Accelerating execution of the integrated TIGER series Monte Carlo radiation transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, L.M.; Hochstedler, R.D.

1997-02-01

Execution of the integrated TIGER series (ITS) of coupled electron/photon Monte Carlo radiation transport codes has been accelerated by modifying the FORTRAN source code for more efficient computation. Each member code of ITS was benchmarked and profiled with a specific test case that directed the acceleration effort toward the most computationally intensive subroutines. Techniques for accelerating these subroutines included replacing linear search algorithms with binary versions, replacing the pseudo-random number generator, reducing program memory allocation, and proofing the input files for geometrical redundancies. All techniques produced identical or statistically similar results to the original code. Final benchmark timing of themore » accelerated code resulted in speed-up factors of 2.00 for TIGER (the one-dimensional slab geometry code), 1.74 for CYLTRAN (the two-dimensional cylindrical geometry code), and 1.90 for ACCEPT (the arbitrary three-dimensional geometry code).« less

A Guide to Axial-Flow Turbine Off-Design Computer Program AXOD2

NASA Technical Reports Server (NTRS)

Chen, Shu-Cheng S.

2014-01-01

A Users Guide for the axial flow turbine off-design computer program AXOD2 is composed in this paper. This Users Guide is supplementary to the original Users Manual of AXOD. Three notable contributions of AXOD2 to its predecessor AXOD, both in the context of the Guide or in the functionality of the code, are described and discussed in length. These are: 1) a rational representation of the mathematical principles applied, with concise descriptions of the formulas implemented in the actual coding. Their physical implications are addressed; 2) the creation and documentation of an Addendum Listing of input namelist-parameters unique to AXOD2, that differ from or are in addition to the original input-namelists given in the Manual of AXOD. Their usages are discussed; and 3) the institution of proper stoppages of the code execution, encoding termination messaging and error messages of the execution to AXOD2. These measures are to safe-guard the integrity of the code execution, such that a failure mode encountered during a case-study would not plunge the code execution into indefinite loop, or cause a blow-out of the program execution. Details on these are discussed and illustrated in this paper. Moreover, this computer program has since been reconstructed substantially. Standard FORTRAN Langue was instituted, and the code was formatted in Double Precision (REAL*8). As the result, the code is now suited for use in a local Desktop Computer Environment, is perfectly portable to any Operating System, and can be executed by any FORTRAN compiler equivalent to a FORTRAN 9095 compiler. AXOD2 will be available through NASA Glenn Research Center (GRC) Software Repository.

Performance Analysis and Optimization on the UCLA Parallel Atmospheric General Circulation Model Code

NASA Technical Reports Server (NTRS)

Lou, John; Ferraro, Robert; Farrara, John; Mechoso, Carlos

1996-01-01

An analysis is presented of several factors influencing the performance of a parallel implementation of the UCLA atmospheric general circulation model (AGCM) on massively parallel computer systems. Several modificaitons to the original parallel AGCM code aimed at improving its numerical efficiency, interprocessor communication cost, load-balance and issues affecting single-node code performance are discussed.

A computer-aided design system geared toward conceptual design in a research environment. [for hypersonic vehicles

NASA Technical Reports Server (NTRS)

STACK S. H.

1981-01-01

A computer-aided design system has recently been developed specifically for the small research group environment. The system is implemented on a Prime 400 minicomputer linked with a CDC 6600 computer. The goal was to assign the minicomputer specific tasks, such as data input and graphics, thereby reserving the large mainframe computer for time-consuming analysis codes. The basic structure of the design system consists of GEMPAK, a computer code that generates detailed configuration geometry from a minimum of input; interface programs that reformat GEMPAK geometry for input to the analysis codes; and utility programs that simplify computer access and data interpretation. The working system has had a large positive impact on the quantity and quality of research performed by the originating group. This paper describes the system, the major factors that contributed to its particular form, and presents examples of its application.

Emergence of Coding and its Specificity as a Physico-Informatic Problem

NASA Astrophysics Data System (ADS)

Wills, Peter R.; Nieselt, Kay; McCaskill, John S.

2015-06-01

We explore the origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events. Cells are cybernetic: they use genetic information in processes of communication and control, subjecting physical events to a system of integrated governance. The genetic code is the most obvious example of how cells use information computationally, but the historical origin of the usefulness of molecular information is not well understood. Genetic coding made information useful because it imposed a modular metric on the evolutionary search and thereby offered a general solution to the problem of finding catalysts of any specificity. We use the term "quasispecies symmetry breaking" to describe the iterated process of self-organisation whereby the alphabets of distinguishable codons and amino acids increased, step by step.

Los Alamos radiation transport code system on desktop computing platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Briesmeister, J.F.; Brinkley, F.W.; Clark, B.A.

The Los Alamos Radiation Transport Code System (LARTCS) consists of state-of-the-art Monte Carlo and discrete ordinates transport codes and data libraries. These codes were originally developed many years ago and have undergone continual improvement. With a large initial effort and continued vigilance, the codes are easily portable from one type of hardware to another. The performance of scientific work-stations (SWS) has evolved to the point that such platforms can be used routinely to perform sophisticated radiation transport calculations. As the personal computer (PC) performance approaches that of the SWS, the hardware options for desk-top radiation transport calculations expands considerably. Themore » current status of the radiation transport codes within the LARTCS is described: MCNP, SABRINA, LAHET, ONEDANT, TWODANT, TWOHEX, and ONELD. Specifically, the authors discuss hardware systems on which the codes run and present code performance comparisons for various machines.« less

Additional extensions to the NASCAP computer code, volume 3

NASA Technical Reports Server (NTRS)

Mandell, M. J.; Cooke, D. L.

1981-01-01

The ION computer code is designed to calculate charge exchange ion densities, electric potentials, plasma temperatures, and current densities external to a neutralized ion engine in R-Z geometry. The present version assumes the beam ion current and density to be known and specified, and the neutralizing electrons to originate from a hot-wire ring surrounding the beam orifice. The plasma is treated as being resistive, with an electron relaxation time comparable to the plasma frequency. Together with the thermal and electrical boundary conditions described below and other straightforward engine parameters, these assumptions suffice to determine the required quantities. The ION code, written in ASCII FORTRAN for UNIVAC 1100 series computers, is designed to be run interactively, although it can also be run in batch mode. The input is free-format, and the output is mainly graphical, using the machine-independent graphics developed for the NASCAP code. The executive routine calls the code's major subroutines in user-specified order, and the code allows great latitude for restart and parameter change.

Computer Viruses: Prevention, Detection, and Treatment

DTIC Science & Technology

1990-03-12

executed, also carries out its covert function, potentially undetected. This class of attack earned the term "Trojan horse" from the original of Greek ... mythology , signifying a gift which conceals a malicious purpose. 1 cause harm. The offending code may be present in a code segment the user "touches," which

Validation of CFD/Heat Transfer Software for Turbine Blade Analysis

NASA Technical Reports Server (NTRS)

Kiefer, Walter D.

2004-01-01

I am an intern in the Turbine Branch of the Turbomachinery and Propulsion Systems Division. The division is primarily concerned with experimental and computational methods of calculating heat transfer effects of turbine blades during operation in jet engines and land-based power systems. These include modeling flow in internal cooling passages and film cooling, as well as calculating heat flux and peak temperatures to ensure safe and efficient operation. The branch is research-oriented, emphasizing the development of tools that may be used by gas turbine designers in industry. The branch has been developing a computational fluid dynamics (CFD) and heat transfer code called GlennHT to achieve the computational end of this analysis. The code was originally written in FORTRAN 77 and run on Silicon Graphics machines. However the code has been rewritten and compiled in FORTRAN 90 to take advantage of more modem computer memory systems. In addition the branch has made a switch in system architectures from SGI's to Linux PC's. The newly modified code therefore needs to be tested and validated. This is the primary goal of my internship. To validate the GlennHT code, it must be run using benchmark fluid mechanics and heat transfer test cases, for which there are either analytical solutions or widely accepted experimental data. From the solutions generated by the code, comparisons can be made to the correct solutions to establish the accuracy of the code. To design and create these test cases, there are many steps and programs that must be used. Before a test case can be run, pre-processing steps must be accomplished. These include generating a grid to describe the geometry, using a software package called GridPro. Also various files required by the GlennHT code must be created including a boundary condition file, a file for multi-processor computing, and a file to describe problem and algorithm parameters. A good deal of this internship will be to become familiar with these programs and the structure of the GlennHT code. Additional information is included in the original extended abstract.

Software for Collaborative Engineering of Launch Rockets

NASA Technical Reports Server (NTRS)

Stanley, Thomas Troy

2003-01-01

The Rocket Evaluation and Cost Integration for Propulsion and Engineering software enables collaborative computing with automated exchange of information in the design and analysis of launch rockets and other complex systems. RECIPE can interact with and incorporate a variety of programs, including legacy codes, that model aspects of a system from the perspectives of different technological disciplines (e.g., aerodynamics, structures, propulsion, trajectory, aeroheating, controls, and operations) and that are used by different engineers on different computers running different operating systems. RECIPE consists mainly of (1) ISCRM a file-transfer subprogram that makes it possible for legacy codes executed in their original operating systems on their original computers to exchange data and (2) CONES an easy-to-use filewrapper subprogram that enables the integration of legacy codes. RECIPE provides a tightly integrated conceptual framework that emphasizes connectivity among the programs used by the collaborators, linking these programs in a manner that provides some configuration control while facilitating collaborative engineering tradeoff studies, including design to cost studies. In comparison with prior collaborative-engineering schemes, one based on the use of RECIPE enables fewer engineers to do more in less time.

A performance comparison of the Cray-2 and the Cray X-MP

NASA Technical Reports Server (NTRS)

Schmickley, Ronald; Bailey, David H.

1986-01-01

A suite of thirteen large Fortran benchmark codes were run on Cray-2 and Cray X-MP supercomputers. These codes were a mix of compute-intensive scientific application programs (mostly Computational Fluid Dynamics) and some special vectorized computation exercise programs. For the general class of programs tested on the Cray-2, most of which were not specially tuned for speed, the floating point operation rates varied under a variety of system load configurations from 40 percent up to 125 percent of X-MP performance rates. It is concluded that the Cray-2, in the original system configuration studied (without memory pseudo-banking) will run untuned Fortran code, on average, about 70 percent of X-MP speeds.

New Parallel computing framework for radiation transport codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostin, M.A.; /Michigan State U., NSCL; Mokhov, N.V.

A new parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was integrated with the MARS15 code, and an effort is under way to deploy it in PHITS. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility canmore » be used in single process calculations as well as in the parallel regime. Several checkpoint files can be merged into one thus combining results of several calculations. The framework also corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

PIES free boundary stellarator equilibria with improved initial conditions

NASA Astrophysics Data System (ADS)

Drevlak, M.; Monticello, D.; Reiman, A.

2005-07-01

The MFBE procedure developed by Strumberger (1997 Nucl. Fusion 37 19) is used to provide an improved starting point for free boundary equilibrium computations in the case of W7-X (Nührenberg and Zille 1986 Phys. Lett. A 114 129) using the Princeton iterative equilibrium solver (PIES) code (Reiman and Greenside 1986 Comput. Phys. Commun. 43 157). Transferring the consistent field found by the variational moments equilibrium code (VMEC) (Hirshmann and Whitson 1983 Phys. Fluids 26 3553) to an extended coordinate system using the VMORPH code, a safe margin between plasma boundary and PIES domain is established. The new EXTENDER_P code implements a generalization of the virtual casing principle, which allows field extension both for VMEC and PIES equilibria. This facilitates analysis of the 5/5 islands of the W7-X standard case without including them in the original PIES computation.

New features and applications of PRESTO, a computer code for the performance of regenerative, superheated steam turbine cycles

NASA Technical Reports Server (NTRS)

Choo, Y. K.; Staiger, P. J.

1982-01-01

The code was designed to analyze performance at valves-wide-open design flow. The code can model conventional steam cycles as well as cycles that include such special features as process steam extraction and induction and feedwater heating by external heat sources. Convenience features and extensions to the special features were incorporated into the PRESTO code. The features are described, and detailed examples illustrating the use of both the original and the special features are given.

Computer program for the Kendall family of trend tests

USGS Publications Warehouse

Helsel, Dennis R.; Mueller, David K.; Slack, James R.

2006-01-01

The Seasonal Kendall (SK) test for trend was developed by the U.S. Geological Survey and has become the most frequently used test for trend in the environmental sciences. Recently the test was modified to form the Regional Kendall (RK) test for trend. In this form, trends at numerous locations within a region are tested to determine whether the direction of trend is consistent across the entire region. Computer code developed at the USGS in the 1980s to perform the SK test is no longer widely available. Other versions written by other scientists may or may not be easily available, and may require commercial software in order to be run. These other versions do not explicitly compute the RK test. Therefore, the original code for computing the SK test has been repackaged into a program that runs under the Windows operating system. This program may be used to verify that other implementations of the test give the same results as the original. The program also provides a means for computing the RK test and the simpler Mann-Kendall test for trend.

Development of Parallel Computing Framework to Enhance Radiation Transport Code Capabilities for Rare Isotope Beam Facility Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostin, Mikhail; Mokhov, Nikolai; Niita, Koji

A parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. It is intended to be used with older radiation transport codes implemented in Fortran77, Fortran 90 or C. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was developed and tested in conjunction with the MARS15 code. It is possible to use it with other codes such as PHITS, FLUKA andmore » MCNP after certain adjustments. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility can be used in single process calculations as well as in the parallel regime. The framework corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

Implementing Scientific Simulation Codes Highly Tailored for Vector Architectures Using Custom Configurable Computing Machines

NASA Technical Reports Server (NTRS)

Rutishauser, David

2006-01-01

The motivation for this work comes from an observation that amidst the push for Massively Parallel (MP) solutions to high-end computing problems such as numerical physical simulations, large amounts of legacy code exist that are highly optimized for vector supercomputers. Because re-hosting legacy code often requires a complete re-write of the original code, which can be a very long and expensive effort, this work examines the potential to exploit reconfigurable computing machines in place of a vector supercomputer to implement an essentially unmodified legacy source code. Custom and reconfigurable computing resources could be used to emulate an original application's target platform to the extent required to achieve high performance. To arrive at an architecture that delivers the desired performance subject to limited resources involves solving a multi-variable optimization problem with constraints. Prior research in the area of reconfigurable computing has demonstrated that designing an optimum hardware implementation of a given application under hardware resource constraints is an NP-complete problem. The premise of the approach is that the general issue of applying reconfigurable computing resources to the implementation of an application, maximizing the performance of the computation subject to physical resource constraints, can be made a tractable problem by assuming a computational paradigm, such as vector processing. This research contributes a formulation of the problem and a methodology to design a reconfigurable vector processing implementation of a given application that satisfies a performance metric. A generic, parametric, architectural framework for vector processing implemented in reconfigurable logic is developed as a target for a scheduling/mapping algorithm that maps an input computation to a given instance of the architecture. This algorithm is integrated with an optimization framework to arrive at a specification of the architecture parameters that attempts to minimize execution time, while staying within resource constraints. The flexibility of using a custom reconfigurable implementation is exploited in a unique manner to leverage the lessons learned in vector supercomputer development. The vector processing framework is tailored to the application, with variable parameters that are fixed in traditional vector processing. Benchmark data that demonstrates the functionality and utility of the approach is presented. The benchmark data includes an identified bottleneck in a real case study example vector code, the NASA Langley Terminal Area Simulation System (TASS) application.

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

Documentation of probabilistic fracture mechanics codes used for reactor pressure vessels subjected to pressurized thermal shock loading: Parts 1 and 2. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balkey, K.; Witt, F.J.; Bishop, B.A.

1995-06-01

Significant attention has been focused on the issue of reactor vessel pressurized thermal shock (PTS) for many years. Pressurized thermal shock transient events are characterized by a rapid cooldown at potentially high pressure levels that could lead to a reactor vessel integrity concern for some pressurized water reactors. As a result of regulatory and industry efforts in the early 1980`s, a probabilistic risk assessment methodology has been established to address this concern. Probabilistic fracture mechanics analyses are performed as part of this methodology to determine conditional probability of significant flaw extension for given pressurized thermal shock events. While recent industrymore » efforts are underway to benchmark probabilistic fracture mechanics computer codes that are currently used by the nuclear industry, Part I of this report describes the comparison of two independent computer codes used at the time of the development of the original U.S. Nuclear Regulatory Commission (NRC) pressurized thermal shock rule. The work that was originally performed in 1982 and 1983 to compare the U.S. NRC - VISA and Westinghouse (W) - PFM computer codes has been documented and is provided in Part I of this report. Part II of this report describes the results of more recent industry efforts to benchmark PFM computer codes used by the nuclear industry. This study was conducted as part of the USNRC-EPRI Coordinated Research Program for reviewing the technical basis for pressurized thermal shock (PTS) analyses of the reactor pressure vessel. The work focused on the probabilistic fracture mechanics (PFM) analysis codes and methods used to perform the PTS calculations. An in-depth review of the methodologies was performed to verify the accuracy and adequacy of the various different codes. The review was structured around a series of benchmark sample problems to provide a specific context for discussion and examination of the fracture mechanics methodology.« less

Second Generation Integrated Composite Analyzer (ICAN) Computer Code

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Ginty, Carol A.; Sanfeliz, Jose G.

1993-01-01

This manual updates the original 1986 NASA TP-2515, Integrated Composite Analyzer (ICAN) Users and Programmers Manual. The various enhancements and newly added features are described to enable the user to prepare the appropriate input data to run this updated version of the ICAN code. For reference, the micromechanics equations are provided in an appendix and should be compared to those in the original manual for modifications. A complete output for a sample case is also provided in a separate appendix. The input to the code includes constituent material properties, factors reflecting the fabrication process, and laminate configuration. The code performs micromechanics, macromechanics, and laminate analyses, including the hygrothermal response of polymer-matrix-based fiber composites. The output includes the various ply and composite properties, the composite structural response, and the composite stress analysis results with details on failure. The code is written in FORTRAN 77 and can be used efficiently as a self-contained package (or as a module) in complex structural analysis programs. The input-output format has changed considerably from the original version of ICAN and is described extensively through the use of a sample problem.

