaviors. The implementation of DNAS framework into the obXML schema will facilitate the development of occupant information modeling by providing interoperability between occupant behavior models and building energy modeling programs.

Hong, Tianzhen↗
DOE OSTI2024

Replication Package for "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifier

This replication package is a case study on automated deductive verification for Rust for practical programs. It is a companion artifact to a corresponding usability study on verification titled "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifiers". It seeks to answer the question "Can Rust developers today use Rust verifiers to verify their code?". To answer this question, the study contrasts the verification experience of two mature Rust verifiers, Creusot and Prusti, by using the tools to develop a verified implementation of union-find in Rust. The union-find implementation is based on real-world code as used in the popular egg E-graph library. The artifact consists of two different verified libraries, one using Creusot and one using Prusti. The libraries have similar Rust interfaces and high-level proofs but differ in their details: Creusot and Prusti have different annotation languages and support different proof styles. Each implementation can be verified with its respective tool and compiles as a traditional Rust development.

Sarracino, John↗
DOE OSTI2022

Machine Learning Modeling Pipeline for Extracting Nuclear Proliferation Events of Interest from Open Data Sources (U)

In FY2020, the Savannah River National Laboratory (SRNL) and the Sanghani Center for Artificial Intelligence and Data Analytics at Virginia Polytechnic Institute and State University entered a collaboration funded by Department of Energy’s (DOE) Office of Defense Nuclear Nonproliferation Research and Development. The project’s mission was to take the first steps toward developing a demonstration prototype system that uses multiple machine learning and data analytics methods on largescale open data sources to identify new, developing, and/or undeclared nuclear programs. Given the SRNL team’s on-site perspective of events culminating in the DOE’s decision to pursue the Savannah River Plutonium Processing Facility (SRPPF), the team targeted the identification of events and indicators in retrospective datasets that pointed to the activity of “fissile core fabrication at the Savannah River Site” prior to the official announcement in May of 2018. A preliminary modeling pipeline was developed in FY20 that showed the datasets contained adequate signal for continuation of efforts. In FY21, a modular demonstration prototype modeling pipeline has continued in development for two text-based data sources: a broad internet archive (Webhose Ltd.) and a decahose Twitter database (i.e., a global sampling of one in every ten Tweets). The techniques that have been developed rely on graph theory and anomaly detection to identify contextual shifts in key words and phrases at various points in time such that indicators of events of interest could be identified and subsequently, events could be extracted from the corpuses. The foundational concept behind the approaches is that contextual shifts in key words and phrases can act as indicators of events of interest. Both datasets have proven successful in extracting events of interest related to pit production at the Savannah River Site prior to the official announcement. In addition, the pipelines have generated a wide range of events broadly summarized as: the awarding of DOE contracts at major sites, DOE investments in various programs, accidents at DOE national laboratories, speculations about the fate of pit production in the DOE complex, domestic and international shipments and receipts of nuclear materials at DOE sites, termination of non-proliferation agreements with Russia, termination of MOX, new weapons development approvals/testing, nuclear posture reviews, major DOE cleanup/production milestones, political opinions, and nuclear watch groups’ opinions, among many others.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

History and State of the Art in Advanced Thermal Protection Systems

This report documents the current state of the art of thermal protection systems (TPS) relevant to missile application materials and MTCR control language. The information is intended to provide data on current TPS for determining the current state of development and identifying potential research directions. Various vehicle configurations and types of TPS are described, including the evolution of materials and systems. Vehicle configurations such as high drag rocket and capsule systems and low-drag air-breathers are discussed. TPS are complex, transitioning from often very low temperatures to temperatures exceeding 3000°C and heat fluxes of up to 30,000 W/cm 2 . They can take the form of blankets, sheets, tiles and fabricated rigid structures, and can be made from high temperature capable alloys, refractory metals, ceramics, ceramic matrix composites, ultra-high temperature ceramics, carbon-carbon composites or ablative carbonaceous materials. Current state of the art in TPS is based on materials any systems developed for the initial space program. TPS was upgraded to the point of the Space Shuttle development and has stagnated since them.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Establishing a Common Definition for Zero Energy Buildings: Time to Move the Market

