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DOE OSTI2012

An Analysis of Multi-type Relational Interactions in FMA Using Graph Motifs with Disjointness Constraints

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions. MOCH represents patterns of multitype interaction as small labeled sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology (OWL, RDF and SPARQL) and Virtuoso, we performed exhaustive analyses of three 2-node motifs, resulting in 638 matching FMA configurations; twelve 3-node motifs, resulting in 202,960 configurations. Using the Principal Ideal Explorer (PIE) methodology as an extension of MOCH, we were able to identify 755 root nodes with 4,100 respective descendants with opposing antonyms in their class names for arbitrary-length motifs. With possible disjointness implied by antonyms, we performed manual inspection of a subset of the resulting FMA fragments and tracked down a source of abnormal inferred conclusions (captured by the motifs), coming from a gender-neutral class being modeled as a part of gender-specific class, such as “Urinary system” is a part of “Female human body.” Our results demonstrate that MOCH and PIE provide a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.

Zhang, Guo Qiang↗

DOE OSTI2015

RVA: A Plugin for ParaView 3.14

RVA is a plugin developed for the 64-bit Windows version of the ParaView 3.14 visualization package. RVA is designed to provide support in the visualization and analysis of complex reservoirs being managed using multi-fluid EOR techniques. RVA, for Reservoir Visualization and Analysis, was developed at the University of Illinois at Urbana-Champaign, with contributions from the Illinois State Geological Survey, Department of Computer Science and National Center for Supercomputing Applications. RVA was designed to utilize and enhance the state-of-the-art visualization capabilities within ParaView, readily allowing joint visualization of geologic framework and reservoir fluid simulation model results. Particular emphasis was placed on enabling visualization and analysis of simulation results highlighting multiple fluid phases, multiple properties for each fluid phase (including flow lines), multiple geologic models and multiple time steps. Additional advanced functionality was provided through the development of custom code to implement data mining capabilities. The built-in functionality of ParaView provides the capacity to process and visualize data sets ranging from small models on local desktop systems to extremely large models created and stored on remote supercomputers. The RVA plugin that we developed and the associated User Manual provide improved functionality through new software tools, and instruction in the use of ParaView-RVA, targeted to petroleum engineers and geologists in industry and research. The RVA web site (http://rva.cs.illinois.edu) provides an overview of functions, and the development web site (https://github.com/shaffer1/RVA) provides ready access to the source code, compiled binaries, user manual, and a suite of demonstration data sets. Key functionality has been included to support a range of reservoirs visualization and analysis needs, including: sophisticated connectivity analysis, cross sections through simulation results between selected wells, simplified volumetric calculations, global vertical exaggeration adjustments, ingestion of UTChem simulation results, ingestion of Isatis geostatistical framework models, interrogation of joint geologic and reservoir modeling results, joint visualization and analysis of well history files, location-targeted visualization, advanced correlation analysis, visualization of flow paths, and creation of static images and animations highlighting targeted reservoir features.

Source record↗

DOE OSTI2021

Achieving Integrated Daylighting and Electric Lighting Systems: Current State of the Art and Needed Research

This paper presents the results of a multi-disciplinary scoping study, the goals of which were to see the seamless integration and application of light in buildings, regardless of source, that is purposely modulated to illuminate surfaces and designed in a way that is comfortable, healthy, pleasing, cost effective, and energy efficient. The scoping study was performed in order to set the stage for transforming the design and realization of lighting systems integration (daylight and electric). This, in turn, will support achieving the the U.S. Department of Energy’s (DOE) Building Technologies Office (BTO) long-term energy savings goals. Holistic lighting systems of the future should include components that are adaptable to change, resilient to disruption, and robust. The system of codes, standards, guidelines, and contracts employed to design and implement lighting systems should be structured to help them to flourish, rather than being barriers to realization. Finally, the research thrusts and mechanisms should be engaged with these goals in mind. While integrated lighting systems may reduce lighting energy use in buildings, a broader web of non-energy impacts affecting occupant’s overall health, comfort, and satisfaction may also guide technology investment goals when the entire lighting systems lifecycle is considered. Daylighting systems are separated from electric lighting systems, and both are characteristically detached from other systems such as safety, security, communications, and information systems. Being disconnected from the inputs and outputs of other building systems precludes the ability to acquire and utilize information about occupation, status of systems, and interior and exterior environmental conditions. The outcome of this separation is that the standard building is not fulfilling the potential for creating dynamic and holistic lighting for building occupants.