Upgrades of Two Computer Codes for Analysis of Turbomachinery

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.; Liou, Meng-Sing

2005-01-01

Major upgrades have been made in two of the programs reported in "ive Computer Codes for Analysis of Turbomachinery". The affected programs are: Swift -- a code for three-dimensional (3D) multiblock analysis; and TCGRID, which generates a 3D grid used with Swift. Originally utilizing only a central-differencing scheme for numerical solution, Swift was augmented by addition of two upwind schemes that give greater accuracy but take more computing time. Other improvements in Swift include addition of a shear-stress-transport turbulence model for better prediction of adverse pressure gradients, addition of an H-grid capability for flexibility in modeling flows in pumps and ducts, and modification to enable simultaneous modeling of hub and tip clearances. Improvements in TCGRID include modifications to enable generation of grids for more complicated flow paths and addition of an option to generate grids compatible with the ADPAC code used at NASA and in industry. For both codes, new test cases were developed and documentation was updated. Both codes were converted to Fortran 90, with dynamic memory allocation. Both codes were also modified for ease of use in both UNIX and Windows operating systems.

WDEC: A Code for Modeling White Dwarf Structure and Pulsations

NASA Astrophysics Data System (ADS)

Bischoff-Kim, Agnès; Montgomery, Michael H.

2018-05-01

The White Dwarf Evolution Code (WDEC), written in Fortran, makes models of white dwarf stars. It is fast, versatile, and includes the latest physics. The code evolves hot (∼100,000 K) input models down to a chosen effective temperature by relaxing the models to be solutions of the equations of stellar structure. The code can also be used to obtain g-mode oscillation modes for the models. WDEC has a long history going back to the late 1960s. Over the years, it has been updated and re-packaged for modern computer architectures and has specifically been used in computationally intensive asteroseismic fitting. Generations of white dwarf astronomers and dozens of publications have made use of the WDEC, although the last true instrument paper is the original one, published in 1975. This paper discusses the history of the code, necessary to understand why it works the way it does, details the physics and features in the code today, and points the reader to where to find the code and a user guide.

Application of a personal computer for the uncoupled vibration analysis of wind turbine blade and counterweight assemblies

NASA Technical Reports Server (NTRS)

White, P. R.; Little, R. R.

1985-01-01

A research effort was undertaken to develop personal computer based software for vibrational analysis. The software was developed to analytically determine the natural frequencies and mode shapes for the uncoupled lateral vibrations of the blade and counterweight assemblies used in a single bladed wind turbine. The uncoupled vibration analysis was performed in both the flapwise and chordwise directions for static rotor conditions. The effects of rotation on the uncoupled flapwise vibration of the blade and counterweight assemblies were evaluated for various rotor speeds up to 90 rpm. The theory, used in the vibration analysis codes, is based on a lumped mass formulation for the blade and counterweight assemblies. The codes are general so that other designs can be readily analyzed. The input for the codes is generally interactive to facilitate usage. The output of the codes is both tabular and graphical. Listings of the codes are provided. Predicted natural frequencies of the first several modes show reasonable agreement with experimental results. The analysis codes were originally developed on a DEC PDP 11/34 minicomputer and then downloaded and modified to run on an ITT XTRA personal computer. Studies conducted to evaluate the efficiency of running the programs on a personal computer as compared with the minicomputer indicated that, with the proper combination of hardware and software options, the efficiency of using a personal computer exceeds that of a minicomputer.

Experimental QR code optical encryption: noise-free data recovering.

PubMed

Barrera, John Fredy; Mira-Agudelo, Alejandro; Torroba, Roberto

2014-05-15

We report, to our knowledge for the first time, the experimental implementation of a quick response (QR) code as a "container" in an optical encryption system. A joint transform correlator architecture in an interferometric configuration is chosen as the experimental scheme. As the implementation is not possible in a single step, a multiplexing procedure to encrypt the QR code of the original information is applied. Once the QR code is correctly decrypted, the speckle noise present in the recovered QR code is eliminated by a simple digital procedure. Finally, the original information is retrieved completely free of any kind of degradation after reading the QR code. Additionally, we propose and implement a new protocol in which the reception of the encrypted QR code and its decryption, the digital block processing, and the reading of the decrypted QR code are performed employing only one device (smartphone, tablet, or computer). The overall method probes to produce an outcome far more attractive to make the adoption of the technique a plausible option. Experimental results are presented to demonstrate the practicality of the proposed security system.

Aeroacoustic Analysis of Turbofan Noise Generation

NASA Technical Reports Server (NTRS)

Meyer, Harold D.; Envia, Edmane

1996-01-01

This report provides an updated version of analytical documentation for the V072 Rotor Wake/Stator Interaction Code. It presents the theoretical derivation of the equations used in the code and, where necessary, it documents the enhancements and changes made to the original code since its first release. V072 is a package of FORTRAN computer programs which calculate the in-duct acoustic modes excited by a fan/stator stage operating in a subsonic mean flow. Sound is generated by the stator vanes interacting with the mean wakes of the rotor blades. In this updated version, only the tonal noise produced at the blade passing frequency and its harmonics, is described. The broadband noise component analysis, which was part of the original report, is not included here. The code provides outputs of modal pressure and power amplitudes generated by the rotor-wake/stator interaction. The rotor/stator stage is modeled as an ensemble of blades and vanes of zero camber and thickness enclosed within an infinite hard-walled annular duct. The amplitude of each propagating mode is computed and summed to obtain the harmonics of sound power flux within the duct for both upstream and downstream propagating modes.

Computational logic: its origins and applications.

PubMed

Paulson, Lawrence C

2018-02-01

Computational logic is the use of computers to establish facts in a logical formalism. Originating in nineteenth century attempts to understand the nature of mathematical reasoning, the subject now comprises a wide variety of formalisms, techniques and technologies. One strand of work follows the 'logic for computable functions (LCF) approach' pioneered by Robin Milner, where proofs can be constructed interactively or with the help of users' code (which does not compromise correctness). A refinement of LCF, called Isabelle, retains these advantages while providing flexibility in the choice of logical formalism and much stronger automation. The main application of these techniques has been to prove the correctness of hardware and software systems, but increasingly researchers have been applying them to mathematics itself.

MAVIS III -- A Windows 95/NT Upgrade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hardwick, M.F.

1997-12-01

MAVIS (Modeling and Analysis of Explosive Valve Interactions) is a computer program that simulates operation of explosively actuated valve. MAVIS was originally written in Fortran in the mid 1970`s and was primarily run on the Sandia Vax computers in use through the early 1990`s. During the mid to late 1980`s MAVIS was upgraded to include the effects of plastic deformation and it became MAVIS II. When the Vax computers were retired, the Gas Transfer System (GTS) Development Department ported the code to the Macintosh and PC platforms, where it ran as a simple console application. All graphical output was lostmore » during these ports. GTS code developers recently completed an upgrade that provides a Windows 95/NT MAVIS application and restores all of the original graphical output. This upgrade is called MAVIS III version 1.0. This report serves both as a user`s manual for MAVIS III v 1.0 and as a general software development reference.« less

Reply to comment by Melsen et al. on "Most computational hydrology is not reproducible, so is it really science?"

NASA Astrophysics Data System (ADS)

Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

2017-03-01

In this article, we reply to a comment made by Melsen et al. [2017] on our previous commentary regarding reproducibility in computational hydrology. Re-executing someone else's code and workflow to derive a set of published results does not by itself constitute reproducibility. However, it forms a key part of the process: it demonstrates that all the degrees of freedom and choices made by the scientist in running the experiment are contained within that code and workflow. This does not only allow us to build and extend directly from the original work, but with full knowledge of decisions made in the original experimental setup, we can then focus our attention to the degrees of freedom of interest: those that occur in hydrological systems that are ultimately our subject of study.

Computation of Thermally Perfect Properties of Oblique Shock Waves

NASA Technical Reports Server (NTRS)

Tatum, Kenneth E.

1996-01-01

A set of compressible flow relations describing flow properties across oblique shock waves, derived for a thermally perfect, calorically imperfect gas, is applied within the existing thermally perfect gas (TPG) computer code. The relations are based upon a value of cp expressed as a polynomial function of temperature. The updated code produces tables of compressible flow properties of oblique shock waves, as well as the original properties of normal shock waves and basic isentropic flow, in a format similar to the tables for normal shock waves found in NACA Rep. 1135. The code results are validated in both the calorically perfect and the calorically imperfect, thermally perfect temperature regimes through comparisons with the theoretical methods of NACA Rep. 1135, and with a state-of-the-art computational fluid dynamics code. The advantages of the TPG code for oblique shock wave calculations, as well as for the properties of isentropic flow and normal shock waves, are its ease of use, and its applicability to any type of gas (monatomic, diatomic, triatomic, polyatomic, or any specified mixture thereof).

A method of non-contact reading code based on computer vision

NASA Astrophysics Data System (ADS)

Zhang, Chunsen; Zong, Xiaoyu; Guo, Bingxuan

2018-03-01

With the purpose of guarantee the computer information exchange security between internal and external network (trusted network and un-trusted network), A non-contact Reading code method based on machine vision has been proposed. Which is different from the existing network physical isolation method. By using the computer monitors, camera and other equipment. Deal with the information which will be on exchanged, Include image coding ,Generate the standard image , Display and get the actual image , Calculate homography matrix, Image distort correction and decoding in calibration, To achieve the computer information security, Non-contact, One-way transmission between the internal and external network , The effectiveness of the proposed method is verified by experiments on real computer text data, The speed of data transfer can be achieved 24kb/s. The experiment shows that this algorithm has the characteristics of high security, fast velocity and less loss of information. Which can meet the daily needs of the confidentiality department to update the data effectively and reliably, Solved the difficulty of computer information exchange between Secret network and non-secret network, With distinctive originality, practicability, and practical research value.

Current and anticipated uses of the thermal hydraulics codes at the NRC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caruso, R.

1997-07-01

The focus of Thermal-Hydraulic computer code usage in nuclear regulatory organizations has undergone a considerable shift since the codes were originally conceived. Less work is being done in the area of {open_quotes}Design Basis Accidents,{close_quotes}, and much more emphasis is being placed on analysis of operational events, probabalistic risk/safety assessment, and maintenance practices. All of these areas need support from Thermal-Hydraulic computer codes to model the behavior of plant fluid systems, and they all need the ability to perform large numbers of analyses quickly. It is therefore important for the T/H codes of the future to be able to support thesemore » needs, by providing robust, easy-to-use, tools that produce easy-to understand results for a wider community of nuclear professionals. These tools need to take advantage of the great advances that have occurred recently in computer software, by providing users with graphical user interfaces for both input and output. In addition, reduced costs of computer memory and other hardware have removed the need for excessively complex data structures and numerical schemes, which make the codes more difficult and expensive to modify, maintain, and debug, and which increase problem run-times. Future versions of the T/H codes should also be structured in a modular fashion, to allow for the easy incorporation of new correlations, models, or features, and to simplify maintenance and testing. Finally, it is important that future T/H code developers work closely with the code user community, to ensure that the code meet the needs of those users.« less

A GPU-accelerated implicit meshless method for compressible flows

NASA Astrophysics Data System (ADS)

Zhang, Jia-Le; Ma, Zhi-Hua; Chen, Hong-Quan; Cao, Cheng

2018-05-01

This paper develops a recently proposed GPU based two-dimensional explicit meshless method (Ma et al., 2014) by devising and implementing an efficient parallel LU-SGS implicit algorithm to further improve the computational efficiency. The capability of the original 2D meshless code is extended to deal with 3D complex compressible flow problems. To resolve the inherent data dependency of the standard LU-SGS method, which causes thread-racing conditions destabilizing numerical computation, a generic rainbow coloring method is presented and applied to organize the computational points into different groups by painting neighboring points with different colors. The original LU-SGS method is modified and parallelized accordingly to perform calculations in a color-by-color manner. The CUDA Fortran programming model is employed to develop the key kernel functions to apply boundary conditions, calculate time steps, evaluate residuals as well as advance and update the solution in the temporal space. A series of two- and three-dimensional test cases including compressible flows over single- and multi-element airfoils and a M6 wing are carried out to verify the developed code. The obtained solutions agree well with experimental data and other computational results reported in the literature. Detailed analysis on the performance of the developed code reveals that the developed CPU based implicit meshless method is at least four to eight times faster than its explicit counterpart. The computational efficiency of the implicit method could be further improved by ten to fifteen times on the GPU.

Web Services Provide Access to SCEC Scientific Research Application Software

NASA Astrophysics Data System (ADS)

Gupta, N.; Gupta, V.; Okaya, D.; Kamb, L.; Maechling, P.

2003-12-01

Web services offer scientific communities a new paradigm for sharing research codes and communicating results. While there are formal technical definitions of what constitutes a web service, for a user community such as the Southern California Earthquake Center (SCEC), we may conceptually consider a web service to be functionality provided on-demand by an application which is run on a remote computer located elsewhere on the Internet. The value of a web service is that it can (1) run a scientific code without the user needing to install and learn the intricacies of running the code; (2) provide the technical framework which allows a user's computer to talk to the remote computer which performs the service; (3) provide the computational resources to run the code; and (4) bundle several analysis steps and provide the end results in digital or (post-processed) graphical form. Within an NSF-sponsored ITR project coordinated by SCEC, we are constructing web services using architectural protocols and programming languages (e.g., Java). However, because the SCEC community has a rich pool of scientific research software (written in traditional languages such as C and FORTRAN), we also emphasize making existing scientific codes available by constructing web service frameworks which wrap around and directly run these codes. In doing so we attempt to broaden community usage of these codes. Web service wrapping of a scientific code can be done using a "web servlet" construction or by using a SOAP/WSDL-based framework. This latter approach is widely adopted in IT circles although it is subject to rapid evolution. Our wrapping framework attempts to "honor" the original codes with as little modification as is possible. For versatility we identify three methods of user access: (A) a web-based GUI (written in HTML and/or Java applets); (B) a Linux/OSX/UNIX command line "initiator" utility (shell-scriptable); and (C) direct access from within any Java application (and with the correct API interface from within C++ and/or C/Fortran). This poster presentation will provide descriptions of the following selected web services and their origin as scientific application codes: 3D community velocity models for Southern California, geocoordinate conversions (latitude/longitude to UTM), execution of GMT graphical scripts, data format conversions (Gocad to Matlab format), and implementation of Seismic Hazard Analysis application programs that calculate hazard curve and hazard map data sets.

Real-time computer treatment of THz passive device images with the high image quality

NASA Astrophysics Data System (ADS)

Trofimov, Vyacheslav A.; Trofimov, Vladislav V.

2012-06-01

We demonstrate real-time computer code improving significantly the quality of images captured by the passive THz imaging system. The code is not only designed for a THz passive device: it can be applied to any kind of such devices and active THz imaging systems as well. We applied our code for computer processing of images captured by four passive THz imaging devices manufactured by different companies. It should be stressed that computer processing of images produced by different companies requires using the different spatial filters usually. The performance of current version of the computer code is greater than one image per second for a THz image having more than 5000 pixels and 24 bit number representation. Processing of THz single image produces about 20 images simultaneously corresponding to various spatial filters. The computer code allows increasing the number of pixels for processed images without noticeable reduction of image quality. The performance of the computer code can be increased many times using parallel algorithms for processing the image. We develop original spatial filters which allow one to see objects with sizes less than 2 cm. The imagery is produced by passive THz imaging devices which captured the images of objects hidden under opaque clothes. For images with high noise we develop an approach which results in suppression of the noise after using the computer processing and we obtain the good quality image. With the aim of illustrating the efficiency of the developed approach we demonstrate the detection of the liquid explosive, ordinary explosive, knife, pistol, metal plate, CD, ceramics, chocolate and other objects hidden under opaque clothes. The results demonstrate the high efficiency of our approach for the detection of hidden objects and they are a very promising solution for the security problem.

Modified Laser and Thermos cell calculations on microcomputers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shapiro, A.; Huria, H.C.

1987-01-01

In the course of designing and operating nuclear reactors, many fuel pin cell calculations are required to obtain homogenized cell cross sections as a function of burnup. In the interest of convenience and cost, it would be very desirable to be able to make such calculations on microcomputers. In addition, such a microcomputer code would be very helpful for educational course work in reactor computations. To establish the feasibility of making detailed cell calculations on a microcomputer, a mainframe cell code was compiled and run on a microcomputer. The computer code Laser, originally written in Fortran IV for the IBM-7090more » class of mainframe computers, is a cylindrical, one-dimensional, multigroup lattice cell program that includes burnup. It is based on the MUFT code for epithermal and fast group calculations, and Thermos for the thermal calculations. There are 50 fast and epithermal groups and 35 thermal groups. Resonances are calculated assuming a homogeneous system and then corrected for self-shielding, Dancoff, and Doppler by self-shielding factors. The Laser code was converted to run on a microcomputer. In addition, the Thermos portion of Laser was extracted and compiled separately to have available a stand alone thermal code.« less

Algorithm 782 : codes for rank-revealing QR factorizations of dense matrices.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bischof, C. H.; Quintana-Orti, G.; Mathematics and Computer Science

1998-06-01

This article describes a suite of codes as well as associated testing and timing drivers for computing rank-revealing QR (RRQR) factorizations of dense matrices. The main contribution is an efficient block algorithm for approximating an RRQR factorization, employing a windowed version of the commonly used Golub pivoting strategy and improved versions of the RRQR algorithms for triangular matrices originally suggested by Chandrasekaran and Ipsen and by Pan and Tang, respectively, We highlight usage and features of these codes.

The generation of meaningful information in molecular systems.

PubMed

Wills, Peter R

2016-03-13

The physico-chemical processes occurring inside cells are under the computational control of genetic (DNA) and epigenetic (internal structural) programming. The origin and evolution of genetic information (nucleic acid sequences) is reasonably well understood, but scant attention has been paid to the origin and evolution of the molecular biological interpreters that give phenotypic meaning to the sequence information that is quite faithfully replicated during cellular reproduction. The near universality and age of the mapping from nucleotide triplets to amino acids embedded in the functionality of the protein synthetic machinery speaks to the early development of a system of coding which is still extant in every living organism. We take the origin of genetic coding as a paradigm of the emergence of computation in natural systems, focusing on the requirement that the molecular components of an interpreter be synthesized autocatalytically. Within this context, it is seen that interpreters of increasing complexity are generated by series of transitions through stepped dynamic instabilities (non-equilibrium phase transitions). The early phylogeny of the amino acyl-tRNA synthetase enzymes is discussed in such terms, leading to the conclusion that the observed optimality of the genetic code is a natural outcome of the processes of self-organization that produced it. © 2016 The Author(s).

