Performance Portability in the Uintah Runtime System Through the Use of Kokkos.
Abstract not provided.
Sunderland, Daniel↗
SEARCH · Engineering Papers
Results for “Software Library”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Replicated computational results (RCR) report for "BLIS: A framework for rapidly instantiating BLAS functionality"
“BLIS: A Framework for Rapidly Instantiating BLAS Functionality” includes single-platform BLIS performance results for both level-2 and level-3 operations that is competitive with OpenBLAS, ATLAS, and Intel MKL. A detailed description of the configuration used to generate the performance results was provided to the reviewer by the authors. All the software components used in the comparison were reinstalled and new performance results were generated and compared to the original results. After completing this process, the published results are deemed replicable by the reviewer.
97 MATHEMATICS AND COMPUTING↗
A computational modeling framework for pre-clinical evaluation of cardiac mapping systems
There are a variety of difficulties in evaluating clinical cardiac mapping systems, most notably the inability to record the transmembrane potential throughout the entire heart during patient procedures which prevents the comparison to a relevant “gold standard”. Cardiac mapping systems are comprised of hardware and software elements including sophisticated mathematical algorithms, both of which continue to undergo rapid innovation. The purpose of this study is to develop a computational modeling framework to evaluate the performance of cardiac mapping systems. The framework enables rigorous evaluation of a mapping system’s ability to localize and characterize (i.e., focal or reentrant) arrhythmogenic sources in the heart. The main component of our tool is a library of computer simulations of various dynamic patterns throughout the entire heart in which the type and location of the arrhythmogenic sources are known. Our framework allows for performance evaluation for various electrode configurations, heart geometries, arrhythmias, and electrogram noise levels and involves blind comparison of mapping systems against a “silver standard” comprised of computer simulations in which the precise transmembrane potential patterns throughout the heart are known. A feasibility study was performed using simulations of patterns in the human left atria and three hypothetical virtual catheter electrode arrays. Activation times (AcT) and patterns (AcP) were computed for three virtual electrode arrays: two basket arrays with good and poor contact and one high-resolution grid with uniform spacing. The average root mean squared difference of AcTs of electrograms and those of the nearest endocardial action potential was less than 1 ms and therefore appears to be a poor performance metric. In an effort to standardize performance evaluation of mapping systems a novel performance metric is introduced based on the number of AcPs identified correctly and those considered spurious as well as misclassifications of arrhythmia type; spatial and temporal localization accuracy of correctly identified patterns was also quantified. This approach provides a rigorous quantitative analysis of cardiac mapping system performance. Proof of concept of this computational evaluation framework suggests that it could help safeguard that mapping systems perform as expected as well as provide estimates of system accuracy.
59 BASIC BIOLOGICAL SCIENCES↗
Using PVM to host CLIPS in distributed environments
It is relatively easy to enhance CLIPS (C Language Integrated Production System) to support multiple expert systems running in a distributed environment with heterogeneous machines. The task is minimized by using the PVM (Parallel Virtual Machine) code from Oak Ridge Labs to provide the distributed utility. PVM is a library of C and FORTRAN subprograms that supports distributive computing on many different UNIX platforms. A PVM deamon is easily installed on each CPU that enters the virtual machine environment. Any user with rsh or rexec access to a machine can use the one PVM deamon to obtain a generous set of distributed facilities. The ready availability of both CLIPS and PVM makes the combination of software particularly attractive for budget conscious experimentation of heterogeneous distributive computing with multiple CLIPS executables. This paper presents a design that is sufficient to provide essential message passing functions in CLIPS and enable the full range of PVM facilities.
Myers, Leonard↗
Development and Operations of the Astrophysics Data System
The ADS was represented at the AAS meeting with 3 poster papers and a demonstration booth. We have setup a mirror site of the Vizier data base system at the CDS. functionality of the ADC at Goddard. This will replace the Preparations for the APS and LPSC meetings in March started. We will have demonstrations at both meetings. Preparations for the APS and LPSC meetings in March continued. We will have demonstrations at both meetings. The ADS was represented with a poster at the joint AGUEGU meeting in Nice, France. Discussions about the on-going collaboration between the ADS and the CDS in Strasbourg, France were held in Strasbourg. The ADS was invited to organize a session about the ADS and its mirror sites at the next United Nations Workshop on Basic Space Sciences in the Developing World. Efforts are under way to enter the tables of contents of all conference proceedings in the SA0 library into the ADS. This requires copying the tables of contents from all volumes in the library and have them typed in. This will greatly enhance the coverage of the literature in the ADS. We started the development of a search system for the full text of all scanned material in the ADS. This will eventually allow our users search capabilities that so far do not exist in any form. I order to enable the full text searching, we have purchased OCR software and are in the process of OCRing the scanned pages in the ADS. Efforts are in progress to handle the inclusion of data set identifiers in article manuscripts. The ADS will be the central system that will allow the journals to verify data set identifiers. The "master verifier" has been implemented in prototype form at the ADS. We started to include more journals in Geosciences/Geophysics in the ADS. The Royal astronomical Society has decided to archive their on-line journals in the ADS three years after publication. We have started to process these older on-line articles in order to archive them in the ADS. Our mirror site in Korea now has a full article mirror. We developed XML output capability in the ADS. This will make it easier to exchange data with other data systems. We started the development of new indexing software that will eventually reduce the indexing time for a database from days to hours or less. The ADS was represented at the IAU General Assembly with a poster. Discussions with the IAU management were held about extending the ADS IAU collaborations.