Davis, Robert G.↗

NASA NTRSDate not supplied

Interoperable Map Services with Performance Tuning for Earth Science Data through API-Tiles and Dynamic API-Styles

NASA’s Goddard Earth Sciences Data and Information Services Center (GES DISC) provides access to a wide range of global climate data from various satellite missions and models. However, the visualization and analysis of these data can be challenging due to their large volume, complex structure, and diverse formats. This study presents the implementation of interoperable map services (API-Maps) with performance tuning using API-Tiles and dynamic API-Styles. API-Maps is a standard for defining and exposing map services through RESTful (representational state transfer) APIs (application programming interfaces). API-Tiles is a technique for generating and delivering map tiles on demand from any data source. API-Styles is a method for dynamically applying styles to map tiles based on user preferences or data attributes. The use of API-Tiles and dynamic API-Styles enhances the performance and scalability of the map services, allowing for smooth and interactive visualization of large datasets. Two types of Earth Science data sources from the NASA GES DISC are used in the experiment: regularly gridded data, such as Global Precipitation Measurement (GPM) precipitation data, and low processing level data, such as low-level data of atmospheric composite measurements from the TROPOspheric Monitoring Instrument (TROPOMI) mission. Re-gridding of swath data (low level data - e.g. Level 2) of atmospheric composites (e.g. TROPOMI products, such as nitrogen dioxide, ozone and aerosol optical depth) is applied to enable the Web-based, interoperable, tiled, and styled mapping (rendering) services of such data. The results demonstrate the effectiveness of the proposed approach in providing fast and efficient access to Earth science data through interoperable map services.

Geographic Information System↗

DOE OSTI2015

Best practices mobile application for D and D KM-IT - 15712

The Deactivation and Decommissioning Knowledge Management Information Tool (D and D KM-IT) is the repository of useful information built specifically for D and D community. The knowledge provided by the D and D KM-IT is the experience and expertise gained by people within the field and fellow employees of the Department of Energy (DOE). This information has been the result of gathering, analyzing, storing, and sharing knowledge to help reduce time spent on discovering previously found data. In order to help in organizing all the data from all the professional contributors, the D and D KM-IT has been divided into 12 different modules. Each individual module pertains to a different area of information for users, such as vendor and technology information, collaboration tools, and even a hotline that contains problems posted by the users. Purpose: - Design and develop the module for the Best Practices on D and D KM-IT mobile platform deployed at https://m.dndkm.org; - The Best Practices mobile module should integrate with existing modules seamlessly; - Use the D and D KM-IT existing database to consume information for the mobile system. jQuery Mobile framework was used to develop Best Practices module for mobile devices. jQuery Mobile framework provides support for responsive web design (RWD). RWD allows adaptation of the layout and user interface of web sites and web apps to different device resolutions, screen densities, and views. UI design was implemented with three fundamental elements: CSS media queries, An adaptable grid, Flexible images and media. Advantages/benefits: - A responsive web design adapts to any-sized screen / resolution and orientation view; - ASP.NET compatible which allows the D and D KM-IT database to support all platforms accessing the system; - Navigating pages is more bandwidth efficient by refreshing data in small section with Ajax instead of reloading the entire page; - Multiple parts of a page can perform different tasks resulting in improved user's experience. Results: - Mobile system is accessible on compatible devices running Android, Apple, Blackberry, Palm, and Windows devices; - Best Practices searches through Characterization, Decontamination, Dismantlement, Material Disposition, and Worker Safety; - Keyword search is enabled for the best practices that are available on both the desktop and mobile systems - Documents are formatted into a PDF file format to ensure compatibility on any device. Conclusion: - Fully integrated with the desktop Best Practices module and displays documents that are uploaded on web platform; - Fast-loading with D and D KM-IT mobile system and downloadable documents; - Responsive design which gives the same user experience when either viewed on smart phone or tablet.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2013