Reduction of lithologic-log data to numbers for use in the digital computer

USGS Publications Warehouse

Morgan, C.O.; McNellis, J.M.

1971-01-01

The development of a standardized system for conveniently coding lithologic-log data for use in the digital computer has long been needed. The technique suggested involves a reduction of the original written alphanumeric log to a numeric log by use of computer programs. This numeric log can then be retrieved as a written log, interrogated for pertinent information, or analyzed statistically. ?? 1971 Plenum Publishing Corporation.

Development and application of GASP 2.0

NASA Technical Reports Server (NTRS)

Mcgrory, W. D.; Huebner, L. D.; Slack, D. C.; Walters, R. W.

1992-01-01

GASP 2.0 represents a major new release of the computational fluid dynamics code in wide use by the aerospace community. The authors have spent the last two years analyzing the strengths and weaknesses of the previous version of the finite-rate chemistry, Navier Stokes solution algorithm. What has resulted is a completely redesigned computer code that offers two to four times the performance of previous versions while requiring as little as one quarter of the memory requirements. In addition to the improvements in efficiency over the original code, Version 2.0 contains many new features. A brief discussion of the improvements made to GASP, and an application using GASP 2.0 which demonstrates some of the new features are presented.

Preconditioning for Numerical Simulation of Low Mach Number Three-Dimensional Viscous Turbomachinery Flows

NASA Technical Reports Server (NTRS)

Tweedt, Daniel L.; Chima, Rodrick V.; Turkel, Eli

1997-01-01

A preconditioning scheme has been implemented into a three-dimensional viscous computational fluid dynamics code for turbomachine blade rows. The preconditioning allows the code, originally developed for simulating compressible flow fields, to be applied to nearly-incompressible, low Mach number flows. A brief description is given of the compressible Navier-Stokes equations for a rotating coordinate system, along with the preconditioning method employed. Details about the conservative formulation of artificial dissipation are provided, and different artificial dissipation schemes are discussed and compared. The preconditioned code was applied to a well-documented case involving the NASA large low-speed centrifugal compressor for which detailed experimental data are available for comparison. Performance and flow field data are compared for the near-design operating point of the compressor, with generally good agreement between computation and experiment. Further, significant differences between computational results for the different numerical implementations, revealing different levels of solution accuracy, are discussed.

Computational logic: its origins and applications

PubMed Central

2018-01-01

Computational logic is the use of computers to establish facts in a logical formalism. Originating in nineteenth century attempts to understand the nature of mathematical reasoning, the subject now comprises a wide variety of formalisms, techniques and technologies. One strand of work follows the ‘logic for computable functions (LCF) approach’ pioneered by Robin Milner, where proofs can be constructed interactively or with the help of users’ code (which does not compromise correctness). A refinement of LCF, called Isabelle, retains these advantages while providing flexibility in the choice of logical formalism and much stronger automation. The main application of these techniques has been to prove the correctness of hardware and software systems, but increasingly researchers have been applying them to mathematics itself. PMID:29507522

Development of a 3-D upwind PNS code for chemically reacting hypersonic flowfields

NASA Technical Reports Server (NTRS)

Tannehill, J. C.; Wadawadigi, G.

1992-01-01

Two new parabolized Navier-Stokes (PNS) codes were developed to compute the three-dimensional, viscous, chemically reacting flow of air around hypersonic vehicles such as the National Aero-Space Plane (NASP). The first code (TONIC) solves the gas dynamic and species conservation equations in a fully coupled manner using an implicit, approximately-factored, central-difference algorithm. This code was upgraded to include shock fitting and the capability of computing the flow around complex body shapes. The revised TONIC code was validated by computing the chemically-reacting (M(sub infinity) = 25.3) flow around a 10 deg half-angle cone at various angles of attack and the Ames All-Body model at 0 deg angle of attack. The results of these calculations were in good agreement with the results from the UPS code. One of the major drawbacks of the TONIC code is that the central-differencing of fluxes across interior flowfield discontinuities tends to introduce errors into the solution in the form of local flow property oscillations. The second code (UPS), originally developed for a perfect gas, has been extended to permit either perfect gas, equilibrium air, or nonequilibrium air computations. The code solves the PNS equations using a finite-volume, upwind TVD method based on Roe's approximate Riemann solver that was modified to account for real gas effects. The dissipation term associated with this algorithm is sufficiently adaptive to flow conditions that, even when attempting to capture very strong shock waves, no additional smoothing is required. For nonequilibrium calculations, the code solves the fluid dynamic and species continuity equations in a loosely-coupled manner. This code was used to calculate the hypersonic, laminar flow of chemically reacting air over cones at various angles of attack. In addition, the flow around the McDonnel Douglas generic option blended-wing-body was computed and comparisons were made between the perfect gas, equilibrium air, and the nonequilibrium air results.

Fast ITTBC using pattern code on subband segmentation

NASA Astrophysics Data System (ADS)

Koh, Sung S.; Kim, Hanchil; Lee, Kooyoung; Kim, Hongbin; Jeong, Hun; Cho, Gangseok; Kim, Chunghwa

2000-06-01

Iterated Transformation Theory-Based Coding suffers from very high computational complexity in encoding phase. This is due to its exhaustive search. In this paper, our proposed image coding algorithm preprocess an original image to subband segmentation image by wavelet transform before image coding to reduce encoding complexity. A similar block is searched by using the 24 block pattern codes which are coded by the edge information in the image block on the domain pool of the subband segmentation. As a result, numerical data shows that the encoding time of the proposed coding method can be reduced to 98.82% of that of Joaquin's method, while the loss in quality relative to the Jacquin's is about 0.28 dB in PSNR, which is visually negligible.

Research in Computational Astrobiology

NASA Technical Reports Server (NTRS)

Chaban, Galina; Colombano, Silvano; Scargle, Jeff; New, Michael H.; Pohorille, Andrew; Wilson, Michael A.

2003-01-01

We report on several projects in the field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. Research projects included modifying existing computer simulation codes to use efficient, multiple time step algorithms, statistical methods for analysis of astrophysical data via optimal partitioning methods, electronic structure calculations on water-nuclei acid complexes, incorporation of structural information into genomic sequence analysis methods and calculations of shock-induced formation of polycylic aromatic hydrocarbon compounds.

Cross-indexing of binary SIFT codes for large-scale image search.

PubMed

Liu, Zhen; Li, Houqiang; Zhang, Liyan; Zhou, Wengang; Tian, Qi

2014-05-01

In recent years, there has been growing interest in mapping visual features into compact binary codes for applications on large-scale image collections. Encoding high-dimensional data as compact binary codes reduces the memory cost for storage. Besides, it benefits the computational efficiency since the computation of similarity can be efficiently measured by Hamming distance. In this paper, we propose a novel flexible scale invariant feature transform (SIFT) binarization (FSB) algorithm for large-scale image search. The FSB algorithm explores the magnitude patterns of SIFT descriptor. It is unsupervised and the generated binary codes are demonstrated to be dispreserving. Besides, we propose a new searching strategy to find target features based on the cross-indexing in the binary SIFT space and original SIFT space. We evaluate our approach on two publicly released data sets. The experiments on large-scale partial duplicate image retrieval system demonstrate the effectiveness and efficiency of the proposed algorithm.

Numerical ‘health check’ for scientific codes: the CADNA approach

NASA Astrophysics Data System (ADS)

Scott, N. S.; Jézéquel, F.; Denis, C.; Chesneaux, J.-M.

2007-04-01

Scientific computation has unavoidable approximations built into its very fabric. One important source of error that is difficult to detect and control is round-off error propagation which originates from the use of finite precision arithmetic. We propose that there is a need to perform regular numerical 'health checks' on scientific codes in order to detect the cancerous effect of round-off error propagation. This is particularly important in scientific codes that are built on legacy software. We advocate the use of the CADNA library as a suitable numerical screening tool. We present a case study to illustrate the practical use of CADNA in scientific codes that are of interest to the Computer Physics Communications readership. In doing so we hope to stimulate a greater awareness of round-off error propagation and present a practical means by which it can be analyzed and managed.

Initial results on computational performance of Intel Many Integrated Core (MIC) architecture: implementation of the Weather and Research Forecasting (WRF) Purdue-Lin microphysics scheme

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen H.

2014-10-01

Purdue-Lin scheme is a relatively sophisticated microphysics scheme in the Weather Research and Forecasting (WRF) model. The scheme includes six classes of hydro meteors: water vapor, cloud water, raid, cloud ice, snow and graupel. The scheme is very suitable for massively parallel computation as there are no interactions among horizontal grid points. In this paper, we accelerate the Purdue Lin scheme using Intel Many Integrated Core Architecture (MIC) hardware. The Intel Xeon Phi is a high performance coprocessor consists of up to 61 cores. The Xeon Phi is connected to a CPU via the PCI Express (PICe) bus. In this paper, we will discuss in detail the code optimization issues encountered while tuning the Purdue-Lin microphysics Fortran code for Xeon Phi. In particularly, getting a good performance required utilizing multiple cores, the wide vector operations and make efficient use of memory. The results show that the optimizations improved performance of the original code on Xeon Phi 5110P by a factor of 4.2x. Furthermore, the same optimizations improved performance on Intel Xeon E5-2603 CPU by a factor of 1.2x compared to the original code.

Original analytic solution of a half-bridge modelled as a statically indeterminate system

NASA Astrophysics Data System (ADS)

Oanta, Emil M.; Panait, Cornel; Raicu, Alexandra; Barhalescu, Mihaela

2016-12-01

The paper presents an original computer based analytical model of a half-bridge belonging to a circular settling tank. The primary unknown is computed using the force method, the coefficients of the canonical equation being calculated using either the discretization of the bending moment diagram in trapezoids, or using the relations specific to the polygons. A second algorithm based on the method of initial parameters is also presented. Analyzing the new solution we came to the conclusion that most of the computer code developed for other model may be reused. The results are useful to evaluate the behavior of the structure and to compare with the results of the finite element models.

Parallelization of Lower-Upper Symmetric Gauss-Seidel Method for Chemically Reacting Flow

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Jost, Gabriele; Chang, Sherry

2005-01-01

Development of technologies for exploration of the solar system has revived an interest in computational simulation of chemically reacting flows since planetary probe vehicles exhibit non-equilibrium phenomena during the atmospheric entry of a planet or a moon as well as the reentry to the Earth. Stability in combustion is essential for new propulsion systems. Numerical solution of real-gas flows often increases computational work by an order-of-magnitude compared to perfect gas flow partly because of the increased complexity of equations to solve. Recently, as part of Project Columbia, NASA has integrated a cluster of interconnected SGI Altix systems to provide a ten-fold increase in current supercomputing capacity that includes an SGI Origin system. Both the new and existing machines are based on cache coherent non-uniform memory access architecture. Lower-Upper Symmetric Gauss-Seidel (LU-SGS) relaxation method has been implemented into both perfect and real gas flow codes including Real-Gas Aerodynamic Simulator (RGAS). However, the vectorized RGAS code runs inefficiently on cache-based shared-memory machines such as SGI system. Parallelization of a Gauss-Seidel method is nontrivial due to its sequential nature. The LU-SGS method has been vectorized on an oblique plane in INS3D-LU code that has been one of the base codes for NAS Parallel benchmarks. The oblique plane has been called a hyperplane by computer scientists. It is straightforward to parallelize a Gauss-Seidel method by partitioning the hyperplanes once they are formed. Another way of parallelization is to schedule processors like a pipeline using software. Both hyperplane and pipeline methods have been implemented using openMP directives. The present paper reports the performance of the parallelized RGAS code on SGI Origin and Altix systems.

High performance optical encryption based on computational ghost imaging with QR code and compressive sensing technique

NASA Astrophysics Data System (ADS)

Zhao, Shengmei; Wang, Le; Liang, Wenqiang; Cheng, Weiwen; Gong, Longyan

2015-10-01

In this paper, we propose a high performance optical encryption (OE) scheme based on computational ghost imaging (GI) with QR code and compressive sensing (CS) technique, named QR-CGI-OE scheme. N random phase screens, generated by Alice, is a secret key and be shared with its authorized user, Bob. The information is first encoded by Alice with QR code, and the QR-coded image is then encrypted with the aid of computational ghost imaging optical system. Here, measurement results from the GI optical system's bucket detector are the encrypted information and be transmitted to Bob. With the key, Bob decrypts the encrypted information to obtain the QR-coded image with GI and CS techniques, and further recovers the information by QR decoding. The experimental and numerical simulated results show that the authorized users can recover completely the original image, whereas the eavesdroppers can not acquire any information about the image even the eavesdropping ratio (ER) is up to 60% at the given measurement times. For the proposed scheme, the number of bits sent from Alice to Bob are reduced considerably and the robustness is enhanced significantly. Meantime, the measurement times in GI system is reduced and the quality of the reconstructed QR-coded image is improved.

Liquid rocket combustor computer code development

NASA Technical Reports Server (NTRS)

Liang, P. Y.

1985-01-01

The Advanced Rocket Injector/Combustor Code (ARICC) that has been developed to model the complete chemical/fluid/thermal processes occurring inside rocket combustion chambers are highlighted. The code, derived from the CONCHAS-SPRAY code originally developed at Los Alamos National Laboratory incorporates powerful features such as the ability to model complex injector combustion chamber geometries, Lagrangian tracking of droplets, full chemical equilibrium and kinetic reactions for multiple species, a fractional volume of fluid (VOF) description of liquid jet injection in addition to the gaseous phase fluid dynamics, and turbulent mass, energy, and momentum transport. Atomization and droplet dynamic models from earlier generation codes are transplated into the present code. Currently, ARICC is specialized for liquid oxygen/hydrogen propellants, although other fuel/oxidizer pairs can be easily substituted.

An analysis of thermal response factors and how to reduce their computational time requirement

NASA Technical Reports Server (NTRS)

Wiese, M. R.

1982-01-01

Te RESFAC2 version of the Thermal Response Factor Program (RESFAC) is the result of numerous modifications and additions to the original RESFAC. These modifications and additions have significantly reduced the program's computational time requirement. As a result of this work, the program is more efficient and its code is both readable and understandable. This report describes what a thermal response factor is; analyzes the original matrix algebra calculations and root finding techniques; presents a new root finding technique and streamlined matrix algebra; supplies ten validation cases and their results.

Analysis of random point images with the use of symbolic computation codes and generalized Catalan numbers

NASA Astrophysics Data System (ADS)

Reznik, A. L.; Tuzikov, A. V.; Solov'ev, A. A.; Torgov, A. V.

2016-11-01

Original codes and combinatorial-geometrical computational schemes are presented, which are developed and applied for finding exact analytical formulas that describe the probability of errorless readout of random point images recorded by a scanning aperture with a limited number of threshold levels. Combinatorial problems encountered in the course of the study and associated with the new generalization of Catalan numbers are formulated and solved. An attempt is made to find the explicit analytical form of these numbers, which is, on the one hand, a necessary stage of solving the basic research problem and, on the other hand, an independent self-consistent problem.

Three-dimensional magnetic induction model of an octagonal edge-defined film-fed growth system

NASA Astrophysics Data System (ADS)

Rajendran, S.; Holmes, K.; Menna, A.

1994-03-01

Silicon wafers for the photovoltaic industry are produced by growing thin octagonal tubes by the edge-defined film-fed growth (EFG) process. The thermal origin of the wafer thickness variations was studied with a three-dimensional (3D) magnetic induction model. The implementation of the computer code and the significance of the computed results for improving the thickness uniformity are discussed.

Research on Image Encryption Based on DNA Sequence and Chaos Theory

NASA Astrophysics Data System (ADS)

Tian Zhang, Tian; Yan, Shan Jun; Gu, Cheng Yan; Ren, Ran; Liao, Kai Xin

2018-04-01

Nowadays encryption is a common technique to protect image data from unauthorized access. In recent years, many scientists have proposed various encryption algorithms based on DNA sequence to provide a new idea for the design of image encryption algorithm. Therefore, a new method of image encryption based on DNA computing technology is proposed in this paper, whose original image is encrypted by DNA coding and 1-D logistic chaotic mapping. First, the algorithm uses two modules as the encryption key. The first module uses the real DNA sequence, and the second module is made by one-dimensional logistic chaos mapping. Secondly, the algorithm uses DNA complementary rules to encode original image, and uses the key and DNA computing technology to compute each pixel value of the original image, so as to realize the encryption of the whole image. Simulation results show that the algorithm has good encryption effect and security.

Improvements to Busquet's Non LTE algorithm in NRL's Hydro code

NASA Astrophysics Data System (ADS)

Klapisch, M.; Colombant, D.

1996-11-01

Implementation of the Non LTE model RADIOM (M. Busquet, Phys. Fluids B, 5, 4191 (1993)) in NRL's RAD2D Hydro code in conservative form was reported previously(M. Klapisch et al., Bull. Am. Phys. Soc., 40, 1806 (1995)).While the results were satisfactory, the algorithm was slow and not always converging. We describe here modifications that address the latter two shortcomings. This method is quicker and more stable than the original. It also gives information about the validity of the fitting. It turns out that the number and distribution of groups in the multigroup diffusion opacity tables - a basis for the computation of radiation effects in the ionization balance in RADIOM- has a large influence on the robustness of the algorithm. These modifications give insight about the algorithm, and allow to check that the obtained average charge state is the true average. In addition, code optimization resulted in greatly reduced computing time: The ratio of Non LTE to LTE computing times being now between 1.5 and 2.