Murray, Stephen S.↗
Enhanced Graphics for Extended Scale Range
Enhanced Graphics for Extended Scale Range is a computer program for rendering fly-through views of scene models that include visible objects differing in size by large orders of magnitude. An example would be a scene showing a person in a park at night with the moon, stars, and galaxies in the background sky. Prior graphical computer programs exhibit arithmetic and other anomalies when rendering scenes containing objects that differ enormously in scale and distance from the viewer. The present program dynamically repartitions distance scales of objects in a scene during rendering to eliminate almost all such anomalies in a way compatible with implementation in other software and in hardware accelerators. By assigning depth ranges correspond ing to rendering precision requirements, either automatically or under program control, this program spaces out object scales to match the precision requirements of the rendering arithmetic. This action includes an intelligent partition of the depth buffer ranges to avoid known anomalies from this source. The program is written in C++, using OpenGL, GLUT, and GLUI standard libraries, and nVidia GEForce Vertex Shader extensions. The program has been shown to work on several computers running UNIX and Windows operating systems.
Hanson, Andrew J.↗
Software Development and Testing Support for the Avionics Systems Telemetry Tool Suite
The Customer Avionics Interface Development and Analysis (CAIDA) team helps to provide modeling and simulation software for the verification of the Launch Control System (LCS). With a new iteration of telemetry tools being developed, extensive work must be done to ensure features are implemented in an efficient manner. The authors worked to develop new functionalities in the telemetry tools, update documentation, and perform various tests on the CAIDA Advanced Telemetry Tool (CATT). This was accomplished with Python through built-in library frameworks. In addition, work needed to be performed to set up a training document for new engineers and interns joining the team in the future. The outcome of this internship was the completion of several new features, unit and functional tests on CATT, thorough documentation, and a developer’s guide to programming under CAIDA.
Negron-Martinez, Antonio Jose↗
MODIS Technical Report Series. Volume 4: MODIS data access user's guide: Scan cube format
The software described in this document provides I/O functions to be used with Moderate Resolution Spectroradiometer (MODIS) level 1 and 2 data, and could be easily extended to other data sources. This data is in a scan cube data format: a 3-dimensional ragged array containing multiple bands which have resolutions ranging from 250 to 1000 meters. The complexity of the data structure is handled internally by the library. The I/O calls allow the user to access any pixel in any band through 'C' structure syntax. The high MODIS data volume (approaching half a terabyte per day) has been a driving factor in the library design. To avoid recopying data for user access, all I/O is performed through dynamic 'C' pointer manipulation. This manual contains background material on MODIS, several coding examples of library usage, in-depth discussions of each function, reference 'man' type pages, and several appendices with details of the included files used to customize a user's data product for use with the library.