Low Cost Electrochromic Film on Plastic for Net-Zero Energy Buildings

Over 4 Quads of energy are lost through windows annually. Passive coatings reduce wasted energy, but energy lost through windows would remain over 2 Quads with complete replacement of Low-E glass. Active control of transmitted light and solar heating with electrochromic (EC) windows can transform the efficiency of energy use within buildings, thereby reducing energy footprints and corresponding greenhouse emissions. High production, integration, and distribution cost limits adoption of current EC products. ITN aimed to utilize its proven heritage of efficiently transitioning technologies from rigid to flexible substrates employing roll-to-roll manufacturing to capture the emerging EC window market opportunity. The project focused on three main efforts (1) Transition Small Scale Prototypes To Limited 0.5 Meter Wide, Web Coater Production, (2) Satisfy Market Driven EC Performance Metrics on Plastic Substrates, and (3) Product Development and Commercialization. The overall goal was to substantially reduce investor risk to motivate private investment in a production facility to further transition and scale this promising technology. A 0.5 meter roll-to-roll web coater was designed, constructed, and commissioned at ITN to support EC development effort. With this tool, we were able to establish the feasibility of roll-to-roll production of EC devices. Individually layers were continuously produced at lengths up to 3 meters with good uniformity, both down web and cross web. Solid state devices were produced, and device performance was being enhanced through hardware modifications underway at the close of the project. When deployed in composite device structures, we were able to verify that individual layers were able to achieve a transmission range of 3-70% transmission average over the visible portion of the spectrum. Initial development of intelligent process controls led to verification of a 2-state controller employed during deposition of the electrochromic layer. The project also successfully increased device performance in line with market needs. Improved device materials provided increased transmission range to a 5-65% transmission over the visible spectrum and faster switching times for both small area batch parts and large area composite materials. We were able to demonstrate durable cycling over 10,000-20,000 cycles in a variety of architectures including suspended films in an IGU and films laminated to glass tested in open air representative of retrofit applications. Robust packaging techniques were identified and samples proved durable even in 40C and 100% relative humidity outside the IGU environment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2017

Facilitating the Use of Epidemiological Models for Infectious Disease Surveillance

1. To develop a comprehensive model characterization framework to describe epidemiological models in an operational context. 2. To apply the framework to characterize “operational” models for specific infectious diseases and provide a web-based directory, the biosurveillance analytics resource directory (BARD) to the global infectious disease surveillance community. Epidemiological modeling for infectious disease is useful for disease management and routine implementation needs to be facilitated through better description of models in an operational context. A standardized model characterization process that allows selection or making manual comparisons of available models and their results is currently lacking. Los Alamos National Laboratory(LANL) has developed a comprehensive framework that can be used to characterize an infectious disease model in an operational context. We offer this framework and an associated database to stakeholders of the infectious disease modeling field as a tool for standardizing model description and facilitating the use of epidemiological models. Such a framework could help the understanding of diverse models by various stakeholders with different preconceptions, backgrounds, expertise ,and needs, and can foster greater use of epidemiological models as tools in infectious disease surveillance. We define, “operational” as the application of an epidemiological model to a real-world event for decision support and can be used by experts and non-experts alike. The term “model” covers three major types, risk mapping, disease dynamics and anomaly detection. To develop a framework for characterizing epidemiological models we collected information via a three-step process: a literature search of model characteristics, a review of current operational infectious disease epidemiological models, and subject matter expert (SME)panel consultation. We limited selection of operational models to five infectious diseases: influenza, malaria, dengue, cholera and foot-and-mouth disease (FMD). These diseases capture a variety of transmission modes, represent high or potentially high epidemic or endemic burden, and are well represented in the literature. We also developed working criteria for what attributes can be used to comprehensively describe an operational model including a model’s documentation, accessibility, and sustainability. To apply the model characterization framework, we built the BARD, which is publicly available (http://brd.bsvgateway.org).A document was also developed to describe the usability requirements for the BARD; potential users (and non-users) and use cases are formally described to explain the scope of use. 1. Framework for model characterization. The framework is divided into six major components (Figure 1):Model Purpose, Model Objective, Model Scope, Biosurveillance(BSV) goals, Conceptual Model and Model Utility; each of which has several sub-categories for characterizing each aspect of a model.2. Application to model characterization Models for five infectious diseases—cholera, malaria, influenza, FMD and dengue were characterized using the framework and are included in the BARD database. Our framework characterized disparate models in a streamlined fashion. Model information could be binned into the same categories, allowing easy manual comparison and understanding of the models.3. Development of the BARD. Our model characterization framework was implemented into an actionable tool which provides specific information about a model that has been systematically categorized. It allows manual category-to-category comparison of multiple models for a single disease and while the tool does not rank models it provides model information in a format that allows a user to make a ranking or an assessment of the utility of the model. With the model characterization framework we hope to encourage model developers to start describing the many features of their models using a common format. We illustrate the application of the framework through the development of the BARD which is a scientific and non-biased tool for selecting an appropriate epidemiological model for infectious disease surveillance. Epidemiological models are not necessarily being developed with decision makers in mind. This gap between model developers and decision makers needs to be narrowed before modeling becomes routinely implemented in decision making. The characterization framework and the tool developed (BARD) area first step towards addressing this gap.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2008