Validation of a Computational Fluid Dynamics (CFD) Code for Supersonic Axisymmetric Base Flow

NASA Technical Reports Server (NTRS)

Tucker, P. Kevin

1993-01-01

The ability to accurately and efficiently calculate the flow structure in the base region of bodies of revolution in supersonic flight is a significant step in CFD code validation for applications ranging from base heating for rockets to drag for protectives. The FDNS code is used to compute such a flow and the results are compared to benchmark quality experimental data. Flowfield calculations are presented for a cylindrical afterbody at M = 2.46 and angle of attack a = O. Grid independent solutions are compared to mean velocity profiles in the separated wake area and downstream of the reattachment point. Additionally, quantities such as turbulent kinetic energy and shear layer growth rates are compared to the data. Finally, the computed base pressures are compared to the measured values. An effort is made to elucidate the role of turbulence models in the flowfield predictions. The level of turbulent eddy viscosity, and its origin, are used to contrast the various turbulence models and compare the results to the experimental data.

Performance of the OVERFLOW-MLP and LAURA-MLP CFD Codes on the NASA Ames 512 CPU Origin System

NASA Technical Reports Server (NTRS)

Taft, James R.

2000-01-01

The shared memory Multi-Level Parallelism (MLP) technique, developed last year at NASA Ames has been very successful in dramatically improving the performance of important NASA CFD codes. This new and very simple parallel programming technique was first inserted into the OVERFLOW production CFD code in FY 1998. The OVERFLOW-MLP code's parallel performance scaled linearly to 256 CPUs on the NASA Ames 256 CPU Origin 2000 system (steger). Overall performance exceeded 20.1 GFLOP/s, or about 4.5x the performance of a dedicated 16 CPU C90 system. All of this was achieved without any major modification to the original vector based code. The OVERFLOW-MLP code is now in production on the inhouse Origin systems as well as being used offsite at commercial aerospace companies. Partially as a result of this work, NASA Ames has purchased a new 512 CPU Origin 2000 system to further test the limits of parallel performance for NASA codes of interest. This paper presents the performance obtained from the latest optimization efforts on this machine for the LAURA-MLP and OVERFLOW-MLP codes. The Langley Aerothermodynamics Upwind Relaxation Algorithm (LAURA) code is a key simulation tool in the development of the next generation shuttle, interplanetary reentry vehicles, and nearly all "X" plane development. This code sustains about 4-5 GFLOP/s on a dedicated 16 CPU C90. At this rate, expected workloads would require over 100 C90 CPU years of computing over the next few calendar years. It is not feasible to expect that this would be affordable or available to the user community. Dramatic performance gains on cheaper systems are needed. This code is expected to be perhaps the largest consumer of NASA Ames compute cycles per run in the coming year.The OVERFLOW CFD code is extensively used in the government and commercial aerospace communities to evaluate new aircraft designs. It is one of the largest consumers of NASA supercomputing cycles and large simulations of highly resolved full aircraft are routinely undertaken. Typical large problems might require 100s of Cray C90 CPU hours to complete. The dramatic performance gains with the 256 CPU steger system are exciting. Obtaining results in hours instead of months is revolutionizing the way in which aircraft manufacturers are looking at future aircraft simulation work. Figure 2 below is a current state of the art plot of OVERFLOW-MLP performance on the 512 CPU Lomax system. As can be seen, the chart indicates that OVERFLOW-MLP continues to scale linearly with CPU count up to 512 CPUs on a large 35 million point full aircraft RANS simulation. At this point performance is such that a fully converged simulation of 2500 time steps is completed in less than 2 hours of elapsed time. Further work over the next few weeks will improve the performance of this code even further.The LAURA code has been converted to the MLP format as well. This code is currently being optimized for the 512 CPU system. Performance statistics indicate that the goal of 100 GFLOP/s will be achieved by year's end. This amounts to 20x the 16 CPU C90 result and strongly demonstrates the viability of the new parallel systems rapidly solving very large simulations in a production environment.

Towards Holography via Quantum Source-Channel Codes.

PubMed

Pastawski, Fernando; Eisert, Jens; Wilming, Henrik

2017-07-14

While originally motivated by quantum computation, quantum error correction (QEC) is currently providing valuable insights into many-body quantum physics, such as topological phases of matter. Furthermore, mounting evidence originating from holography research (AdS/CFT) indicates that QEC should also be pertinent for conformal field theories. With this motivation in mind, we introduce quantum source-channel codes, which combine features of lossy compression and approximate quantum error correction, both of which are predicted in holography. Through a recent construction for approximate recovery maps, we derive guarantees on its erasure decoding performance from calculations of an entropic quantity called conditional mutual information. As an example, we consider Gibbs states of the transverse field Ising model at criticality and provide evidence that they exhibit nontrivial protection from local erasure. This gives rise to the first concrete interpretation of a bona fide conformal field theory as a quantum error correcting code. We argue that quantum source-channel codes are of independent interest beyond holography.

Towards Holography via Quantum Source-Channel Codes

NASA Astrophysics Data System (ADS)

Pastawski, Fernando; Eisert, Jens; Wilming, Henrik

2017-07-01

While originally motivated by quantum computation, quantum error correction (QEC) is currently providing valuable insights into many-body quantum physics, such as topological phases of matter. Furthermore, mounting evidence originating from holography research (AdS/CFT) indicates that QEC should also be pertinent for conformal field theories. With this motivation in mind, we introduce quantum source-channel codes, which combine features of lossy compression and approximate quantum error correction, both of which are predicted in holography. Through a recent construction for approximate recovery maps, we derive guarantees on its erasure decoding performance from calculations of an entropic quantity called conditional mutual information. As an example, we consider Gibbs states of the transverse field Ising model at criticality and provide evidence that they exhibit nontrivial protection from local erasure. This gives rise to the first concrete interpretation of a bona fide conformal field theory as a quantum error correcting code. We argue that quantum source-channel codes are of independent interest beyond holography.

Computing travel time when the exact address is unknown: a comparison of point and polygon ZIP code approximation methods.

PubMed

Berke, Ethan M; Shi, Xun

2009-04-29

Travel time is an important metric of geographic access to health care. We compared strategies of estimating travel times when only subject ZIP code data were available. Using simulated data from New Hampshire and Arizona, we estimated travel times to nearest cancer centers by using: 1) geometric centroid of ZIP code polygons as origins, 2) population centroids as origin, 3) service area rings around each cancer center, assigning subjects to rings by assuming they are evenly distributed within their ZIP code, 4) service area rings around each center, assuming the subjects follow the population distribution within the ZIP code. We used travel times based on street addresses as true values to validate estimates. Population-based methods have smaller errors than geometry-based methods. Within categories (geometry or population), centroid and service area methods have similar errors. Errors are smaller in urban areas than in rural areas. Population-based methods are superior to the geometry-based methods, with the population centroid method appearing to be the best choice for estimating travel time. Estimates in rural areas are less reliable.

Error suppression for Hamiltonian quantum computing in Markovian environments

NASA Astrophysics Data System (ADS)

Marvian, Milad; Lidar, Daniel A.

2017-03-01

Hamiltonian quantum computing, such as the adiabatic and holonomic models, can be protected against decoherence using an encoding into stabilizer subspace codes for error detection and the addition of energy penalty terms. This method has been widely studied since it was first introduced by Jordan, Farhi, and Shor (JFS) in the context of adiabatic quantum computing. Here, we extend the original result to general Markovian environments, not necessarily in Lindblad form. We show that the main conclusion of the original JFS study holds under these general circumstances: Assuming a physically reasonable bath model, it is possible to suppress the initial decay out of the encoded ground state with an energy penalty strength that grows only logarithmically in the system size, at a fixed temperature.

Mode-dependent templates and scan order for H.264/AVC-based intra lossless coding.

PubMed

Gu, Zhouye; Lin, Weisi; Lee, Bu-Sung; Lau, Chiew Tong; Sun, Ming-Ting

2012-09-01

In H.264/advanced video coding (AVC), lossless coding and lossy coding share the same entropy coding module. However, the entropy coders in the H.264/AVC standard were original designed for lossy video coding and do not yield adequate performance for lossless video coding. In this paper, we analyze the problem with the current lossless coding scheme and propose a mode-dependent template (MD-template) based method for intra lossless coding. By exploring the statistical redundancy of the prediction residual in the H.264/AVC intra prediction modes, more zero coefficients are generated. By designing a new scan order for each MD-template, the scanned coefficients sequence fits the H.264/AVC entropy coders better. A fast implementation algorithm is also designed. With little computation increase, experimental results confirm that the proposed fast algorithm achieves about 7.2% bit saving compared with the current H.264/AVC fidelity range extensions high profile.

WOLF: a computer code package for the calculation of ion beam trajectories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogel, D.L.

1985-10-01

The WOLF code solves POISSON'S equation within a user-defined problem boundary of arbitrary shape. The code is compatible with ANSI FORTRAN and uses a two-dimensional Cartesian coordinate geometry represented on a triangular lattice. The vacuum electric fields and equipotential lines are calculated for the input problem. The use may then introduce a series of emitters from which particles of different charge-to-mass ratios and initial energies can originate. These non-relativistic particles will then be traced by WOLF through the user-defined region. Effects of ion and electron space charge are included in the calculation. A subprogram PISA forms part of this codemore » and enables optimization of various aspects of the problem. The WOLF package also allows detailed graphics analysis of the computed results to be performed.« less

Calculation of transonic aileron buzz

NASA Technical Reports Server (NTRS)

Steger, J. L.; Bailey, H. E.

1979-01-01

An implicit finite-difference computer code that uses a two-layer algebraic eddy viscosity model and exact geometric specification of the airfoil has been used to simulate transonic aileron buzz. The calculated results, which were performed on both the Illiac IV parallel computer processor and the Control Data 7600 computer, are in essential agreement with the original expository wind-tunnel data taken in the Ames 16-Foot Wind Tunnel just after World War II. These results and a description of the pertinent numerical techniques are included.

Photoplus: auxiliary information for printed images based on distributed source coding

NASA Astrophysics Data System (ADS)

Samadani, Ramin; Mukherjee, Debargha

2008-01-01

A printed photograph is difficult to reuse because the digital information that generated the print may no longer be available. This paper describes a mechanism for approximating the original digital image by combining a scan of the printed photograph with small amounts of digital auxiliary information kept together with the print. The auxiliary information consists of a small amount of digital data to enable accurate registration and color-reproduction, followed by a larger amount of digital data to recover residual errors and lost frequencies by distributed Wyner-Ziv coding techniques. Approximating the original digital image enables many uses, including making good quality reprints from the original print, even when they are faded many years later. In essence, the print itself becomes the currency for archiving and repurposing digital images, without requiring computer infrastructure.

Adapting a Navier-Stokes code to the ICL-DAP

NASA Technical Reports Server (NTRS)

Grosch, C. E.

1985-01-01

The results of an experiment are reported, i.c., to adapt a Navier-Stokes code, originally developed on a serial computer, to concurrent processing on the CL Distributed Array Processor (DAP). The algorithm used in solving the Navier-Stokes equations is briefly described. The architecture of the DAP and DAP FORTRAN are also described. The modifications of the algorithm so as to fit the DAP are given and discussed. Finally, performance results are given and conclusions are drawn.

Computation of turbulent boundary layers employing the defect wall-function method. M.S. Thesis

NASA Technical Reports Server (NTRS)

Brown, Douglas L.

1994-01-01

In order to decrease overall computational time requirements of spatially-marching parabolized Navier-Stokes finite-difference computer code when applied to turbulent fluid flow, a wall-function methodology, originally proposed by R. Barnwell, was implemented. This numerical effort increases computational speed and calculates reasonably accurate wall shear stress spatial distributions and boundary-layer profiles. Since the wall shear stress is analytically determined from the wall-function model, the computational grid near the wall is not required to spatially resolve the laminar-viscous sublayer. Consequently, a substantially increased computational integration step size is achieved resulting in a considerable decrease in net computational time. This wall-function technique is demonstrated for adiabatic flat plate test cases from Mach 2 to Mach 8. These test cases are analytically verified employing: (1) Eckert reference method solutions, (2) experimental turbulent boundary-layer data of Mabey, and (3) finite-difference computational code solutions with fully resolved laminar-viscous sublayers. Additionally, results have been obtained for two pressure-gradient cases: (1) an adiabatic expansion corner and (2) an adiabatic compression corner.

Mathematical Description of Complex Chemical Kinetics and Application to CFD Modeling Codes

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1993-01-01

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.

Mathematical description of complex chemical kinetics and application to CFD modeling codes

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1993-01-01

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.

Time-Dependent Simulation of Incompressible Flow in a Turbopump Using Overset Grid Approach

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan

2001-01-01

This paper reports the progress being made towards complete unsteady turbopump simulation capability by using overset grid systems. A computational model of a turbo-pump impeller is used as a test case for the performance evaluation of the MPI, hybrid MPI/Open-MP, and MLP versions of the INS3D code. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Unsteady computations for a turbo-pump, which contains 114 zones with 34.3 Million grid points, are performed on Origin 2000 systems at NASA Ames Research Center. The approach taken for these simulations, and the performance of the parallel versions of the code are presented.

JSPAM: A restricted three-body code for simulating interacting galaxies

NASA Astrophysics Data System (ADS)

Wallin, J. F.; Holincheck, A. J.; Harvey, A.

2016-07-01

Restricted three-body codes have a proven ability to recreate much of the disturbed morphology of actual interacting galaxies. As more sophisticated n-body models were developed and computer speed increased, restricted three-body codes fell out of favor. However, their supporting role for performing wide searches of parameter space when fitting orbits to real systems demonstrates a continuing need for their use. Here we present the model and algorithm used in the JSPAM code. A precursor of this code was originally described in 1990, and was called SPAM. We have recently updated the software with an alternate potential and a treatment of dynamical friction to more closely mimic the results from n-body tree codes. The code is released publicly for use under the terms of the Academic Free License ("AFL") v. 3.0 and has been added to the Astrophysics Source Code Library.

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Al-Nasra, M.; Zhang, Y.; Baddourah, M. A.; Agarwal, T. K.; Storaasli, O. O.; Carmona, E. A.

1991-01-01

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

SciDAC-3: Searching for Physics Beyond the Standard Model, University of Arizona component, Year 2 progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toussaint, Doug

2014-03-21

The Arizona component of the SciDAC-3 Lattice Gauge Theory program consisted of partial support for a postdoctoral position. In the original budget this covered three fourths of a postdoc, but the University of Arizona changed its ERE rate for postdoctoral positions from 4.3% to 21%, so the support level was closer to two-thirds of a postdoc. The grant covered the work of postdoc Thomas Primer. Dr. Primer's first task was an urgent one, although it was not forseen in our proposed work. It turned out that on the large lattices used in some of our current computations the gauge fixingmore » code was not working as expected, and this revealed itself in inconsistent results in the correlators needed to compute the semileptonic form factors for K and D decays. Dr. Primer participated in the effort to understand this problem and to modify our codes to deal with the large lattices we are now generating (as large as 144 3 x 288). Corrected code was incorporated in our standard codes, and workarounds that allow us to use the correlators already computed with the unexpected gauge fixing were been implemented.« less

A Non-Cut Cell Immersed Boundary Method for Use in Icing Simulations

NASA Technical Reports Server (NTRS)

Sarofeen, Christian M.; Noack, Ralph W.; Kreeger, Richard E.

2013-01-01

This paper describes a computational fluid dynamic method used for modelling changes in aircraft geometry due to icing. While an aircraft undergoes icing, the accumulated ice results in a geometric alteration of the aerodynamic surfaces. In computational simulations for icing, it is necessary that the corresponding geometric change is taken into consideration. The method used, herein, for the representation of the geometric change due to icing is a non-cut cell Immersed Boundary Method (IBM). Computational cells that are in a body fitted grid of a clean aerodynamic geometry that are inside a predicted ice formation are identified. An IBM is then used to change these cells from being active computational cells to having properties of viscous solid bodies. This method has been implemented in the NASA developed node centered, finite volume computational fluid dynamics code, FUN3D. The presented capability is tested for two-dimensional airfoils including a clean airfoil, an iced airfoil, and an airfoil in harmonic pitching motion about its quarter chord. For these simulations velocity contours, pressure distributions, coefficients of lift, coefficients of drag, and coefficients of pitching moment about the airfoil's quarter chord are computed and used for comparison against experimental results, a higher order panel method code with viscous effects, XFOIL, and the results from FUN3D's original solution process. The results of the IBM simulations show that the accuracy of the IBM compares satisfactorily with the experimental results, XFOIL results, and the results from FUN3D's original solution process.

Compressive Sampling based Image Coding for Resource-deficient Visual Communication.

PubMed

Liu, Xianming; Zhai, Deming; Zhou, Jiantao; Zhang, Xinfeng; Zhao, Debin; Gao, Wen

2016-04-14

In this paper, a new compressive sampling based image coding scheme is developed to achieve competitive coding efficiency at lower encoder computational complexity, while supporting error resilience. This technique is particularly suitable for visual communication with resource-deficient devices. At the encoder, compact image representation is produced, which is a polyphase down-sampled version of the input image; but the conventional low-pass filter prior to down-sampling is replaced by a local random binary convolution kernel. The pixels of the resulting down-sampled pre-filtered image are local random measurements and placed in the original spatial configuration. The advantages of local random measurements are two folds: 1) preserve high-frequency image features that are otherwise discarded by low-pass filtering; 2) remain a conventional image and can therefore be coded by any standardized codec to remove statistical redundancy of larger scales. Moreover, measurements generated by different kernels can be considered as multiple descriptions of the original image and therefore the proposed scheme has the advantage of multiple description coding. At the decoder, a unified sparsity-based soft-decoding technique is developed to recover the original image from received measurements in a framework of compressive sensing. Experimental results demonstrate that the proposed scheme is competitive compared with existing methods, with a unique strength of recovering fine details and sharp edges at low bit-rates.

Prioritized LT Codes

NASA Technical Reports Server (NTRS)

Woo, Simon S.; Cheng, Michael K.