Kalb, Virginia L.↗
Light Output Fitting Software
Light output response of scintillators is crucial to the utilization of organic scintillators as effective tools in radiation detection and measurement. While the response is a continuous distribution, the light output corresponding to the maximum energy deposition is crucial in effectively understanding and simulating a detector. There are a variety of fits derived in literature that will vary for every detector material. The Light Output Response Fitter, or LORF Program is a python script designed to easily and quickly compute and plot fits for a variety of scintillator light output models. It includes a stopping power library constructed from SRIM including Organic Glass, EJ309, EJ301, Stilbene, EJ276, and their deuterated counterparts by default, with the ability for the user to add custom stopping power libraries. The user is also capable of importing the python package and utilizing its in-built functions as appropriate. Uses for this capability include plotting and computing a model with known parameters.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Modeling liquid organic thin films on substrates
We present the rationale, methods, and results of modeling of thin film organic liquids on various substrates. These liquids may coat surfaces (substrates) either as a result of their production, dispersal via aerosols or spills. Identification of unknown coated surfaces using either reflectance or emittance spectroscopy cannot be accomplished simply through reference to reflectance signature libraries since neither the thickness of the liquid layer nor the substrate type is known beforehand and both contribute to the signature. Liquid spectral libraries offer the complex index of refraction (n,k) as a function of wavelength which by itself is useful only for thick (bulk) liquid layers via computation of reflectance and transmittance coefficients using the Fresnel equations. Thin liquid layers both reflect and refract incident light in combination with reflectance from the substrate. We show modeling of various organic liquids on substrates using commercial thin film design and modeling software, as well as Monte Carlo ray tracing software to demonstrate the variety of potential signatures encountered that depend on the thickness of the liquid layer as well as the characteristics of the substrate (metal or dielectric). These substrates give rise to transflectance behavior, while many dielectric substrates have rich absorption features that provide complex signatures that combine attributes of both the liquid and the substrate. Knowledge of the complex index of refraction of both target liquids and substrates is essential in order to synthesize spectra necessary in the application of target identification algorithms.
complex index of refraction↗
The MCDB System for Management and Analysis of Petabyte-Scale Uncertain Data
Analysts working with very large data sets often use statistical models to “guess” at unknown, inaccurate, or missing information associated with the data. For example, a distant object viewed through an optical lens will have its position slightly shifted by imperfections in the lens. Thus, rather than considering the object’s observed position to be absolutely correct, it makes sense to take into account the lens’s imperfections to obtain a probabilistic guess as to the object’s true position. For another example, it might be important to associate some sort of error distribution with each of the individual sensors in an array of magnetometers. This error distribution may be complex and include spatially-driven covariances, because errors in nearby sensors are likely to be correlated (caused, for example, by the presence of some nearby, fixed metal object). This project is concerned with the design and implementation of a prototype data management system called the Monte Carlo Database System, or MCDB for short. MCDB allows an expert-level analyst or statistician to attach arbitrary stochastic models to very large data sets in order to “guess” the values for unknown or inaccurate data, such as the actual position of the observed object in the lens example above. When the resulting data set is analyzed, the underlying stochastic models are used to generate hundreds or thousands of possible data set instances, and each of those possible instances is analyzed separately by MCDB. Thus, MCDB does not just give a single answer to the analysis, but it actually gives an empirical distribution of query results that embody the underlying uncertainty, and can in turn be analyzed using standard statistical techniques. The stochastic models in MCDB are implemented as user-defined, external C++ libraries called Variable Generation functions (VG functions for short). Because the VG function interface is exceedingly general, it allows MCDB to be used in a very wide variety of application domains, in conjunction with virtually any stochastic model. Ultimately, we ended up calling the system that we developed over the course of the project SimSQL, to denote the fact that it allowed for stochastic simulation of data. The software developed during the lifetime of the project is available for download from the SimSQL project website: http://cmj4.web.rice.edu/SimSQL/SimSQL.html.
42 ENGINEERING↗
Eigenvalue routines in NASTRAN: A comparison with the Block Lanczos method
The NASA STRuctural ANalysis (NASTRAN) program is one of the most extensively used engineering applications software in the world. It contains a wealth of matrix operations and numerical solution techniques, and they were used to construct efficient eigenvalue routines. The purpose of this paper is to examine the current eigenvalue routines in NASTRAN and to make efficiency comparisons with a more recent implementation of the Block Lanczos algorithm by Boeing Computer Services (BCS). This eigenvalue routine is now available in the BCS mathematics library as well as in several commercial versions of NASTRAN. In addition, CRAY maintains a modified version of this routine on their network. Several example problems, with a varying number of degrees of freedom, were selected primarily for efficiency bench-marking. Accuracy is not an issue, because they all gave comparable results. The Block Lanczos algorithm was found to be extremely efficient, in particular, for very large size problems.