Providing Internet Access to High-Resolution Lunar Images

The OnMoon server is a computer program that provides Internet access to high-resolution Lunar images, maps, and elevation data, all suitable for use in geographical information system (GIS) software for generating images, maps, and computational models of the Moon. The OnMoon server implements the Open Geospatial Consortium (OGC) Web Map Service (WMS) server protocol and supports Moon-specific extensions. Unlike other Internet map servers that provide Lunar data using an Earth coordinate system, the OnMoon server supports encoding of data in Moon-specific coordinate systems. The OnMoon server offers access to most of the available high-resolution Lunar image and elevation data. This server can generate image and map files in the tagged image file format (TIFF) or the Joint Photographic Experts Group (JPEG), 8- or 16-bit Portable Network Graphics (PNG), or Keyhole Markup Language (KML) format. Image control is provided by use of the OGC Style Layer Descriptor (SLD) protocol. Full-precision spectral arithmetic processing is also available, by use of a custom SLD extension. This server can dynamically add shaded relief based on the Lunar elevation to any image layer. This server also implements tiled WMS protocol and super-overlay KML for high-performance client application programs.

Plesea, Lucian↗

DOE OSTI2020

Application of physiologically based pharmacokinetic modeling for sertraline dosing recommendations in pregnancy

Pregnancy is a period of significant change that impacts physiological and metabolic status leading to alterations in the disposition of drugs. Uncertainty in drug dosing in pregnancy can lead to suboptimal therapy, which can contribute to disease exacerbation. A few studies show there are increased dosing requirements for antidepressants in late pregnancy; however, the quantitative data to guide dose adjustments are sparse. We aimed to develop a physiologically based pharmacokinetic (PBPK) model that allows gestational-age dependent prediction of sertraline dosing in pregnancy. A minimal physiological model with defined gut, liver, plasma, and lumped placental-fetal compartments was constructed using the ordinary differential equation solver package, ‘mrgsolve’, in R. We extracted data from the literature to parameterize the model, including sertraline physicochemical properties, in vitro metabolism studies, disposition in nonpregnant women, and physiological changes during pregnancy. The model predicted the pharmacokinetic parameters from a clinical study with eight subjects for the second trimester and six subjects for the third trimester. Based on the model, gestational-dependent changes in physiology and metabolism account for increased clearance of sertraline (up to 143% at 40 weeks gestational age), potentially leading to under-dosing of pregnant women when nonpregnancy doses are used. The PBPK model was converted to a prototype web-based interactive dosing tool to demonstrate how the output of a PBPK model may translate into optimal sertraline dosing in pregnancy. Quantitative prediction of drug exposure using PBPK modeling in pregnancy will support clinically appropriate dosing and increase the therapeutic benefit for pregnant women.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Application of Manufacturing Quality Management Principles to PV System Installations