To change the current paradigm from buildings being consumers of energy to producers of energy requires a common language to facilitate market transformation. Common definitions help create market movement by sharing concepts across market actors. While the term 'zero energy buildings' has been in the marketplace for over 20 years, no common definition had been established. US DOE, last year, embarked on a process to evaluate current definitions and solicit industry input to formulate a common definition and nomenclature for zero energy buildings. This definition uses commonly available site measurements and national conversion factors to define zero energy buildings on a source energy basis for a variety of boundary conditions including building, portfolio, campus, and community. Issues addressed include multiple fuel types, cogeneration, and renewable energy certificates. This paper describes the process used to arrive at the definition, looks at methods of calculating site to source energy conversions, and how boundary decisions affect a robust and stable definition that can be used to direct programs and policies for many years to come. This stability is critical to move building investments towards buildings that produce as much energy as they consume.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

The Evolution of Airport Terminal Wayfinding Technologies

This work was presented during the Transportation Research Board (TRB) and Airport Cooperative Research Program (ACRP) webinar "Enhancing the Airport Experience with Wayfinding" on May 23, 2024. The process of navigating within airports has evolved over the years, with various technologies emerging to complement static signage. Historically, wayfinding began with static signage and airport staff members providing personal guidance, before progressing into digital signs, interactive kiosks, and displays. In recent years, wayfinding has continued along its digital path using mobile applications, indoor positioning technology, and even robot guides. With ever- larger airport facilities and a growing number of travelers, the future of wayfinding will likely be heavily linked to further digital developments such as facial recognition, augmented-reality technology, and autonomous vehicle navigation. This presentation delves into the history of interior wayfinding in airports, its present state, and the anticipated future. Key wayfinding technologies are discussed with an emphasis on emerging smartphone applications. Other considerations such as legal issues, language barriers, and human-technology interactions are included. A wayfinding framework is proposed, with static wayfinding technologies serving as the base upon which dynamic and personalized digital technologies are built. In this framework, electronic wayfinding technologies do not replace - but rather augment - traditional methods. These technologies can be integrated into existing wayfinding systems for a seamless traveler experience.

airport↗
DOE OSTI2025

MontePy: a Python library for reading, editing, and writing MCNP input files.

The Monte Carlo N-Particle (MCNP) radiation transport code is a highly capable and accurate code with a long legacy. MCNP uses the Monte Carlo simulation process to simulate the path of particles (e.g., neutrons, photons, charged particles, etc.), and their interaction with materials. It is widely used in nuclear engineering, high-energy physics, and other fields. Its origins in the mid-twentieth century predate many modern software conventions. MCNP users provide an input file to MCNP, which it then uses to create an internal representation of the simulation problem. These input files originally had to be stored as punchcard decks, and the user manual still uses the terminology of cards and decks, despite moving beyond punchcards. MCNP predates nearly all modern human readable markup or data serialization languages, such as the extensible Markup Language (XML), the Standard Generalized Markup Language (SGML), YAML (YAML Ain’t Markup Language), and Javascript Object Notation (JSON). Due to this, MCNP uses an entirely custom defined syntax language for its input, making off-the-shelf libraries for XML, YAML, and JSON impossible to use for scripting various operations on MCNP input files (Kulesza et al., 2022).