Tischler, V. A.↗
SNPP and NOAA-20 VIIRS On-Orbit Geolocation Trending and Improvements
Two Visible Infrared Imaging Radiometer Suite (VIIRS) sensors have been in operations for more than 8.5 and 2.5 years since they were launched in October 2011 on SNPP satellite and in November 2017 on NOAA-20 satellite, respectively. These are two satellites in the Join Polar Satellite System (JPSS) constellation, of which Suomi National Polar-orbiting Partnership (SNPP) is a risk reduction satellite and NOAA-20 is the first of four JPSS satellites(JPSS-1 became NOAA-20 after launch). Accurate geolocation is a critical element in data calibration for accurate retrieval of global biogeophysical parameters. In this paper, we describe the latest trends in the continuously improved geolocation accuracy in VIIRS Collection-1 (C1) and C2 re-processing. We implemented a VIIRS instrument geometric model update (VIGMU)for both sensors that correct for geolocation error oscilations in the scan direction. We borrowed code from Moderate Resolution Imaging Spectroradiometer (MODIS) geolocation software to correct for time-dependent pointing variations, that are particularly acute in NOAA-20 VIIRS, and some pointing anomalies in SNPP VIIRS. We developed a Kalman Filter using gyrodata to correct for attitude errors due to the degradation of the star trackers performance from the SNPP satellite. We also present an improved ground control point matching (CPM) tool, in which the ground control point (GCP) chips library is refreshed using recently launched Landsat-8 images.
SNPP↗
THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA
Nobody is better suited to “describe” data than the scientist who created it. This “description” about a data is called Metadata. In general terms, Metadata represents the who, what, when, where, why and how of the dataset [1]. eXtensible Markup Language (XML) is the preferred output format for metadata, as it makes it portable and, more importantly, suitable for system discoverability. The newly developed ORNL Metadata Editor (OME) is a Web-based tool that allows users to create and maintain XML files containing key information, or metadata, about the research. Metadata include information about the specific projects, parameters, time periods, and locations associated with the data. Such information helps put the research findings in context. In addition, the metadata produced using OME will allow other researchers to find these data via Metadata clearinghouses like Mercury [2][4]. OME is part of ORNL’s Mercury software fleet [2][3]. It was jointly developed to support projects funded by the United States Geological Survey (USGS), U.S. Department of Energy (DOE), National Aeronautics and Space Administration (NASA) and National Oceanic and Atmospheric Administration (NOAA). OME’s architecture provides a customizable interface to support project-specific requirements. Using this new architecture, the ORNL team developed OME instances for USGS’s Core Science Analytics, Synthesis, and Libraries (CSAS&L), DOE’s Next Generation Ecosystem Experiments (NGEE) and Atmospheric Radiation Measurement (ARM) Program, and the international Surface Ocean Carbon Dioxide ATlas (SOCAT).Researchers simply use the ORNL Metadata Editor to enter relevant metadata into a Web-based form. From the information on the form, the Metadata Editor can create an XML file on the server that the editor is installed or to the user’s personal computer. Researchers can also use the ORNL Metadata Editor to modify existing XML metadata files.As an example, an NGEE Arctic scientist use OME to register their datasets to the NGEE data archive and allows the NGEE archive to publish these datasets via a data search portal (http://ngee.ornl.gov/data). These highly descriptive metadata created using OME allows the Archive to enable advanced data search options using keyword, geo-spatial, temporal and ontology filters. Similarly, ARM OME allows scientists or principal investigators (PIs) to submit their data products to the ARM data archive.How would OME help Big Data Centers like the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC)?The ORNL DAAC is one of NASA’s Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of the Earth's environment. Typically data produced, archived and analyzed is at a scale of multiple petabytes, which makes the discoverability of the data very challenging. Without proper metadata associated with the data, it is difficult to find the data you are looking for and equally difficult to use and understand the data.OME will allow data centers like the NGEE and ORNL DAAC to produce meaningful, high quality, standards-based, descriptive information about their data products in-turn helping with the data discoverability and interoperability. Useful Links:USGS OME: http://mercury.ornl.gov/OME/NGEE OME: http://ngee-arctic.ornl.gov/ngeemetadata/ARM OME: http://archive2.ornl.gov/armome/Contact: Ranjeet Devarakonda (devarakondar@ornl.gov)References:[1] Federal Geographic Data Committee. Content standard for digital geospatial metadata. Federal Geographic Data Committee, 1998.[2] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94.[3] Wilson, B. E., Palanisamy, G., Devarakonda, R., Rhyne, B. T., Lindsley, C., & Green, J. (2010). Mercury Toolset for Spatiotemporal Metadata.[4] Pouchard, L. C., Branstetter, M. L., Cook, R. B., Devarakonda, R., Green, J., Palanisamy, G., ... & Noy, N. F. (2013). A Linked Science investigation: enhancing climate change data discovery with semantic technologies. Earth science informatics, 6(3), 175-185.