2011-01-01

The original Luby Transform (LT) coding scheme is extended to account for data transmissions where some information symbols in a message block are more important than others. Prioritized LT codes provide unequal error protection (UEP) of data on an erasure channel by modifying the original LT encoder. The prioritized algorithm improves high-priority data protection without penalizing low-priority data recovery. Moreover, low-latency decoding is also obtained for high-priority data due to fast encoding. Prioritized LT codes only require a slight change in the original encoding algorithm, and no changes at all at the decoder. Hence, with a small complexity increase in the LT encoder, an improved UEP and low-decoding latency performance for high-priority data can be achieved. LT encoding partitions a data stream into fixed-sized message blocks each with a constant number of information symbols. To generate a code symbol from the information symbols in a message, the Robust-Soliton probability distribution is first applied in order to determine the number of information symbols to be used to compute the code symbol. Then, the specific information symbols are chosen uniform randomly from the message block. Finally, the selected information symbols are XORed to form the code symbol. The Prioritized LT code construction includes an additional restriction that code symbols formed by a relatively small number of XORed information symbols select some of these information symbols from the pool of high-priority data. Once high-priority data are fully covered, encoding continues with the conventional LT approach where code symbols are generated by selecting information symbols from the entire message block including all different priorities. Therefore, if code symbols derived from high-priority data experience an unusual high number of erasures, Prioritized LT codes can still reliably recover both high- and low-priority data. This hybrid approach decides not only "how to encode" but also "what to encode" to achieve UEP. Another advantage of the priority encoding process is that the majority of high-priority data can be decoded sooner since only a small number of code symbols are required to reconstruct high-priority data. This approach increases the likelihood that high-priority data is decoded first over low-priority data. The Prioritized LT code scheme achieves an improvement in high-priority data decoding performance as well as overall information recovery without penalizing the decoding of low-priority data, assuming high-priority data is no more than half of a message block. The cost is in the additional complexity required in the encoder. If extra computation resource is available at the transmitter, image, voice, and video transmission quality in terrestrial and space communications can benefit from accurate use of redundancy in protecting data with varying priorities.

1DTempPro V2: new features for inferring groundwater/surface-water exchange

USGS Publications Warehouse

Koch, Franklin W.; Voytek, Emily B.; Day-Lewis, Frederick D.; Healy, Richard W.; Briggs, Martin A.; Lane, John W.; Werkema, Dale D.

2016-01-01

A new version of the computer program 1DTempPro extends the original code to include new capabilities for (1) automated parameter estimation, (2) layer heterogeneity, and (3) time-varying specific discharge. The code serves as an interface to the U.S. Geological Survey model VS2DH and supports analysis of vertical one-dimensional temperature profiles under saturated flow conditions to assess groundwater/surface-water exchange and estimate hydraulic conductivity for cases where hydraulic head is known.

f1: a code to compute Appell's F1 hypergeometric function

NASA Astrophysics Data System (ADS)

Colavecchia, F. D.; Gasaneo, G.

2004-02-01

In this work we present the FORTRAN code to compute the hypergeometric function F1( α, β1, β2, γ, x, y) of Appell. The program can compute the F1 function for real values of the variables { x, y}, and complex values of the parameters { α, β1, β2, γ}. The code uses different strategies to calculate the function according to the ideas outlined in [F.D. Colavecchia et al., Comput. Phys. Comm. 138 (1) (2001) 29]. Program summaryTitle of the program: f1 Catalogue identifier: ADSJ Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSJ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Computers: PC compatibles, SGI Origin2∗ Operating system under which the program has been tested: Linux, IRIX Programming language used: Fortran 90 Memory required to execute with typical data: 4 kbytes No. of bits in a word: 32 No. of bytes in distributed program, including test data, etc.: 52 325 Distribution format: tar gzip file External subprograms used: Numerical Recipes hypgeo [W.H. Press et al., Numerical Recipes in Fortran 77, Cambridge Univ. Press, 1996] or chyp routine of R.C. Forrey [J. Comput. Phys. 137 (1997) 79], rkf45 [L.F. Shampine and H.H. Watts, Rep. SAND76-0585, 1976]. Keywords: Numerical methods, special functions, hypergeometric functions, Appell functions, Gauss function Nature of the physical problem: Computing the Appell F1 function is relevant in atomic collisions and elementary particle physics. It is usually the result of multidimensional integrals involving Coulomb continuum states. Method of solution: The F1 function has a convergent-series definition for | x|<1 and | y|<1, and several analytic continuations for other regions of the variable space. The code tests the values of the variables and selects one of the precedent cases. In the convergence region the program uses the series definition near the origin of coordinates, and a numerical integration of the third-order differential parametric equation for the F1 function. Also detects several special cases according to the values of the parameters. Restrictions on the complexity of the problem: The code is restricted to real values of the variables { x, y}. Also, there are some parameter domains that are not covered. These usually imply differences between integer parameters that lead to negative integer arguments of Gamma functions. Typical running time: Depends basically on the variables. The computation of Table 4 of [F.D. Colavecchia et al., Comput. Phys. Comm. 138 (1) (2001) 29] (64 functions) requires approximately 0.33 s in a Athlon 900 MHz processor.

An analysis of the metabolic theory of the origin of the genetic code

NASA Technical Reports Server (NTRS)

Amirnovin, R.; Bada, J. L. (Principal Investigator)

1997-01-01

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature.

Injecting Artificial Memory Errors Into a Running Computer Program

NASA Technical Reports Server (NTRS)

Bornstein, Benjamin J.; Granat, Robert A.; Wagstaff, Kiri L.

2008-01-01

Single-event upsets (SEUs) or bitflips are computer memory errors caused by radiation. BITFLIPS (Basic Instrumentation Tool for Fault Localized Injection of Probabilistic SEUs) is a computer program that deliberately injects SEUs into another computer program, while the latter is running, for the purpose of evaluating the fault tolerance of that program. BITFLIPS was written as a plug-in extension of the open-source Valgrind debugging and profiling software. BITFLIPS can inject SEUs into any program that can be run on the Linux operating system, without needing to modify the program s source code. Further, if access to the original program source code is available, BITFLIPS offers fine-grained control over exactly when and which areas of memory (as specified via program variables) will be subjected to SEUs. The rate of injection of SEUs is controlled by specifying either a fault probability or a fault rate based on memory size and radiation exposure time, in units of SEUs per byte per second. BITFLIPS can also log each SEU that it injects and, if program source code is available, report the magnitude of effect of the SEU on a floating-point value or other program variable.

The MCNP6 Analytic Criticality Benchmark Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Forrest B.

2016-06-16

Analytical benchmarks provide an invaluable tool for verifying computer codes used to simulate neutron transport. Several collections of analytical benchmark problems [1-4] are used routinely in the verification of production Monte Carlo codes such as MCNP® [5,6]. Verification of a computer code is a necessary prerequisite to the more complex validation process. The verification process confirms that a code performs its intended functions correctly. The validation process involves determining the absolute accuracy of code results vs. nature. In typical validations, results are computed for a set of benchmark experiments using a particular methodology (code, cross-section data with uncertainties, and modeling)more » and compared to the measured results from the set of benchmark experiments. The validation process determines bias, bias uncertainty, and possibly additional margins. Verification is generally performed by the code developers, while validation is generally performed by code users for a particular application space. The VERIFICATION_KEFF suite of criticality problems [1,2] was originally a set of 75 criticality problems found in the literature for which exact analytical solutions are available. Even though the spatial and energy detail is necessarily limited in analytical benchmarks, typically to a few regions or energy groups, the exact solutions obtained can be used to verify that the basic algorithms, mathematics, and methods used in complex production codes perform correctly. The present work has focused on revisiting this benchmark suite. A thorough review of the problems resulted in discarding some of them as not suitable for MCNP benchmarking. For the remaining problems, many of them were reformulated to permit execution in either multigroup mode or in the normal continuous-energy mode for MCNP. Execution of the benchmarks in continuous-energy mode provides a significant advance to MCNP verification methods.« less

Supersonic propulsion simulation by incorporating component models in the large perturbation inlet (LAPIN) computer code

NASA Technical Reports Server (NTRS)

Cole, Gary L.; Richard, Jacques C.

1991-01-01

An approach to simulating the internal flows of supersonic propulsion systems is presented. The approach is based on a fairly simple modification of the Large Perturbation Inlet (LAPIN) computer code. LAPIN uses a quasi-one dimensional, inviscid, unsteady formulation of the continuity, momentum, and energy equations. The equations are solved using a shock capturing, finite difference algorithm. The original code, developed for simulating supersonic inlets, includes engineering models of unstart/restart, bleed, bypass, and variable duct geometry, by means of source terms in the equations. The source terms also provide a mechanism for incorporating, with the inlet, propulsion system components such as compressor stages, combustors, and turbine stages. This requires each component to be distributed axially over a number of grid points. Because of the distributed nature of such components, this representation should be more accurate than a lumped parameter model. Components can be modeled by performance map(s), which in turn are used to compute the source terms. The general approach is described. Then, simulation of a compressor/fan stage is discussed to show the approach in detail.

Correlation of transonic-cone Preston-tube data and skin friction. [characterizing the flow quality of a transonic wind tunnel

NASA Technical Reports Server (NTRS)

Reed, T. D.

1981-01-01

The distribution of Preston tube pressures within turbulent boundary layers along the surface of a sharp-nosed, ten degree cone was correlated with theoretical values of turbulent skin friction for freestream Mach numbers less than one. The mini-basic computer code, the Wu and Lock computer code, and the STAN-5 computer code were used to analyze the data and to solve the boundary layer conservation equations. The skin friction which results from using Preston tube pressures in the correlation equation, has a rms error of 1.125 percent. It was found that the effective center of the probe is not a constant but increases as the surface distance increases. For a specified unit Reynolds number, the effective center of the probe decreases as the Mach number increases. The variation of the fluid (air) properties across the face of the probe may be neglected for subsonic flows. The possible transverse errors caused by the use of the concept of a virtual origin for the turbulent boundary layer were investigated and found to be negligible.

Remote control missile model test

NASA Technical Reports Server (NTRS)

Allen, Jerry M.; Shaw, David S.; Sawyer, Wallace C.

1989-01-01

An extremely large, systematic, axisymmetric body/tail fin data base was gathered through tests of an innovative missile model design which is described herein. These data were originally obtained for incorporation into a missile aerodynamics code based on engineering methods (Program MISSILE3), but can also be used as diagnostic test cases for developing computational methods because of the individual-fin data included in the data base. Detailed analysis of four sample cases from these data are presented to illustrate interesting individual-fin force and moment trends. These samples quantitatively show how bow shock, fin orientation, fin deflection, and body vortices can produce strong, unusual, and computationally challenging effects on individual fin loads. Comparisons between these data and calculations from the SWINT Euler code are also presented.

Flood predictions using the parallel version of distributed numerical physical rainfall-runoff model TOPKAPI

NASA Astrophysics Data System (ADS)

Boyko, Oleksiy; Zheleznyak, Mark

2015-04-01

The original numerical code TOPKAPI-IMMS of the distributed rainfall-runoff model TOPKAPI ( Todini et al, 1996-2014) is developed and implemented in Ukraine. The parallel version of the code has been developed recently to be used on multiprocessors systems - multicore/processors PC and clusters. Algorithm is based on binary-tree decomposition of the watershed for the balancing of the amount of computation for all processors/cores. Message passing interface (MPI) protocol is used as a parallel computing framework. The numerical efficiency of the parallelization algorithms is demonstrated for the case studies for the flood predictions of the mountain watersheds of the Ukrainian Carpathian regions. The modeling results is compared with the predictions based on the lumped parameters models.

Dust Dynamics in Protoplanetary Disks: Parallel Computing with PVM

NASA Astrophysics Data System (ADS)

de La Fuente Marcos, Carlos; Barge, Pierre; de La Fuente Marcos, Raúl

2002-03-01

We describe a parallel version of our high-order-accuracy particle-mesh code for the simulation of collisionless protoplanetary disks. We use this code to carry out a massively parallel, two-dimensional, time-dependent, numerical simulation, which includes dust particles, to study the potential role of large-scale, gaseous vortices in protoplanetary disks. This noncollisional problem is easy to parallelize on message-passing multicomputer architectures. We performed the simulations on a cache-coherent nonuniform memory access Origin 2000 machine, using both the parallel virtual machine (PVM) and message-passing interface (MPI) message-passing libraries. Our performance analysis suggests that, for our problem, PVM is about 25% faster than MPI. Using PVM and MPI made it possible to reduce CPU time and increase code performance. This allows for simulations with a large number of particles (N ~ 105-106) in reasonable CPU times. The performances of our implementation of the pa! rallel code on an Origin 2000 supercomputer are presented and discussed. They exhibit very good speedup behavior and low load unbalancing. Our results confirm that giant gaseous vortices can play a dominant role in giant planet formation.

Extensible Computational Chemistry Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-08-09

ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE was conceived as part of the Environmental Molecular Sciences Laboratory construction to solve the problem of researchers being able to effectively utilize complex computational chemistry codes and massively parallel high performance compute resources. Bringing the power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of themore » inner workings of either the theoretical codes or the supercomputers needed to run them was a grand challenge problem in the original version of the EMSL. ECCE allows collaboration among researchers using a web-based data repository where the inputs and results for all calculations done within ECCE are organized. ECCE is a first of kind end-to-end problem solving environment for all phases of computational chemistry research: setting up calculations with sophisticated GUI and direct manipulation visualization tools, submitting and monitoring calculations on remote high performance supercomputers without having to be familiar with the details of using these compute resources, and performing results visualization and analysis including creating publication quality images. ECCE is a suite of tightly integrated applications that are employed as the user moves through the modeling process.« less

Automatic Generation of Algorithms for the Statistical Analysis of Planetary Nebulae Images

NASA Technical Reports Server (NTRS)

Fischer, Bernd

2004-01-01

Analyzing data sets collected in experiments or by observations is a Core scientific activity. Typically, experimentd and observational data are &aught with uncertainty, and the analysis is based on a statistical model of the conjectured underlying processes, The large data volumes collected by modern instruments make computer support indispensible for this. Consequently, scientists spend significant amounts of their time with the development and refinement of the data analysis programs. AutoBayes [GF+02, FS03] is a fully automatic synthesis system for generating statistical data analysis programs. Externally, it looks like a compiler: it takes an abstract problem specification and translates it into executable code. Its input is a concise description of a data analysis problem in the form of a statistical model as shown in Figure 1; its output is optimized and fully documented C/C++ code which can be linked dynamically into the Matlab and Octave environments. Internally, however, it is quite different: AutoBayes derives a customized algorithm implementing the given model using a schema-based process, and then further refines and optimizes the algorithm into code. A schema is a parameterized code template with associated semantic constraints which define and restrict the template s applicability. The schema parameters are instantiated in a problem-specific way during synthesis as AutoBayes checks the constraints against the original model or, recursively, against emerging sub-problems. AutoBayes schema library contains problem decomposition operators (which are justified by theorems in a formal logic in the domain of Bayesian networks) as well as machine learning algorithms (e.g., EM, k-Means) and nu- meric optimization methods (e.g., Nelder-Mead simplex, conjugate gradient). AutoBayes augments this schema-based approach by symbolic computation to derive closed-form solutions whenever possible. This is a major advantage over other statistical data analysis systems which use numerical approximations even in cases where closed-form solutions exist. AutoBayes is implemented in Prolog and comprises approximately 75.000 lines of code. In this paper, we take one typical scientific data analysis problem-analyzing planetary nebulae images taken by the Hubble Space Telescope-and show how AutoBayes can be used to automate the implementation of the necessary anal- ysis programs. We initially follow the analysis described by Knuth and Hajian [KHO2] and use AutoBayes to derive code for the published models. We show the details of the code derivation process, including the symbolic computations and automatic integration of library procedures, and compare the results of the automatically generated and manually implemented code. We then go beyond the original analysis and use AutoBayes to derive code for a simple image segmentation procedure based on a mixture model which can be used to automate a manual preproceesing step. Finally, we combine the original approach with the simple segmentation which yields a more detailed analysis. This also demonstrates that AutoBayes makes it easy to combine different aspects of data analysis.

Analysis of rotor vibratory loads using higher harmonic pitch control

NASA Technical Reports Server (NTRS)

Quackenbush, Todd R.; Bliss, Donald B.; Boschitsch, Alexander H.; Wachspress, Daniel A.

1992-01-01

Experimental studies of isolated rotors in forward flight have indicated that higher harmonic pitch control can reduce rotor noise. These tests also show that such pitch inputs can generate substantial vibratory loads. The modification is summarized of the RotorCRAFT (Computation of Rotor Aerodynamics in Forward flighT) analysis of isolated rotors to study the vibratory loading generated by high frequency pitch inputs. The original RotorCRAFT code was developed for use in the computation of such loading, and uses a highly refined rotor wake model to facilitate this task. The extended version of RotorCRAFT incorporates a variety of new features including: arbitrary periodic root pitch control; computation of blade stresses and hub loads; improved modeling of near wake unsteady effects; and preliminary implementation of a coupled prediction of rotor airloads and noise. Correlation studies are carried out with existing blade stress and vibratory hub load data to assess the performance of the extended code.

Rotordynamics on the PC: Transient Analysis With ARDS

NASA Technical Reports Server (NTRS)

Fleming, David P.

1997-01-01

Personal computers can now do many jobs that formerly required a large mainframe computer. An example is NASA Lewis Research Center's program Analysis of RotorDynamic Systems (ARDS), which uses the component mode synthesis method to analyze the dynamic motion of up to five rotating shafts. As originally written in the early 1980's, this program was considered large for the mainframe computers of the time. ARDS, which was written in Fortran 77, has been successfully ported to a 486 personal computer. Plots appear on the computer monitor via calls programmed for the original CALCOMP plotter; plots can also be output on a standard laser printer. The executable code, which uses the full array sizes of the mainframe version, easily fits on a high-density floppy disk. The program runs under DOS with an extended memory manager. In addition to transient analysis of blade loss, step turns, and base acceleration, with simulation of squeeze-film dampers and rubs, ARDS calculates natural frequencies and unbalance response.

APORT: a program for the area-based apportionment of county variables to cells of a polar grid. [Airborne pollutant transport models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fields, D.E.; Little, C.A.