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2015

CRADA: Data Acquisition and Tomographic Software Development

Dr. Raymond R. Raylman, Professor and Vice Chair for Research, Radiology Department at WVU was the Principal Investigator for the project. The Jefferson Lab partner on this project was the Radiation Detector and Imaging Group in the Physics Division, led by Dr. Drew Weisenberger who was the coordinator of the project execution and the chief contact with WVU. The responsibility of Jefferson Lab was to facilitate optimization of data acquisition software, conversion of JLab Fortran iterative positron emission mammography computer code to C++ and to act as a computer code repository. During the two year project interactions and exchange of information was directed by Dr. Raylman and Dr. Wesienberger. WVU provided the expertise that allowed JLab to continue development of the current JLab data acquisition software referred to as JDAQ. JDAQ is a highly flexible Java language based data acquisition tool that helps to minimize software induced dead-time while maintaining the highest possible data rates from a JLab built FPGA based analog-to-digital convertor (ADC). JDAQ interfaces directly with the FPGA based multi-channel ADCs. Using JDAQ it is possible process data from a number of different detector types such as the PET systems at WVU. Because of the inherent flexibility of our processing software, we are also able adjust detector readout parameters during operation to provide the best possible data presentation and calibration parameters. To accommodate the high rate nature of PET detector systems JDAQ was designed to be scalable across an Ethernet network as well as for multi-cpu computer systems, and it also has the capability to synchronize many ADCs connected to multiple computers. During the project WVU will provided iterative reconstruction algorithm expertise and Fortran programming assistance to facilitate the conversion to C++ of a JLab developed Fortran positron emission mammography (PEM) reconstruction code. Also WVU provided acceptance testing of the new C++ based PEM reconstruction code. The PEM code is a maximization (MLEM) image reconstruction program that created images from the list-mode data acquired from the PET system.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Retaining Systems Engineering Model Meaning Through Transformation: Demo 2

Digital engineering strategies typically assume that digital engineering models interoperate seamlessly across the multiple different engineering modeling software applications involved, such as model- based systems engineering (MBSE), mechanical computer-aided design (MCAD), electrical computer-aided design (ECAD), and other engineering modeling applications. The presumption is that the data schema in these modeling software applications are structured in the familiar flat- tabular schema like any other software application. Engineering domain-specific applications (e.g., systems, mechanical, electrical, simulation) are typically designed to solve domain-specific problems, necessarily excluding explicit representations of non-domain information to help the engineer focus on the domain problems (system definition, design, simulation). Such exclusions become problematic in inter-domain information exchange. The obvious assumptions of one domain might not be so obvious to experts in another domain. Ambiguity in domain-specific language can erode the ability to enable different domain modeling applications to interoperate, unless the underlying language is understood and used as the basis for translation from one application to another. The engineering modeling software application industry has struggled for decades to enable these applications to interoperate. Industry standards have been developed, but they have not unified the industry. Why is this? The authors assert that the industry has relied on traditional database integration methods. The basic issue prohibiting successful application integration then is that traditional database-driven integration does not consider the distinct languages of each domain. An engineering models meaning is expressed through the underlying language of that engineering domain. In essence, traditional integration methods do not retain the semantic context (meaning) of the model. The basis of this research stems from the widely held assumption that systems engineering models are (or can be) structured according to the underlying semantic ontology of the model. This assumption can be imagined from two thoughts. 1) Digital systems engineering models are often represented using graph theory (the graph of a complex systems model can contain millions of nodes and edges). When examining the nodes one at a time and following the outbound edges of each node one by one, one can end up with rudimentary statements about the model (i.e., node A relates to node B), as in a semantic graph. 2) Likewise, from the study of natural languages, a sentence can be structured into unambiguous triples of subject-predicate-object within formal and highly expressive semantic ontologies. The rudimentary statements about a systems model discerned with graph theory closely mimic the triples used in the ontologies that try to structure natural languages. In other words, a systems models semantic graph can be (or is) structured into an ontology. Additionally, it is well established in industry that through natural language processing (NLP), which provides the means to create language structures, that computers can interpret ontological graphs. Therefore, the authors hypothesized that if the integrity of the underlying semantic structure of a systems model is retained, the contextual meaning of the model is retained. By structuring system models into the triples of the underlying ontology during the transformation from one MBSE application to another, the authors have provided a proof of the concept that the meaning of a system model can be retained during transformation. The authors assert that this is the missing ingredient in effective systems model-to-model interoperability. ACKNOWLEDGEMENTS The authors would like to thank the FY19 Model Interoperability team members who provided a solid foundation for the FY20 team to leverage: John McCloud, for the work he did to guide us toward the right use of technology that will appropriately discover and manipulate ontologies. Carlos Tafoya, for the work he did to develop an application programming interface (API)/Adapter that would export ontology-based data from GENESYS. Peter Chandler, for the work he did to architect our overall integration solution, with an eye toward the future that would influence a large-scale federated production-level systems engineering digital model ecosystem.