FGDC CSDGM↗
Calculating uncertainty on K-effective with MONK10 - 14583
Criticality safety assessments require a demonstration that a particular configuration of fissile material has an adequate sub-critical margin (k-effective sufficiently below unity) to ensure that the risk of criticality under normal operation and accident conditions is acceptable. The required sub-critical margin depends upon the uncertainty in the estimated value of k-effective. The uncertainty in the calculated value of k-effective arises from a number of sources, including: manufacturing tolerances on input data to the code (affecting geometry, compositions and densities), uncertainty in the nuclear data used by the code, stochastic uncertainty resulting from Monte Carlo simulation and modelling approximations/errors, including the inevitable bugs in the software. The ANSWERS Software Service, in collaboration with industrial partners, is developing a number of techniques to better understand and quantify uncertainty on predicted values of k-effective, using MONK. The SPRUCE utility code has been developed to allow uncertainty to be estimated using sampling methods. This can include the sampling of input parameters (including dimensions, compositions and densities) from statistical distributions. It can also include sampling different nuclear data libraries. A set of nuclear data libraries has been generated for this purpose by sampling from statistical distributions that represent the uncertainties in the published nuclear data evaluated files; a set of libraries has been produced for Latin Hypercube Sampling. By varying the input data and nuclear data, separate and combined uncertainties due to manufacturing tolerances and nuclear data can be derived. By performing least squares fitting on the results it is also possible to estimate the contribution of each of the uncertain inputs and a sensitivity method in MONK can break down the nuclear data uncertainty. (authors)
42 ENGINEERING↗
Software for Processing Flight and Simulated Data of the ATIC Experiment
ATIC (Advanced Thin Ionization Calorimeter) is a balloon borne experiment designed to measure the cosmic ray composition for elements from hydrogen to iron and their energy spectra from approx.50 GeV to near 100 TeV. It consists of a Si-matrix detector to determine the charge of a CR particle, a scintillator hodoscope for tracking, carbon interaction targets and a fully active BGO calorimeter. ATIC had its first flight from McMurdo, Antarctica from 28/12/2000 to 13/01/2001. The ATIC flight collected approximately 25 million events. A C++-class library for building different programs for processing flight and simulated data of the ATIC balloon experiment is described. This library is compatible with the ROOT-system and includes classes and methods for solving a number of problems as the following: Reading data files in different formats (raw-data format, ROOT-format, ASCII-format, different formats for simulated data); Transferring all these formats to the only inner format of the library; Reconstruction of trajectories of primary particles with BGO calorimeter only. The Monte-Carlo simulations with GEANT code were used to obtain the basic tables for computing error corridors and chi(sup 2)-values for the trajectories. Obtaining error corridors for searching for signal of primary particle in the Si-matrix; Searching for hit of primary particle in the Si-matrix with using of error corridor and other criteria (chi(sup 2)-values, agreement between signals in Si-matrix and in the upper layer of scintillator and others); Determination of charge of primary particle; Determination of energy deposit in BGO calorimeter.
Panov, A. D.↗
Performance Debugging and Tuning of Flash-X with Data Analysis Tools
State-of-the-art multiphysics simulations running on large scale leadership computing platforms have many variables contributing to their performance and scaling behavior. We recently encountered an interesting performance anomaly in Flash-X, a multiphysics multicomponent simulation software, when characterizing its performance behavior on several large-scale HPC platforms. The anomaly was tracked down to the interaction between the use of dynamic allocation of scratch data and data locality in the cache hierarchy. In this paper we present the details of unexpected performance variability of Flash-X, its extensive analysis using the performance measurement tool TAU to collect the data and Python data analysis libraries to explore the data, and our insights from this experience. In this process, we discovered and removed or mitigated two additional performance limiting bottlenecks for performance tuning.
Huck, Kevin↗
Geant4 based positron beam source (GPos) v1.0
GPos is a software that was created to determine the properties of positron beams resulting from the interaction of the LBNL BELLA center PetaWatt laser-driven plasma-capillary accelerated electron beam and the atoms of a thin solid target. GPos is written in C++, easily compiled with cmake and the spack package manager, which allows for multi-thread and MPI parallel computing. Its functions expand on the Geant4 toolkit library and allow for propagation of the modelled particles through vacuum drift distances with a focusing element (thin lens approximation). Users can change beam-foil-drift-lens parameters - to adapt GPos to other particle sources and infrastructures - in a simple input file. The code particle data output format, openPMD, which is compatible, for example, with the input of the ECP WarpX project code used to explore the physics of particle acceleration in plasmas. Using GPos in conjunction to WarpX allowed us to test various configurations for designing a high-quality and high-energy positron source at BELLA -required for us to address positron acceleration challenges in the development of future linear colliders. GPos can also be advantageous when tackling the physics of muon sources for future muon colliders as well as for the investigation of positron sources in lower energy regimes for applications like annihilation spectroscopy and astrophysical gamma-ray-bursts.
Pinto de Almeida Amorim, Ligia↗