1978-11-01

The APORT computer code was developed to apportion variables tabulated for polygon-structured civil districts onto cells of a polar grid. The apportionment is based on fractional overlap between the polygon and the grid cells. Centering the origin of the polar system at a pollutant source site yields results that are very useful for assessing and interpreting the effects of airborne pollutant dissemination. The APOPLT graphics code, which uses the same data set as APORT, provides a convenient visual display of the polygon structure and the extent of the polar grid. The APORT/APOPLT methodology was verified by application to county summariesmore » of cattle population for counties surrounding the Oyster Creek, New Jersey, nuclear power plant. These numerical results, which were obtained using approximately 2-min computer time on an IBM System 360/91 computer, compare favorably to results of manual computations in both speed and accuracy.« less

Parallel Computation of the Regional Ocean Modeling System (ROMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, P; Song, Y T; Chao, Y

2005-04-05

The Regional Ocean Modeling System (ROMS) is a regional ocean general circulation modeling system solving the free surface, hydrostatic, primitive equations over varying topography. It is free software distributed world-wide for studying both complex coastal ocean problems and the basin-to-global scale ocean circulation. The original ROMS code could only be run on shared-memory systems. With the increasing need to simulate larger model domains with finer resolutions and on a variety of computer platforms, there is a need in the ocean-modeling community to have a ROMS code that can be run on any parallel computer ranging from 10 to hundreds ofmore » processors. Recently, we have explored parallelization for ROMS using the MPI programming model. In this paper, an efficient parallelization strategy for such a large-scale scientific software package, based on an existing shared-memory computing model, is presented. In addition, scientific applications and data-performance issues on a couple of SGI systems, including Columbia, the world's third-fastest supercomputer, are discussed.« less

Influence of temperature fluctuations on infrared limb radiance: a new simulation code

NASA Astrophysics Data System (ADS)

Rialland, Valérie; Chervet, Patrick

2006-08-01

Airborne infrared limb-viewing detectors may be used as surveillance sensors in order to detect dim military targets. These systems' performances are limited by the inhomogeneous background in the sensor field of view which impacts strongly on target detection probability. This background clutter, which results from small-scale fluctuations of temperature, density or pressure must therefore be analyzed and modeled. Few existing codes are able to model atmospheric structures and their impact on limb-observed radiance. SAMM-2 (SHARC-4 and MODTRAN4 Merged), the Air Force Research Laboratory (AFRL) background radiance code can be used to in order to predict the radiance fluctuation as a result of a normalized temperature fluctuation, as a function of the line-of-sight. Various realizations of cluttered backgrounds can then be computed, based on these transfer functions and on a stochastic temperature field. The existing SIG (SHARC Image Generator) code was designed to compute the cluttered background which would be observed from a space-based sensor. Unfortunately, this code was not able to compute accurate scenes as seen by an airborne sensor especially for lines-of-sight close to the horizon. Recently, we developed a new code called BRUTE3D and adapted to our configuration. This approach is based on a method originally developed in the SIG model. This BRUTE3D code makes use of a three-dimensional grid of temperature fluctuations and of the SAMM-2 transfer functions to synthesize an image of radiance fluctuations according to sensor characteristics. This paper details the working principles of the code and presents some output results. The effects of the small-scale temperature fluctuations on infrared limb radiance as seen by an airborne sensor are highlighted.

Concentration transport calculations by an original C++ program with interediate fidelity physics through user-defined buildings with an emphasis on release scenarios in radiological facilities

NASA Astrophysics Data System (ADS)

Sayre, George Anthony

The purpose of this dissertation was to develop the C ++ program Emergency Dose to calculate transport of radionuclides through indoor spaces using intermediate fidelity physics that provides improved spatial heterogeneity over well-mixed models such as MELCORRTM and much lower computation times than CFD codes such as FLUENTRTM . Modified potential flow theory, which is an original formulation of potential flow theory with additions of turbulent jet and natural convection approximations, calculates spatially heterogeneous velocity fields that well-mixed models cannot predict. Other original contributions of MPFT are: (1) generation of high fidelity boundary conditions relative to well-mixed-CFD coupling methods (conflation), (2) broadening of potential flow applications to arbitrary indoor spaces previously restricted to specific applications such as exhaust hood studies, and (3) great reduction of computation time relative to CFD codes without total loss of heterogeneity. Additionally, the Lagrangian transport module, which is discussed in Sections 1.3 and 2.4, showcases an ensemble-based formulation thought to be original to interior studies. Velocity and concentration transport benchmarks against analogous formulations in COMSOLRTM produced favorable results with discrepancies resulting from the tetrahedral meshing used in COMSOLRTM outperforming the Cartesian method used by Emergency Dose. A performance comparison of the concentration transport modules against MELCORRTM showed that Emergency Dose held advantages over the well-mixed model especially in scenarios with many interior partitions and varied source positions. A performance comparison of velocity module against FLUENTRTM showed that viscous drag provided the largest error between Emergency Dose and CFD velocity calculations, but that Emergency Dose's turbulent jets well approximated the corresponding CFD jets. Overall, Emergency Dose was found to provide a viable intermediate solution method for concentration transport with relatively low computation times.

A project based on multi-configuration Dirac-Fock calculations for plasma spectroscopy

NASA Astrophysics Data System (ADS)

Comet, M.; Pain, J.-C.; Gilleron, F.; Piron, R.

2017-09-01

We present a project dedicated to hot plasma spectroscopy based on a Multi-Configuration Dirac-Fock (MCDF) code, initially developed by J. Bruneau. The code is briefly described and the use of the transition state method for plasma spectroscopy is detailed. Then an opacity code for local-thermodynamic-equilibrium plasmas using MCDF data, named OPAMCDF, is presented. Transition arrays for which the number of lines is too large to be handled in a Detailed Line Accounting (DLA) calculation can be modeled within the Partially Resolved Transition Array method or using the Unresolved Transition Arrays formalism in jj-coupling. An improvement of the original Partially Resolved Transition Array method is presented which gives a better agreement with DLA computations. Comparisons with some absorption and emission experimental spectra are shown. Finally, the capability of the MCDF code to compute atomic data required for collisional-radiative modeling of plasma at non local thermodynamic equilibrium is illustrated. In addition to photoexcitation, this code can be used to calculate photoionization, electron impact excitation and ionization cross-sections as well as autoionization rates in the Distorted-Wave or Close Coupling approximations. Comparisons with cross-sections and rates available in the literature are discussed.

The Navy/NASA Engine Program (NNEP89): A user's manual

NASA Technical Reports Server (NTRS)

Plencner, Robert M.; Snyder, Christopher A.

1991-01-01

An engine simulation computer code called NNEP89 was written to perform 1-D steady state thermodynamic analysis of turbine engine cycles. By using a very flexible method of input, a set of standard components are connected at execution time to simulate almost any turbine engine configuration that the user could imagine. The code was used to simulate a wide range of engine cycles from turboshafts and turboprops to air turborockets and supersonic cruise variable cycle engines. Off design performance is calculated through the use of component performance maps. A chemical equilibrium model is incorporated to adequately predict chemical dissociation as well as model virtually any fuel. NNEP89 is written in standard FORTRAN77 with clear structured programming and extensive internal documentation. The standard FORTRAN77 programming allows it to be installed onto most mainframe computers and workstations without modification. The NNEP89 code was derived from the Navy/NASA Engine program (NNEP). NNEP89 provides many improvements and enhancements to the original NNEP code and incorporates features which make it easier to use for the novice user. This is a comprehensive user's guide for the NNEP89 code.

A hardware-oriented concurrent TZ search algorithm for High-Efficiency Video Coding

NASA Astrophysics Data System (ADS)

Doan, Nghia; Kim, Tae Sung; Rhee, Chae Eun; Lee, Hyuk-Jae

2017-12-01

High-Efficiency Video Coding (HEVC) is the latest video coding standard, in which the compression performance is double that of its predecessor, the H.264/AVC standard, while the video quality remains unchanged. In HEVC, the test zone (TZ) search algorithm is widely used for integer motion estimation because it effectively searches the good-quality motion vector with a relatively small amount of computation. However, the complex computation structure of the TZ search algorithm makes it difficult to implement it in the hardware. This paper proposes a new integer motion estimation algorithm which is designed for hardware execution by modifying the conventional TZ search to allow parallel motion estimations of all prediction unit (PU) partitions. The algorithm consists of the three phases of zonal, raster, and refinement searches. At the beginning of each phase, the algorithm obtains the search points required by the original TZ search for all PU partitions in a coding unit (CU). Then, all redundant search points are removed prior to the estimation of the motion costs, and the best search points are then selected for all PUs. Compared to the conventional TZ search algorithm, experimental results show that the proposed algorithm significantly decreases the Bjøntegaard Delta bitrate (BD-BR) by 0.84%, and it also reduces the computational complexity by 54.54%.

DNA as information.

PubMed

Wills, Peter R

2016-03-13

This article reviews contributions to this theme issue covering the topic 'DNA as information' in relation to the structure of DNA, the measure of its information content, the role and meaning of information in biology and the origin of genetic coding as a transition from uninformed to meaningful computational processes in physical systems. © 2016 The Author(s).

On A Nonlinear Generalization of Sparse Coding and Dictionary Learning.

PubMed

Xie, Yuchen; Ho, Jeffrey; Vemuri, Baba

2013-01-01

Existing dictionary learning algorithms are based on the assumption that the data are vectors in an Euclidean vector space ℝ d , and the dictionary is learned from the training data using the vector space structure of ℝ d and its Euclidean L 2 -metric. However, in many applications, features and data often originated from a Riemannian manifold that does not support a global linear (vector space) structure. Furthermore, the extrinsic viewpoint of existing dictionary learning algorithms becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to the application. This paper proposes a novel framework for sparse coding and dictionary learning for data on a Riemannian manifold, and it shows that the existing sparse coding and dictionary learning methods can be considered as special (Euclidean) cases of the more general framework proposed here. We show that both the dictionary and sparse coding can be effectively computed for several important classes of Riemannian manifolds, and we validate the proposed method using two well-known classification problems in computer vision and medical imaging analysis.

On A Nonlinear Generalization of Sparse Coding and Dictionary Learning

PubMed Central

Xie, Yuchen; Ho, Jeffrey; Vemuri, Baba

2013-01-01

Existing dictionary learning algorithms are based on the assumption that the data are vectors in an Euclidean vector space ℝd, and the dictionary is learned from the training data using the vector space structure of ℝd and its Euclidean L2-metric. However, in many applications, features and data often originated from a Riemannian manifold that does not support a global linear (vector space) structure. Furthermore, the extrinsic viewpoint of existing dictionary learning algorithms becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to the application. This paper proposes a novel framework for sparse coding and dictionary learning for data on a Riemannian manifold, and it shows that the existing sparse coding and dictionary learning methods can be considered as special (Euclidean) cases of the more general framework proposed here. We show that both the dictionary and sparse coding can be effectively computed for several important classes of Riemannian manifolds, and we validate the proposed method using two well-known classification problems in computer vision and medical imaging analysis. PMID:24129583

An update of input instructions to TEMOD

NASA Technical Reports Server (NTRS)

1973-01-01

The theory and operation of a FORTRAN 4 computer code, designated as TEMOD, used to calcuate tubular thermoelectric generator performance is described in WANL-TME-1906. The original version of TEMOD was developed in 1969. A description is given of additions to the mathematical model and an update of the input instructions to the code. Although the basic mathematical model described in WANL-TME-1906 has remained unchanged, a substantial number of input/output options were added to allow completion of module performance parametrics as required in support of the compact thermoelectric converter system technology program.

NPS-NRL-Rice-UIUC Collaboration on Navy Atmosphere-Ocean Coupled Models on Many-Core Computer Architectures Annual Report

DTIC Science & Technology

2014-09-30

portability is difficult to achieve on future supercomputers that use various type of accelerators (GPUs, Xeon - Phi , and SIMD etc). All of these...bottlenecks of NUMA. For example, in the CG code the state vector was originally stored as q(1 : Nvar ,1 : Npoin) where Nvar are the number of...a Global Grid Point (GGP) storage. On the other hand, in the DG code the state vector is typically stored as q(1 : Nvar ,1 : Npts,1 : Nelem) where

Computational-hydrodynamic studies of the Noh compressible flow problem using non-ideal equations of state

NASA Astrophysics Data System (ADS)

Honnell, Kevin; Burnett, Sarah; Yorke, Chloe'; Howard, April; Ramsey, Scott

2017-06-01

The Noh problem is classic verification problem in the field of compressible flows. Simple to conceptualize, it is nonetheless difficult for numerical codes to predict correctly, making it an ideal code-verification test bed. In its original incarnation, the fluid is a simple ideal gas; once validated, however, these codes are often used to study highly non-ideal fluids and solids. In this work the classic Noh problem is extended beyond the commonly-studied polytropic ideal gas to more realistic equations of state (EOS) including the stiff gas, the Nobel-Abel gas, and the Carnahan-Starling hard-sphere fluid, thus enabling verification studies to be performed on more physically-realistic fluids. Exact solutions are compared with numerical results obtained from the Lagrangian hydrocode FLAG, developed at Los Alamos. For these more realistic EOSs, the simulation errors decreased in magnitude both at the origin and at the shock, but also spread more broadly about these points compared to the ideal EOS. The overall spatial convergence rate remained first order.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Viktor K. Decyk

The UCLA work on this grant was to design and help implement an object-oriented version of the GTC code, which is written in Fortran90. The GTC code is the main global gyrokinetic code used in this project, and over the years multiple, incompatible versions have evolved. The reason for this effort is to allow multiple authors to work together on GTC and to simplify future enhancements to GTC. The effort was designed to proceed incrementally. Initially, an upper layer of classes (derived types and methods) was implemented which called the original GTC code 'under the hood.' The derived types pointedmore » to data in the original GTC code, and the methods called the original GTC subroutines. The original GTC code was modified only very slightly. This allowed one to define (and refine) a set of classes which described the important features of the GTC code in a new, more abstract way, with a minimum of implementation. Furthermore, classes could be added one at a time, and at the end of the each day, the code continued to work correctly. This work was done in close collaboration with Y. Nishimura from UC Irvine and Stefan Ethier from PPPL. Ten classes were ultimately defined and implemented: gyrokinetic and drift kinetic particles, scalar and vector fields, a mesh, jacobian, FLR, equilibrium, interpolation, and particles species descriptors. In the second state of this development, some of the scaffolding was removed. The constructors in the class objects now allocated the data and the array data in the original GTC code was removed. This isolated the components and now allowed multiple instantiations of the objects to be created, in particular, multiple ion species. Again, the work was done incrementally, one class at a time, so that the code was always working properly. This work was done in close collaboration with Y. Nishimura and W. Zhang from UC Irvine and Stefan Ethier from PPPL. The third stage of this work was to integrate the capabilities of the various versions of the GTC code into one flexible and extensible version. To do this, we developed a methodology to implement Design Patterns in Fortran90. Design Patterns are abstract solutions to generic programming problems, which allow one to handle increased complexity. This work was done in collaboration with Henry Gardner, a computer scientist (and former plasma physicist) from the Australian National University. As an example, the Strategy Pattern is being used in GTC to support multiple solvers. This new code is currently being used in the study of energetic particles. A document describing the evolution of the GTC code to this new object-oriented version is available to users of GTC.« less

Original data preprocessor for Femap/Nastran

NASA Astrophysics Data System (ADS)

Oanta, Emil M.; Panait, Cornel; Raicu, Alexandra

2016-12-01

Automatic data processing and visualization in the finite elements analysis of the structural problems is a long run concern in mechanical engineering. The paper presents the `common database' concept according to which the same information may be accessed from an analytical model, as well as from a numerical one. In this way, input data expressed as comma-separated-value (CSV) files are loaded into the Femap/Nastran environment using original API codes, being automatically generated: the geometry of the model, the loads and the constraints. The original API computer codes are general, being possible to generate the input data of any model. In the next stages, the user may create the discretization of the model, set the boundary conditions and perform a given analysis. If additional accuracy is needed, the analyst may delete the previous discretizations and using the same information automatically loaded, other discretizations and analyses may be done. Moreover, if new more accurate information regarding the loads or constraints is acquired, they may be modelled and then implemented in the data generating program which creates the `common database'. This means that new more accurate models may be easily generated. Other facility consists of the opportunity to control the CSV input files, several loading scenarios being possible to be generated in Femap/Nastran. In this way, using original intelligent API instruments the analyst is focused to accurately model the phenomena and on creative aspects, the repetitive and time-consuming activities being performed by the original computer-based instruments. Using this data processing technique we apply to the best Asimov's principle `minimum change required / maximum desired response'.

General purpose molecular dynamics simulations fully implemented on graphics processing units

NASA Astrophysics Data System (ADS)

Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A.

2008-05-01

Graphics processing units (GPUs), originally developed for rendering real-time effects in computer games, now provide unprecedented computational power for scientific applications. In this paper, we develop a general purpose molecular dynamics code that runs entirely on a single GPU. It is shown that our GPU implementation provides a performance equivalent to that of fast 30 processor core distributed memory cluster. Our results show that GPUs already provide an inexpensive alternative to such clusters and discuss implications for the future.

WIND Flow Solver Released

NASA Technical Reports Server (NTRS)

Towne, Charles E.

1999-01-01

The WIND code is a general-purpose, structured, multizone, compressible flow solver that can be used to analyze steady or unsteady flow for a wide range of geometric configurations and over a wide range of flow conditions. WIND is the latest product of the NPARC Alliance, a formal partnership between the NASA Lewis Research Center and the Air Force Arnold Engineering Development Center (AEDC). WIND Version 1.0 was released in February 1998, and Version 2.0 will be released in February 1999. The WIND code represents a merger of the capabilities of three existing computational fluid dynamics codes--NPARC (the original NPARC Alliance flow solver), NXAIR (an Air Force code used primarily for unsteady store separation problems), and NASTD (the primary flow solver at McDonnell Douglas, now part of Boeing).

TOSCA calculations and measurements for the SLAC SLC damping ring dipole magnet

NASA Astrophysics Data System (ADS)

Early, R. A.; Cobb, J. K.

1985-04-01

The SLAC damping ring dipole magnet was originally designed with removable nose pieces at the ends. Recently, a set of magnetic measurements was taken of the vertical component of induction along the center of the magnet for four different pole-end configurations and several current settings. The three dimensional computer code TOSCA, which is currently installed on the National Magnetic Fusion Energy Computer Center's Cray X-MP, was used to compute field values for the four configurations at current settings near saturation. Comparisons were made for magnetic induction as well as effective magnetic lengths for the different configurations.