42 ENGINEERING↗
DOE OSTI2016

Approaches for Communicating Technical Information - 16012

Projects within the nuclear industry are generally complex and associated with high hazards. To achieve success there is often a necessity to apply innovation or adopt longer term strategies and solutions. Because of these long timescales and the fact that some approaches revolve around allowing natural radioactive decay to take place prior to visible action, the industry is sometimes perceived to be technically unable to make progress with its environmental and waste management obligations. Work within the industry additionally takes on a high profile and invariably creates greater levels of anxiety and mistrust in the eyes of stakeholders than comparable projects from non-nuclear related industries. Many aspects of the industry are still seen as secretive, environmentally detrimental and 'risky' and all components of the nuclear life-cycle are therefore open to external scrutiny. Although communication and engagement has increased greatly over the years, especially in developed countries, there is still room for improvement in this field. Such improvement might relate to the frequency and level of engagement, the subject matter or the actual process itself. Communication with stakeholders is required throughout the various phases of the nuclear lifecycle whether the activity relates to mining/milling of uranium, fuel production, operational plant activities, decommissioning, remediation or waste management. The concerns and aspirations of stakeholders during these different activities will vary but need to be adequately addressed. Some organisations now have a basic engagement program and convince themselves that they are carrying out true engagement. But just ticking a box to say that an engagement program is in place does not provide evidence of its appropriateness or success as on many occasions' organisations might still not understand how to adequately engage and communicate technical information. It is not always the information we choose to communicate but that which might be withheld that is often perceived to be most relevant to the stakeholder community. Communicating technical information isn't as straightforward as it sounds, but still has to be undertaken, otherwise trust, understanding and acceptance of chosen options will not be achieved. I utilise what I call the 'ten principles of engagement' which I believe can help when communicating technical Information in relation to nuclear and radiological matters. These are; 1. Develop Trust. 2. Educating people and providing information in a transparent manner. 3. Develop an engagement process that is truly a two way process. 4. Openly discuss risk perception and risk communication. 5. Never try to trivialise risk. 6. Where possible, simplify the language you use. 7. Put background and naturally occurring radioactivity into context. 8. Explain how radioactive materials are often used in everyday life. 9. Try to demonstrate that you too are a member of the public. 10.Walk the talk - Try to undertake what you wish others to undertake. Further research is being undertaken to determine if Mental Models might assist with the communication of nuclear and radiological information. A mental model is an explanation of someone's thought process about how something works in the real world. The mental model approach aims to investigate the judgment and decision-making processes of both expert and lay groups, thus allowing a comparison and visualisation of the different views to be made. It is undoubtedly worthwhile keeping a watching brief on the outcome of such research as we strive to improve our communication with the general public. The aim of this paper is to highlight some simple principles and approaches that can assist with the communication of technical information. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

A Conceptual World Information Library (WIL) and Land Use Information System (LUIS) - 16181