To help SETO/DOE achieve its goals, the IBTS team proposed a project addressing system reliability by improving installation standards and quality management. The proposed approach was designed to help achieve measurable reductions in installation defect density and improvements in the performance of PV systems by optimizing design and installation of residential and commercial PV systems. This approach addressed the soft costs associated with installations and quality management. The project demonstrated improved system reliability and reduced PV system installation costs. The software developed improved operations, decreased risk, and increased the overall value of PV systems across their lifecycle. The project used several data collection methods, including extensive industry surveys, face-to-face high-level interviews at industry conferences, stakeholder teleconferences, and in-depth interviews conducted by IBTS staff. Results from the research found the industry needs a uniform assessment method for national providers to be more efficient; the software should support both code officials and installers; most industry stakeholders would find value in a centralized software system that allows them to collect, report, and review information on in-process and completed solar installations; and mobile solutions that bridge existing knowledge gaps with inspectors and integrate with existing methodologies (such as permitting software) are of great value. The software solution developed is web-based, allowing for national access, and is built on a Google Firebase platform that can handle significant users and data. It can be used onsite or remotely, allowing for code compliance to continue despite ongoing pandemic related delays or shutdowns for local economies. The information provided by the software tool allows users to uniformly assess a system for compliance and use that aggregated data to identify training topics or create internal process designed to improving issues and reducing occurrence. This solution has multiple benefits in managing quality at time of use and promoting an increase in future safety and quality through education. Perhaps most importantly, this software increases public safety by ensuring compliance of installed systems and allows for local AHJs to remotely engage specialized and qualified solar specific expertise for oversite of the installation in their jurisdictions. Data analysis provides the quality feedback loop identifying the root cause of failure and drives installation practices to improve through training and education, resulting in systems with higher performance, greater reliability, and reduced operations and maintenance costs. With the successful completion of this project, the industry can expect reduced soft costs and increased performance and safety and will ultimately benefit from longer performing systems that cost less to operate.

14 SOLAR ENERGY↗

DOE OSTI2020

ASCR@40: Highlights and Impacts of ASCR’s Programs

A report compiled by the ASCAC Subcommittee on the 40-year history of ASCR for the U.S. Department of Energy’s Office of Advanced Scientific Computing Research. The Office of Advanced Scientific Computing Research (ASCR) sits within the Office of Science in the Department of Energy (DOE). Per their web pages, “the mission of the ASCR program is to discover, develop, and deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to the DOE.” This succinct statement encompasses a wide range of responsibilities for computing and networking facilities; for procuring, deploying, and operating high performance computing, networking, and storage resources; for basic research in mathematics and computer science; for developing and sustaining a large body of software; and for partnering with organizations across the Office of Science and beyond. While its mission statement may seem very contemporary, the roots of ASCR are quite deep—long predating the creation of DOE. Applied mathematics and advanced computing were both elements of the Theoretical Division of the Manhattan Project. In the early 1950s, the Manhattan Project scientist and mathematician John von Neumann, then a commissioner for the AEC (Atomic Energy Commission), advocated for the creation of a Mathematics program to support the continued development and applications of digital computing. Los Alamos National Laboratory (LANL) scientist John Pasta created such a program to fund researchers at universities and AEC laboratories. Under several organizational name changes, this program has persisted ever since, and would eventually grow to become ASCR.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1997

An Automated Method for Identifying Inconsistencies within Diagrammatic Software Requirements Specifications

The development of large-scale, composite software in a geographically distributed environment is an evolutionary process. Often, in such evolving systems, striving for consistency is complicated by many factors, because development participants have various locations, skills, responsibilities, roles, opinions, languages, terminology and different degrees of abstraction they employ. This naturally leads to many partial specifications or viewpoints. These multiple views on the system being developed usually overlap. From another aspect, these multiple views give rise to the potential for inconsistency. Existing CASE tools do not efficiently manage inconsistencies in distributed development environment for a large-scale project. Based on the ViewPoints framework the WHERE (Web-Based Hypertext Environment for requirements Evolution) toolkit aims to tackle inconsistency management issues within geographically distributed software development projects. Consequently, WHERE project helps make more robust software and support software assurance process. The long term goal of WHERE tools aims to the inconsistency analysis and management in requirements specifications. A framework based on Graph Grammar theory and TCMJAVA toolkit is proposed to detect inconsistencies among viewpoints. This systematic approach uses three basic operations (UNION, DIFFERENCE, INTERSECTION) to study the static behaviors of graphic and tabular notations. From these operations, subgraphs Query, Selection, Merge, Replacement operations can be derived. This approach uses graph PRODUCTIONS (rewriting rules) to study the dynamic transformations of graphs. We discuss the feasibility of implementation these operations. Also, We present the process of porting original TCM (Toolkit for Conceptual Modeling) project from C++ to Java programming language in this thesis. A scenario based on NASA International Space Station Specification is discussed to show the applicability of our approach. Finally, conclusion and future work about inconsistency management issues in WHERE project will be summarized.