Speed and accuracy improvements in FLAASH atmospheric correction of hyperspectral imagery

NASA Astrophysics Data System (ADS)

Perkins, Timothy; Adler-Golden, Steven; Matthew, Michael W.; Berk, Alexander; Bernstein, Lawrence S.; Lee, Jamine; Fox, Marsha

2012-11-01

Remotely sensed spectral imagery of the earth's surface can be used to fullest advantage when the influence of the atmosphere has been removed and the measurements are reduced to units of reflectance. Here, we provide a comprehensive summary of the latest version of the Fast Line-of-sight Atmospheric Analysis of Spectral Hypercubes atmospheric correction algorithm. We also report some new code improvements for speed and accuracy. These include the re-working of the original algorithm in C-language code parallelized with message passing interface and containing a new radiative transfer look-up table option, which replaces executions of the MODTRAN model. With computation times now as low as ~10 s per image per computer processor, automated, real-time, on-board atmospheric correction of hyper- and multi-spectral imagery is within reach.

ODECS -- A computer code for the optimal design of S.I. engine control strategies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arsie, I.; Pianese, C.; Rizzo, G.

1996-09-01

The computer code ODECS (Optimal Design of Engine Control Strategies) for the design of Spark Ignition engine control strategies is presented. This code has been developed starting from the author`s activity in this field, availing of some original contributions about engine stochastic optimization and dynamical models. This code has a modular structure and is composed of a user interface for the definition, the execution and the analysis of different computations performed with 4 independent modules. These modules allow the following calculations: (1) definition of the engine mathematical model from steady-state experimental data; (2) engine cycle test trajectory corresponding to amore » vehicle transient simulation test such as ECE15 or FTP drive test schedule; (3) evaluation of the optimal engine control maps with a steady-state approach; (4) engine dynamic cycle simulation and optimization of static control maps and/or dynamic compensation strategies, taking into account dynamical effects due to the unsteady fluxes of air and fuel and the influences of combustion chamber wall thermal inertia on fuel consumption and emissions. Moreover, in the last two modules it is possible to account for errors generated by a non-deterministic behavior of sensors and actuators and the related influences on global engine performances, and compute robust strategies, less sensitive to stochastic effects. In the paper the four models are described together with significant results corresponding to the simulation and the calculation of optimal control strategies for dynamic transient tests.« less

Common Sense and the Uncommon Bacterium--Is "Life" Patentable?

ERIC Educational Resources Information Center

Kiley, Thomas D.

1978-01-01

The Supreme Court is faced with some difficult issues with a common origin in disagreement between the Patent and Trademark Office and the Court of Customs and Patent Appeals over the code that defines what things are and are not patentable. The patent concerns of the computer software and molecular biology fields are addressed. (JMD)

STARS: An Integrated, Multidisciplinary, Finite-Element, Structural, Fluids, Aeroelastic, and Aeroservoelastic Analysis Computer Program

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1997-01-01

A multidisciplinary, finite element-based, highly graphics-oriented, linear and nonlinear analysis capability that includes such disciplines as structures, heat transfer, linear aerodynamics, computational fluid dynamics, and controls engineering has been achieved by integrating several new modules in the original STARS (STructural Analysis RoutineS) computer program. Each individual analysis module is general-purpose in nature and is effectively integrated to yield aeroelastic and aeroservoelastic solutions of complex engineering problems. Examples of advanced NASA Dryden Flight Research Center projects analyzed by the code in recent years include the X-29A, F-18 High Alpha Research Vehicle/Thrust Vectoring Control System, B-52/Pegasus Generic Hypersonics, National AeroSpace Plane (NASP), SR-71/Hypersonic Launch Vehicle, and High Speed Civil Transport (HSCT) projects. Extensive graphics capabilities exist for convenient model development and postprocessing of analysis results. The program is written in modular form in standard FORTRAN language to run on a variety of computers, such as the IBM RISC/6000, SGI, DEC, Cray, and personal computer; associated graphics codes use OpenGL and IBM/graPHIGS language for color depiction. This program is available from COSMIC, the NASA agency for distribution of computer programs.

Parallel design of JPEG-LS encoder on graphics processing units

NASA Astrophysics Data System (ADS)

Duan, Hao; Fang, Yong; Huang, Bormin

2012-01-01

With recent technical advances in graphic processing units (GPUs), GPUs have outperformed CPUs in terms of compute capability and memory bandwidth. Many successful GPU applications to high performance computing have been reported. JPEG-LS is an ISO/IEC standard for lossless image compression which utilizes adaptive context modeling and run-length coding to improve compression ratio. However, adaptive context modeling causes data dependency among adjacent pixels and the run-length coding has to be performed in a sequential way. Hence, using JPEG-LS to compress large-volume hyperspectral image data is quite time-consuming. We implement an efficient parallel JPEG-LS encoder for lossless hyperspectral compression on a NVIDIA GPU using the computer unified device architecture (CUDA) programming technology. We use the block parallel strategy, as well as such CUDA techniques as coalesced global memory access, parallel prefix sum, and asynchronous data transfer. We also show the relation between GPU speedup and AVIRIS block size, as well as the relation between compression ratio and AVIRIS block size. When AVIRIS images are divided into blocks, each with 64×64 pixels, we gain the best GPU performance with 26.3x speedup over its original CPU code.

cosmoabc: Likelihood-free inference for cosmology

NASA Astrophysics Data System (ADS)

Ishida, Emille E. O.; Vitenti, Sandro D. P.; Penna-Lima, Mariana; Trindade, Arlindo M.; Cisewski, Jessi; M.; de Souza, Rafael; Cameron, Ewan; Busti, Vinicius C.

2015-05-01

Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogs. cosmoabc is a Python Approximate Bayesian Computation (ABC) sampler featuring a Population Monte Carlo variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code can be coupled to an external simulator to allow incorporation of arbitrary distance and prior functions. When coupled with the numcosmo library, it has been used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function.

NOAA/DOE CWP structural analysis package. [CWPFLY, CWPEXT, COTEC, and XOTEC codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pompa, J.A.; Lunz, D.F.

1979-09-01

The theoretical development and computer code user's manual for analysis of the Ocean Thermal Energy Conversion (OTEC) plant cold water pipe (CWP) are presented. The analysis of the CWP includes coupled platform/CWP loadngs and dynamic responses. This report with the exception of the Introduction and Appendix F was orginally published as Hydronautics, Inc., Technical Report No. 7825-2 (by Barr, Chang, and Thasanatorn) in November 1978. A detailed theoretical development of the equations describing the coupled platform/CWP system and preliminary validation efforts are described. The appendices encompass a complete user's manual, describing the inputs, outputs and operation of the four componentmore » programs, and detail changes and updates implemented since the original release of the code by Hydronautics. The code itself is available through NOAA's Office of Ocean Technology and Engineering Services.« less

A hydrodynamic approach to cosmology - Methodology

NASA Technical Reports Server (NTRS)

Cen, Renyue

1992-01-01

The present study describes an accurate and efficient hydrodynamic code for evolving self-gravitating cosmological systems. The hydrodynamic code is a flux-based mesh code originally designed for engineering hydrodynamical applications. A variety of checks were performed which indicate that the resolution of the code is a few cells, providing accuracy for integral energy quantities in the present simulations of 1-3 percent over the whole runs. Six species (H I, H II, He I, He II, He III) are tracked separately, and relevant ionization and recombination processes, as well as line and continuum heating and cooling, are computed. The background radiation field is simultaneously determined in the range 1 eV to 100 keV, allowing for absorption, emission, and cosmological effects. It is shown how the inevitable numerical inaccuracies can be estimated and to some extent overcome.

Posteriori error determination and grid adaptation for AMR and ALE computational fluid dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapenta, G. M.

2002-01-01

We discuss grid adaptation for application to AMR and ALE codes. Two new contributions are presented. First, a new method to locate the regions where the truncation error is being created due to an insufficient accuracy: the operator recovery error origin (OREO) detector. The OREO detector is automatic, reliable, easy to implement and extremely inexpensive. Second, a new grid motion technique is presented for application to ALE codes. The method is based on the Brackbill-Saltzman approach but it is directly linked to the OREO detector and moves the grid automatically to minimize the error.

PACER -- A fast running computer code for the calculation of short-term containment/confinement loads following coolant boundary failure. Volume 2: User information

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sienicki, J.J.

A fast running and simple computer code has been developed to calculate pressure loadings inside light water reactor containments/confinements under loss-of-coolant accident conditions. PACER was originally developed to calculate containment/confinement pressure and temperature time histories for loss-of-coolant accidents in Soviet-designed VVER reactors and is relevant to the activities of the US International Nuclear Safety Center. The code employs a multicompartment representation of the containment volume and is focused upon application to early time containment phenomena during and immediately following blowdown. PACER has been developed for FORTRAN 77 and earlier versions of FORTRAN. The code has been successfully compiled and executedmore » on SUN SPARC and Hewlett-Packard HP-735 workstations provided that appropriate compiler options are specified. The code incorporates both capabilities built around a hardwired default generic VVER-440 Model V230 design as well as fairly general user-defined input. However, array dimensions are hardwired and must be changed by modifying the source code if the number of compartments/cells differs from the default number of nine. Detailed input instructions are provided as well as a description of outputs. Input files and selected output are presented for two sample problems run on both HP-735 and SUN SPARC workstations.« less

Fundamental modeling of pulverized coal and coal-water slurry combustion in a gas turbine combustor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatwani, A.; Turan, A.; Hals, F.

1988-01-01

This work describes the essential features of a coal combustion model which is incorporated into a three-dimensional, steady-state, two-phase, turbulent, reactive flow code. The code is a modified and advanced version of INTERN code originally developed at Imperial College which has gone through many stages of development and validation. Swithenbank et al have reported spray combustion model results for an experimental can combustor. The code has since then been modified by and made public under a US Army program. A number of code modifications and improvements have been made at ARL. The earlier version of code was written for amore » small CDC machine which relied on frequent disk/memory transfer and overlay features to carry the computations resulting in loss of computational speed. These limitations have now been removed. For spray applications, the fuel droplet vaporization generates gaseous fuel of uniform composition; hence the earlier formulation relied upon the use of conserved scalar approximation to reduce the number of species equations to be solved. In applications related to coal fuel, coal pyrolysis leads to the formation of at least two different gaseous fuels and a solid fuel of different composition. The authors have therefore removed the conserved scalar formulation for the sake of generality and easy adaptability to complex fuel situations.« less

CMCpy: Genetic Code-Message Coevolution Models in Python

PubMed Central

Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

2013-01-01

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

XGC developments for a more efficient XGC-GENE code coupling

NASA Astrophysics Data System (ADS)

Dominski, Julien; Hager, Robert; Ku, Seung-Hoe; Chang, Cs

2017-10-01

In the Exascale Computing Program, the High-Fidelity Whole Device Modeling project initially aims at delivering a tightly-coupled simulation of plasma neoclassical and turbulence dynamics from the core to the edge of the tokamak. To permit such simulations, the gyrokinetic codes GENE and XGC will be coupled together. Numerical efforts are made to improve the numerical schemes agreement in the coupling region. One of the difficulties of coupling those codes together is the incompatibility of their grids. GENE is a continuum grid-based code and XGC is a Particle-In-Cell code using unstructured triangular mesh. A field-aligned filter is thus implemented in XGC. Even if XGC originally had an approximately field-following mesh, this field-aligned filter permits to have a perturbation discretization closer to the one solved in the field-aligned code GENE. Additionally, new XGC gyro-averaging matrices are implemented on a velocity grid adapted to the plasma properties, thus ensuring same accuracy from the core to the edge regions.

MMAPDNG: A new, fast code backed by a memory-mapped database for simulating delayed γ-ray emission with MCNPX package

NASA Astrophysics Data System (ADS)

Lou, Tak Pui; Ludewigt, Bernhard

2015-09-01

The simulation of the emission of beta-delayed gamma rays following nuclear fission and the calculation of time-dependent energy spectra is a computational challenge. The widely used radiation transport code MCNPX includes a delayed gamma-ray routine that is inefficient and not suitable for simulating complex problems. This paper describes the code "MMAPDNG" (Memory-Mapped Delayed Neutron and Gamma), an optimized delayed gamma module written in C, discusses usage and merits of the code, and presents results. The approach is based on storing required Fission Product Yield (FPY) data, decay data, and delayed particle data in a memory-mapped file. When compared to the original delayed gamma-ray code in MCNPX, memory utilization is reduced by two orders of magnitude and the ray sampling is sped up by three orders of magnitude. Other delayed particles such as neutrons and electrons can be implemented in future versions of MMAPDNG code using its existing framework.

Adaptation and optimization of a line-by-line radiative transfer program for the STAR-100 (STARSMART)

NASA Technical Reports Server (NTRS)

Rarig, P. L.

1980-01-01

A program to calculate upwelling infrared radiation was modified to operate efficiently on the STAR-100. The modified software processes specific test cases significantly faster than the initial STAR-100 code. For example, a midlatitude summer atmospheric model is executed in less than 2% of the time originally required on the STAR-100. Furthermore, the optimized program performs extra operations to save the calculated absorption coefficients. Some of the advantages and pitfalls of virtual memory and vector processing are discussed along with strategies used to avoid loss of accuracy and computing power. Results from the vectorized code, in terms of speed, cost, and relative error with respect to serial code solutions are encouraging.

Implementation of tetrahedral-mesh geometry in Monte Carlo radiation transport code PHITS

NASA Astrophysics Data System (ADS)

Furuta, Takuya; Sato, Tatsuhiko; Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Brown, Justin L.; Bolch, Wesley E.

2017-06-01

A new function to treat tetrahedral-mesh geometry was implemented in the particle and heavy ion transport code systems. To accelerate the computational speed in the transport process, an original algorithm was introduced to initially prepare decomposition maps for the container box of the tetrahedral-mesh geometry. The computational performance was tested by conducting radiation transport simulations of 100 MeV protons and 1 MeV photons in a water phantom represented by tetrahedral mesh. The simulation was repeated with varying number of meshes and the required computational times were then compared with those of the conventional voxel representation. Our results show that the computational costs for each boundary crossing of the region mesh are essentially equivalent for both representations. This study suggests that the tetrahedral-mesh representation offers not only a flexible description of the transport geometry but also improvement of computational efficiency for the radiation transport. Due to the adaptability of tetrahedrons in both size and shape, dosimetrically equivalent objects can be represented by tetrahedrons with a much fewer number of meshes as compared its voxelized representation. Our study additionally included dosimetric calculations using a computational human phantom. A significant acceleration of the computational speed, about 4 times, was confirmed by the adoption of a tetrahedral mesh over the traditional voxel mesh geometry.

Implementation of tetrahedral-mesh geometry in Monte Carlo radiation transport code PHITS.

PubMed

Furuta, Takuya; Sato, Tatsuhiko; Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Brown, Justin L; Bolch, Wesley E

2017-06-21

A new function to treat tetrahedral-mesh geometry was implemented in the particle and heavy ion transport code systems. To accelerate the computational speed in the transport process, an original algorithm was introduced to initially prepare decomposition maps for the container box of the tetrahedral-mesh geometry. The computational performance was tested by conducting radiation transport simulations of 100 MeV protons and 1 MeV photons in a water phantom represented by tetrahedral mesh. The simulation was repeated with varying number of meshes and the required computational times were then compared with those of the conventional voxel representation. Our results show that the computational costs for each boundary crossing of the region mesh are essentially equivalent for both representations. This study suggests that the tetrahedral-mesh representation offers not only a flexible description of the transport geometry but also improvement of computational efficiency for the radiation transport. Due to the adaptability of tetrahedrons in both size and shape, dosimetrically equivalent objects can be represented by tetrahedrons with a much fewer number of meshes as compared its voxelized representation. Our study additionally included dosimetric calculations using a computational human phantom. A significant acceleration of the computational speed, about 4 times, was confirmed by the adoption of a tetrahedral mesh over the traditional voxel mesh geometry.

Optimization Issues with Complex Rotorcraft Comprehensive Analysis

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Young, Katherine C.; Tarzanin, Frank J.; Hirsh, Joel E.; Young, Darrell K.

1998-01-01

This paper investigates the use of the general purpose automatic differentiation (AD) tool called Automatic Differentiation of FORTRAN (ADIFOR) as a means of generating sensitivity derivatives for use in Boeing Helicopter's proprietary comprehensive rotor analysis code (VII). ADIFOR transforms an existing computer program into a new program that performs a sensitivity analysis in addition to the original analysis. In this study both the pros (exact derivatives, no step-size problems) and cons (more CPU, more memory) of ADIFOR are discussed. The size (based on the number of lines) of the VII code after ADIFOR processing increased by 70 percent and resulted in substantial computer memory requirements at execution. The ADIFOR derivatives took about 75 percent longer to compute than the finite-difference derivatives. However, the ADIFOR derivatives are exact and are not functions of step-size. The VII sensitivity derivatives generated by ADIFOR are compared with finite-difference derivatives. The ADIFOR and finite-difference derivatives are used in three optimization schemes to solve a low vibration rotor design problem.

Computation of a Canadian SCWR unit cell with deterministic and Monte Carlo codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrisson, G.; Marleau, G.

2012-07-01

The Canadian SCWR has the potential to achieve the goals that the generation IV nuclear reactors must meet. As part of the optimization process for this design concept, lattice cell calculations are routinely performed using deterministic codes. In this study, the first step (self-shielding treatment) of the computation scheme developed with the deterministic code DRAGON for the Canadian SCWR has been validated. Some options available in the module responsible for the resonance self-shielding calculation in DRAGON 3.06 and different microscopic cross section libraries based on the ENDF/B-VII.0 evaluated nuclear data file have been tested and compared to a reference calculationmore » performed with the Monte Carlo code SERPENT under the same conditions. Compared to SERPENT, DRAGON underestimates the infinite multiplication factor in all cases. In general, the original Stammler model with the Livolant-Jeanpierre approximations are the most appropriate self-shielding options to use in this case of study. In addition, the 89 groups WIMS-AECL library for slight enriched uranium and the 172 groups WLUP library for a mixture of plutonium and thorium give the most consistent results with those of SERPENT. (authors)« less

The Marshall Engineering Thermosphere (MET) Model. Volume 1; Technical Description

NASA Technical Reports Server (NTRS)

Smith, R. E.