The Organization for Economic Co-operation and Development Nuclear Energy Agency initiative on the Preservation of Records, Knowledge and Memory is addressing the topic of communicating with future generations on the location, specific contents, and potential risks associated with deep geologic nuclear waste repositories. At the Waste Isolation Pilot Plant (WIPP) in the United States, the U.S. Department of Energy (DOE) has committed, prior to the facility closure, to develop a Passive Institutional Controls (PICs) program designed to last as long as practicable. A portion of this PICs program includes development of records packages, selection of data storage materials and methods, and a determination of records retention/storage locations. The approved plan for record retention at WIPP includes the storage of information including hard copies of data, figures and maps in multiple libraries and archive record centers. With this in mind, it is easy to envision reams of various paper documents in a robust physical archive record center similar to one of the museums in Washington D.C., or DOE's Legacy Management facility in Morgantown, West Virginia. While some portion of records for nuclear waste burial sites should be maintained in this fashion for near-term retrieval purposes, it is widely accepted that this is not an efficient way to communicate with future generations even 1,000 years from now. Transmitting large detailed volumes of information to the future should be captured in an electronic format; maintained on computers, translated by computers, and perhaps updated by artificial intelligence as machine and human languages change over the centuries. In addition to a physical records development and storage process for transmittal to future generations, a web-based electronic database system should be developed. A World Electronic Library (WEL) database could be funded from various nations and perhaps sanctioned by the United Nations and/or the IAEA. This WEL could contain information regarding several different subjects with the intent of being a one-stop-information-shop for future generations. This database would require updates and maintenance for as long as there is a recipient. One subset of the WEL would be a spatial database containing all the information available to any set of GPS coordinates, anywhere within the world. This Land Use Information System (LUIS) database would contain information on past and present land use, natural resources, known geology, hydrology and atmospheric conditions, potential warnings, and other pertinent information. The LUIS database is where specific electronic information, a subset of all the records data gathered for a nuclear waste repository, could reside. For not only would LUIS provide the information on a nuclear waste repository when specific GPS coordinates were entered; but a search from the LUIS on 'Nuclear Waste Repositories' could bring up information, including data on location of repositories, radionuclides, operations, D and D, maps, and regulations, plus many other details for locations throughout the world. This tool could be used by future generations for a number of land use or resource exploration decisions. So what can we do now? We can agree to the types of information that should be captured into an electronic database for nuclear waste repositories. We can agree to the levels of detail, the file names and the formats, for ease of combining information sets in the future. Perhaps we can agree to a central electronic data storage site, or sites, where this information will reside for import into a centralized electronic record system, if one is ever developed. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Trends in data locality abstractions for HPC systems

The cost of data movement has always been an important concern in high performance computing (HPC) systems. It has now become the dominant factor in terms of both energy consumption and performance. Support for expression of data locality has been explored in the past, but those efforts have had only modest success in being adopted in HPC applications for various reasons. However, with the increasing complexity of the memory hierarchy and higher parallelism in emerging HPC systems, locality management has acquired a new urgency. Developers can no longer limit themselves to low-level solutions and ignore the potential for productivity and performance portability obtained by using locality abstractions. Fortunately, the trend emerging in recent literature on the topic alleviates many of the concerns that got in the way of their adoption by application developers. Data locality abstractions are available in the forms of libraries, data structures, languages and runtime systems; a common theme is increasing productivity without sacrificing performance. Furthermore, this paper examines these trends and identifies commonalities that can combine various locality concepts to develop a comprehensive approach to expressing and managing data locality on future large-scale high-performance computing systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Integration of Data Analytics with Plant System Health Program

This report summarizes the R&D activities of the Plant Health Management (PHM) project during fiscal year 2020 (FY20). This project focuses on the development of methods that integrate component health data and propagate such information at the system level to evaluate system sources of risk. This project development lives in cooperation with the Risk Informed Asset Management (RIAM) project. The RIAM project, in fact, uses the reliability models and data generated by the PHM project to optimize plant operations (e.g., maintenance/replacement schedule, optimal maintenance posture). This year’s activities for the PHM project focused mainly on the development of two classes of models. The first one includes a series of component reliability models which include aging, testing and maintenance. The second class includes a series of system reliability models which focus on the secondary side of exiting U.S. reactors. These models are based on fault tree logic structures such that they can be used by existing plant PRA software. We also started to focus on the management of health data and we tackled this issue in two directions. The first one focuses on the integration of monitor data with simulation models to assess component health. This approach is moving from a classical data based to a model+data based approach with the goal of improving higher component health information. The second direction focuses on linking equipment reliability data (e.g., maintenance/failure reports, component monitoring data) directly to system reliability models using a safety margin based language rather than a probability based language. The main advantage of a safety margin based language is that it can provide to system engineers more tangible information on system/component health and how it propagates to the system level.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