Zhang, Zhong↗

NASA NTRS2017

A Relevancy Algorithm for Curating Earth Science Data Around Phenomenon

Earth science data are being collected for various science needs and applications, processed using different algorithms at multiple resolutions and coverages, and then archived at different archiving centers for distribution and stewardship causing difficulty in data discovery. Curation, which typically occurs in museums, art galleries, and libraries, is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest. Curating data sets around topics or areas of interest addresses some of the data discovery needs in the field of Earth science, especially for unanticipated users of data. This paper describes a methodology to automate search and selection of data around specific phenomena. Different components of the methodology including the assumptions, the process, and the relevancy ranking algorithm are described. The paper makes two unique contributions to improving data search and discovery capabilities. First, the paper describes a novel methodology developed for automatically curating data around a topic using Earthscience metadata records. Second, the methodology has been implemented as a standalone web service that is utilized to augment search and usability of data in a variety of tools.

earth science phenomena↗

DOE OSTI2019

Operational experience with the new CMS DAQ-Expert

The data acquisition (DAQ) system of the Compact Muon Solenoid (CMS) at CERN reads out the detector at the level-1 trigger accept rate of 100 kHz, assembles events with a bandwidth of 200 GB/s, provides these events to the high level-trigger running on a farm of about 30k cores and records the accepted events. Comprising custom-built and cutting edge commercial hardware and several 1000 instances of software applications, the DAQ system is complex in itself and failures cannot be completely excluded. Moreover, problems in the readout of the detectors,in the first level trigger system or in the high level trigger may provoke anomalous behaviour of the DAQ systemwhich sometimes cannot easily be differentiated from a problem in the DAQ system itself. In order to achieve high data taking efficiency with operators from the entire collaboration and without relying too heavily on the on-call experts, an expert system, the DAQ-Expert, has been developed that can pinpoint the source of most failures and give advice to the shift crew on how to recover in the quickest way. The DAQ-Expert constantly analyzes monitoring data from the DAQ system and the high level trigger by making use of logic modules written in Java that encapsulate the expert knowledge about potential operational problems. The results of the reasoning are presented to the operator in a web-based dashboard, may trigger sound alerts in the control room and are archived for post-mortem analysis - presented in a web-based timeline browser. We present the design of the DAQ-Expert and report on the operational experience since 2017, when it was first put into production.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2013

PETSc Users Manual (Rev. 3.3)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

PETSc Users Manual (Rev. 3.4)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

PETSc Users Manual (Rev. 3.5)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. ;For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2002

Near-Real-Time Detection and Monitoring of Dust Events by Satellite (SeaWIFS, MODIS, and TOMS)

Over the last few years satellites have given us increasingly detailed information on the size, location, and duration of dust events around the world. These data not only provide valuable feedback to the modelling community as to the fidelity of their aerosol models but are also finding increasing use in near real-time applications. In particular, the ability to locate and track the development of aerosol dust clouds on a near real-time basis is being used by scientists and government to provide warning of air pollution episodes over major urban area. This ability has also become a crucial component of recent coordinated campaigns to study the characteristics of tropospheric aerosols such as dust and their effect on climate. One such recent campaign was ACE-Asia, which was designed to obtain the comprehensive set of ground, aircraft, and satellite data necessary to provide a detailed understanding of atmospheric aerosol particles over the Asian-Pacific region. As part of ACE-Asia, we developed a near real-time data processing and access system to provide satellite data from the polar-orbiting instruments Earth Probe TOMS (in the form of absorbing aerosol index) and SeaWiFS (in the form of aerosol optical thickness, AOT, and Angstrom exponent). The results were available via web access. The location and movement information provided by these data were used both in support of the day-to-day flight planning of ACE-Asia and as input into aerosol transport models. While near real-time SeaWiFS data processing can be performed using either the normal global data product or data obtained via direct broadcast to receiving stations close to the area of interest, near real-time MODIS processing of data to provide aerosol retrievals is currently only available using its direct broadcast capability. In this paper, we will briefly discuss the algorithms used to generate these data. The retrieved aerosol optical thickness and Angstrom exponent from SeaWiFS will be compared with those obtained from various AERONET sites over the Asian-Pacific region. The TOMS aerosol index will also be compared with AERONET aerosol optical thickness over different aerosol conditions, and comparisons between the MODIS and SeaWiFS data will also be presented. Finally, we will discuss the climate implication of our studies using the combined satellite and AERONET observations.

Hsu, N. Christina↗