High-performance epistasis detection in quantitative trait GWAS

epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS). A parallel MPI version (EPISNPmpi) was created in 2008 to address this computationally expensive analysis on large data sets with many quantitative traits and SNP markers. However, the falling cost of genotyping has led to an explosion of large-scale GWAS data sets that challenge EPISNPmpi’s ability to compute results in a reasonable amount of time. Therefore, we optimized epiSNP for modern multi-core and highly parallel many-core processors to efficiently handle these large data sets. This paper describes the serial optimizations, dynamic load balancing using MPI-3 RMA operations, and shared-memory parallelization with OpenMP to further enhance load balancing and allow execution on the Intel Xeon Phi coprocessor (MIC). For a large GWAS data set, our optimizations provided a 38.43× speedup over EPISNPmpi on 126 nodes using 2 MICs on TACC’s Stampede Supercomputer. We also describe a Coarray Fortran (CAF) version that demonstrates the suitability of PGAS languages for problems with this computational pattern. We show that the Coarray version performs competitively with the MPI version on the NERSC Edison Cray XC30 supercomputer. Finally, the performance benefits of hyper-threading for this application on Edison (average 1.35× speedup) are demonstrated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

ADVANCING THE TRANSPORTATION – SECURITY, TRACKING, AND REPORTING (T-STAR) SYSTEM

The Transportation – Security, Tracking and Reporting (T-STAR) System was developed by NNSA NA-21 Office of Radiological Security (ORS) to provide a transportation security system for use during transport of Category 1 and Category 2 radiological material to provide detection and tracking capability for shipments. While many off the shelf systems provide asset tracking of the conveyance, few offer detection of a breach into the cargo compartment or the removal of cargo from the conveyance. Systems that do offer such capability need to be permanently installed on the conveyance, requiring drilling of holes and running of cables throughout the conveyance itself. This means that dedicated shipping containers or vehicles are required, and this is not sustainable in many countries where ORS is building capacity for the security of radioactive materials in use, storage, and in transport. T-STAR is leveraging various ORNL technologies for improved communications capability and reduced power requirements; the multimode communications module developed by the Unmanned Aerial Systems group and the low power and extensible Authenticatable Container Tracking System (ACTS) tag developed for the US Department of Energy’s Packaging Certification Program provide a small footprint tracking system which can be installed quickly as needed. T-STAR uses a cellular and an Iridium modem to communicate configuration and alert information to a server used to monitor the shipment and incorporates a Z-wave © wireless security system allowing various intrusion detection sensors to be located in the conveyance. The Z-wave sensors are readily available, inexpensive, and power efficient, making them replaceable and low maintenance. The server software be configured as a standalone system installed on a light duty computer hosted by the competent authority, carrier, or response agency, or hosted as part of an Amazon Cloud Server (AWS) accessible via a secure login. The server has two functions, first is to handle messages to/from the T-STAR field unit, second is to host the user interface which can be accessed using a web browser on desktop or mobile device. The user interface implements roles to determine the level of access to shipment information, define geo-fences, and configure notifications. The user interface also supports multiple languages for display as well as notifications by using a simple lookup file which can be modified by the host country to ensure translations are correct and meaningful to responders receiving notifications and alerts. This paper will detail the overarching T-STAR capabilities, architecture and components, and provide insights on how it is deployed, used, and monitored during transportation of radioactive material.

Schultze, Michael↗