1998-01-01

Volume 1 presents a technical description of the Marshall Engineering Thermosphere (MET) model atmosphere and a summary of its historical development. Various programs developed to augment the original capability of the model are discussed in detail. The report also describes each of the individual subroutines developed to enhance the model. Computer codes for these subroutines are contained in four appendices.

Analysis of reaction cross-section production in neutron induced fission reactions on uranium isotope using computer code COMPLET.

PubMed

Asres, Yihunie Hibstie; Mathuthu, Manny; Birhane, Marelgn Derso

2018-04-22

This study provides current evidence about cross-section production processes in the theoretical and experimental results of neutron induced reaction of uranium isotope on projectile energy range of 1-100 MeV in order to improve the reliability of nuclear stimulation. In such fission reactions of 235 U within nuclear reactors, much amount of energy would be released as a product that able to satisfy the needs of energy to the world wide without polluting processes as compared to other sources. The main objective of this work is to transform a related knowledge in the neutron-induced fission reactions on 235 U through describing, analyzing and interpreting the theoretical results of the cross sections obtained from computer code COMPLET by comparing with the experimental data obtained from EXFOR. The cross section value of 235 U(n,2n) 234 U, 235 U(n,3n) 233 U, 235 U(n,γ) 236 U, 235 U(n,f) are obtained using computer code COMPLET and the corresponding experimental values were browsed by EXFOR, IAEA. The theoretical results are compared with the experimental data taken from EXFOR Data Bank. Computer code COMPLET has been used for the analysis with the same set of input parameters and the graphs were plotted by the help of spreadsheet & Origin-8 software. The quantification of uncertainties stemming from both experimental data and computer code calculation plays a significant role in the final evaluated results. The calculated results for total cross sections were compared with the experimental data taken from EXFOR in the literature, and good agreement was found between the experimental and theoretical data. This comparison of the calculated data was analyzed and interpreted with tabulation and graphical descriptions, and the results were briefly discussed within the text of this research work. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Taking Lessons Learned from a Proxy Application to a Full Application for SNAP and PARTISN

DOE PAGES

Womeldorff, Geoffrey Alan; Payne, Joshua Estes; Bergen, Benjamin Karl

2017-06-09

SNAP is a proxy application which simulates the computational motion of a neutral particle transport code, PARTISN. Here in this work, we have adapted parts of SNAP separately; we have re-implemented the iterative shell of SNAP in the task-model runtime Legion, showing an improvement to the original schedule, and we have created multiple Kokkos implementations of the computational kernel of SNAP, displaying similar performance to the native Fortran. We then translate our Kokkos experiments in SNAP to PARTISN, necessitating engineering development, regression testing, and further thought.

Taking Lessons Learned from a Proxy Application to a Full Application for SNAP and PARTISN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Womeldorff, Geoffrey Alan; Payne, Joshua Estes; Bergen, Benjamin Karl

SNAP is a proxy application which simulates the computational motion of a neutral particle transport code, PARTISN. Here in this work, we have adapted parts of SNAP separately; we have re-implemented the iterative shell of SNAP in the task-model runtime Legion, showing an improvement to the original schedule, and we have created multiple Kokkos implementations of the computational kernel of SNAP, displaying similar performance to the native Fortran. We then translate our Kokkos experiments in SNAP to PARTISN, necessitating engineering development, regression testing, and further thought.

Parallel community climate model: Description and user`s guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drake, J.B.; Flanery, R.E.; Semeraro, B.D.

This report gives an overview of a parallel version of the NCAR Community Climate Model, CCM2, implemented for MIMD massively parallel computers using a message-passing programming paradigm. The parallel implementation was developed on an Intel iPSC/860 with 128 processors and on the Intel Delta with 512 processors, and the initial target platform for the production version of the code is the Intel Paragon with 2048 processors. Because the implementation uses a standard, portable message-passing libraries, the code has been easily ported to other multiprocessors supporting a message-passing programming paradigm. The parallelization strategy used is to decompose the problem domain intomore » geographical patches and assign each processor the computation associated with a distinct subset of the patches. With this decomposition, the physics calculations involve only grid points and data local to a processor and are performed in parallel. Using parallel algorithms developed for the semi-Lagrangian transport, the fast Fourier transform and the Legendre transform, both physics and dynamics are computed in parallel with minimal data movement and modest change to the original CCM2 source code. Sequential or parallel history tapes are written and input files (in history tape format) are read sequentially by the parallel code to promote compatibility with production use of the model on other computer systems. A validation exercise has been performed with the parallel code and is detailed along with some performance numbers on the Intel Paragon and the IBM SP2. A discussion of reproducibility of results is included. A user`s guide for the PCCM2 version 2.1 on the various parallel machines completes the report. Procedures for compilation, setup and execution are given. A discussion of code internals is included for those who may wish to modify and use the program in their own research.« less

Observation of temperature trace, induced by changing of temperature inside the human body, on the human body skin using commercially available IR camera

NASA Astrophysics Data System (ADS)

Trofimov, Vyacheslav A.; Trofimov, Vladislav V.

2015-05-01

As it is well-known, application of the passive THz camera for the security problems is very promising way. It allows seeing concealed object without contact with a person and this camera is non-dangerous for a person. In previous papers, we demonstrate new possibility of the passive THz camera using for a temperature difference observing on the human skin if this difference is caused by different temperatures inside the body. For proof of validity of our statement we make the similar physical experiment using the IR camera. We show a possibility of temperature trace on human body skin, caused by changing of temperature inside the human body due to water drinking. We use as a computer code that is available for treatment of images captured by commercially available IR camera, manufactured by Flir Corp., as well as our developed computer code for computer processing of these images. Using both codes we demonstrate clearly changing of human body skin temperature induced by water drinking. Shown phenomena are very important for the detection of forbidden samples and substances concealed inside the human body using non-destructive control without X-rays using. Early we have demonstrated such possibility using THz radiation. Carried out experiments can be used for counter-terrorism problem solving. We developed original filters for computer processing of images captured by IR cameras. Their applications for computer processing of images results in a temperature resolution enhancing of cameras.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simonen, F.A.; Johnson, K.I.; Liebetrau, A.M.

The VISA-II (Vessel Integrity Simulation Analysis code was originally developed as part of the NRC staff evaluation of pressurized thermal shock. VISA-II uses Monte Carlo simulation to evaluate the failure probability of a pressurized water reactor (PWR) pressure vessel subjected to a pressure and thermal transient specified by the user. Linear elastic fracture mechanics methods are used to model crack initiation and propagation. Parameters for initial crack size and location, copper content, initial reference temperature of the nil-ductility transition, fluence, crack-initiation fracture toughness, and arrest fracture toughness are treated as random variables. This report documents an upgraded version of themore » original VISA code as described in NUREG/CR-3384. Improvements include a treatment of cladding effects, a more general simulation of flaw size, shape and location, a simulation of inservice inspection, an updated simulation of the reference temperature of the nil-ductility transition, and treatment of vessels with multiple welds and initial flaws. The code has been extensively tested and verified and is written in FORTRAN for ease of installation on different computers. 38 refs., 25 figs.« less

Numerical uncertainty in computational engineering and physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hemez, Francois M

2009-01-01

Obtaining a solution that approximates ordinary or partial differential equations on a computational mesh or grid does not necessarily mean that the solution is accurate or even 'correct'. Unfortunately assessing the quality of discrete solutions by questioning the role played by spatial and temporal discretizations generally comes as a distant third to test-analysis comparison and model calibration. This publication is contributed to raise awareness of the fact that discrete solutions introduce numerical uncertainty. This uncertainty may, in some cases, overwhelm in complexity and magnitude other sources of uncertainty that include experimental variability, parametric uncertainty and modeling assumptions. The concepts ofmore » consistency, convergence and truncation error are overviewed to explain the articulation between the exact solution of continuous equations, the solution of modified equations and discrete solutions computed by a code. The current state-of-the-practice of code and solution verification activities is discussed. An example in the discipline of hydro-dynamics illustrates the significant effect that meshing can have on the quality of code predictions. A simple method is proposed to derive bounds of solution uncertainty in cases where the exact solution of the continuous equations, or its modified equations, is unknown. It is argued that numerical uncertainty originating from mesh discretization should always be quantified and accounted for in the overall uncertainty 'budget' that supports decision-making for applications in computational physics and engineering.« less

SKYSINE-II procedure: calculation of the effects of structure design on neutron, primary gamma-ray and secondary gamma-ray dose rates in air

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lampley, C.M.

1979-01-01

An updated version of the SKYSHINE Monte Carlo procedure has been developed. The new computer code, SKYSHINE-II, provides a substantial increase in versatility in that the program possesses the ability to address three types of point-isotropic radiation sources: (1) primary gamma rays, (2) neutrons, and (3) secondary gamma rays. In addition, the emitted radiation may now be characterized by an energy emission spectrum product of a new energy-dependent atmospheric transmission data base developed by Radiation Research Associates, Inc. for each of the three source types described above. Most of the computational options present in the original program have been retainedmore » in the new version. Hence, the SKYSHINE-II computer code provides a versatile and viable tool for the analysis of the radiation environment in the vicinity of a building structure containing radiation sources, situated within the confines of a nuclear power plant. This report describes many of the calculational methods employed within the SKYSHINE-II program. A brief description of the new data base is included. Utilization instructions for the program are provided for operation of the SKYSHINE-II code on the Brookhaven National Laboratory Central Scientific Computing Facility. A listing of the source decks, block data routines, and the new atmospheric transmission data base are provided in the appendices of the report.« less

Enhancing Scalability and Efficiency of the TOUGH2_MP for LinuxClusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Wu, Yu-Shu

2006-04-17

TOUGH2{_}MP, the parallel version TOUGH2 code, has been enhanced by implementing more efficient communication schemes. This enhancement is achieved through reducing the amount of small-size messages and the volume of large messages. The message exchange speed is further improved by using non-blocking communications for both linear and nonlinear iterations. In addition, we have modified the AZTEC parallel linear-equation solver to nonblocking communication. Through the improvement of code structuring and bug fixing, the new version code is now more stable, while demonstrating similar or even better nonlinear iteration converging speed than the original TOUGH2 code. As a result, the new versionmore » of TOUGH2{_}MP is improved significantly in its efficiency. In this paper, the scalability and efficiency of the parallel code are demonstrated by solving two large-scale problems. The testing results indicate that speedup of the code may depend on both problem size and complexity. In general, the code has excellent scalability in memory requirement as well as computing time.« less

Single-intensity-recording optical encryption technique based on phase retrieval algorithm and QR code

NASA Astrophysics Data System (ADS)

Wang, Zhi-peng; Zhang, Shuai; Liu, Hong-zhao; Qin, Yi

2014-12-01

Based on phase retrieval algorithm and QR code, a new optical encryption technology that only needs to record one intensity distribution is proposed. In this encryption process, firstly, the QR code is generated from the information to be encrypted; and then the generated QR code is placed in the input plane of 4-f system to have a double random phase encryption. For only one intensity distribution in the output plane is recorded as the ciphertext, the encryption process is greatly simplified. In the decryption process, the corresponding QR code is retrieved using phase retrieval algorithm. A priori information about QR code is used as support constraint in the input plane, which helps solve the stagnation problem. The original information can be recovered without distortion by scanning the QR code. The encryption process can be implemented either optically or digitally, and the decryption process uses digital method. In addition, the security of the proposed optical encryption technology is analyzed. Theoretical analysis and computer simulations show that this optical encryption system is invulnerable to various attacks, and suitable for harsh transmission conditions.

The EDIT-COMGEOM Code

DTIC Science & Technology

1975-09-01

This report assumes a familiarity with the GIFT and MAGIC computer codes. The EDIT-COMGEOM code is a FORTRAN computer code. The EDIT-COMGEOM code...converts the target description data which was used in the MAGIC computer code to the target description data which can be used in the GIFT computer code

Rosen's (M,R) system in Unified Modelling Language.

PubMed

Zhang, Ling; Williams, Richard A; Gatherer, Derek

2016-01-01

Robert Rosen's (M,R) system is an abstract biological network architecture that is allegedly non-computable on a Turing machine. If (M,R) is truly non-computable, there are serious implications for the modelling of large biological networks in computer software. A body of work has now accumulated addressing Rosen's claim concerning (M,R) by attempting to instantiate it in various software systems. However, a conclusive refutation has remained elusive, principally since none of the attempts to date have unambiguously avoided the critique that they have altered the properties of (M,R) in the coding process, producing merely approximate simulations of (M,R) rather than true computational models. In this paper, we use the Unified Modelling Language (UML), a diagrammatic notation standard, to express (M,R) as a system of objects having attributes, functions and relations. We believe that this instantiates (M,R) in such a way than none of the original properties of the system are corrupted in the process. Crucially, we demonstrate that (M,R) as classically represented in the relational biology literature is implicitly a UML communication diagram. Furthermore, since UML is formally compatible with object-oriented computing languages, instantiation of (M,R) in UML strongly implies its computability in object-oriented coding languages. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

VENTURE/PC manual: A multidimensional multigroup neutron diffusion code system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shapiro, A.; Huria, H.C.; Cho, K.W.

1991-12-01

VENTURE/PC is a recompilation of part of the Oak Ridge BOLD VENTURE code system, which will operate on an IBM PC or compatible computer. Neutron diffusion theory solutions are obtained for multidimensional, multigroup problems. This manual contains information associated with operating the code system. The purpose of the various modules used in the code system, and the input for these modules are discussed. The PC code structure is also given. Version 2 included several enhancements not given in the original version of the code. In particular, flux iterations can be done in core rather than by reading and writing tomore » disk, for problems which allow sufficient memory for such in-core iterations. This speeds up the iteration process. Version 3 does not include any of the special processors used in the previous versions. These special processors utilized formatted input for various elements of the code system. All such input data is now entered through the Input Processor, which produces standard interface files for the various modules in the code system. In addition, a Standard Interface File Handbook is included in the documentation which is distributed with the code, to assist in developing the input for the Input Processor.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Shawn

This code consists of Matlab routines which enable the user to perform non-manifold surface reconstruction via triangulation from high dimensional point cloud data. The code was based on an algorithm originally developed in [Freedman (2007), An Incremental Algorithm for Reconstruction of Surfaces of Arbitrary Codimension Computational Geometry: Theory and Applications, 36(2):106-116]. This algorithm has been modified to accommodate non-manifold surface according to the work described in [S. Martin and J.-P. Watson (2009), Non-Manifold Surface Reconstruction from High Dimensional Point Cloud DataSAND #5272610].The motivation for developing the code was a point cloud describing the molecular conformation space of cyclooctane (C8H16). Cyclooctanemore » conformation space was represented using points in 72 dimensions (3 coordinates for each molecule). The code was used to triangulate the point cloud and thereby study the geometry and topology of cyclooctane. Futures applications are envisioned for peptides and proteins.« less

Applications of statistical physics and information theory to the analysis of DNA sequences

NASA Astrophysics Data System (ADS)

Grosse, Ivo

2000-10-01

DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

Rotordynamics on the PC: Further Capabilities of ARDS

NASA Technical Reports Server (NTRS)

Fleming, David P.

1997-01-01

Rotordynamics codes for personal computers are now becoming available. One of the most capable codes is Analysis of RotorDynamic Systems (ARDS) which uses the component mode synthesis method to analyze a system of up to 5 rotating shafts. ARDS was originally written for a mainframe computer but has been successfully ported to a PC; its basic capabilities for steady-state and transient analysis were reported in an earlier paper. Additional functions have now been added to the PC version of ARDS. These functions include: 1) Estimation of the peak response following blade loss without resorting to a full transient analysis; 2) Calculation of response sensitivity to input parameters; 3) Formulation of optimum rotor and damper designs to place critical speeds in desirable ranges or minimize bearing loads; 4) Production of Poincard plots so the presence of chaotic motion can be ascertained. ARDS produces printed and plotted output. The executable code uses the full array sizes of the mainframe version and fits on a high density floppy disc. Examples of all program capabilities are presented and discussed.

Computing Temperatures in Optically Thick Protoplanetary Disks

NASA Technical Reports Server (NTRS)

Capuder, Lawrence F.. Jr.

2011-01-01

We worked with a Monte Carlo radiative transfer code to simulate the transfer of energy through protoplanetary disks, where planet formation occurs. The code tracks photons from the star into the disk, through scattering, absorption and re-emission, until they escape to infinity. High optical depths in the disk interior dominate the computation time because it takes the photon packet many interactions to get out of the region. High optical depths also receive few photons and therefore do not have well-estimated temperatures. We applied a modified random walk (MRW) approximation for treating high optical depths and to speed up the Monte Carlo calculations. The MRW is implemented by calculating the average number of interactions the photon packet will undergo in diffusing within a single cell of the spatial grid and then updating the packet position, packet frequencies, and local radiation absorption rate appropriately. The MRW approximation was then tested for accuracy and speed compared to the original code. We determined that MRW provides accurate answers to Monte Carlo Radiative transfer simulations. The speed gained from using MRW is shown to be proportional to the disk mass.

RELAP5-3D Resolution of Known Restart/Backup Issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mesina, George L.; Anderson, Nolan A.

2014-12-01

The state-of-the-art nuclear reactor system safety analysis computer program developed at the Idaho National Laboratory (INL), RELAP5-3D, continues to adapt to changes in computer hardware and software and to develop to meet the ever-expanding needs of the nuclear industry. To continue at the forefront, code testing must evolve with both code and industry developments, and it must work correctly. To best ensure this, the processes of Software Verification and Validation (V&V) are applied. Verification compares coding against its documented algorithms and equations and compares its calculations against analytical solutions and the method of manufactured solutions. A form of this, sequentialmore » verification, checks code specifications against coding only when originally written then applies regression testing which compares code calculations between consecutive updates or versions on a set of test cases to check that the performance does not change. A sequential verification testing system was specially constructed for RELAP5-3D to both detect errors with extreme accuracy and cover all nuclear-plant-relevant code features. Detection is provided through a “verification file” that records double precision sums of key variables. Coverage is provided by a test suite of input decks that exercise code features and capabilities necessary to model a nuclear power plant. A matrix of test features and short-running cases that exercise them is presented. This testing system is used to test base cases (called null testing) as well as restart and backup cases. It can test RELAP5-3D performance in both standalone and coupled (through PVM to other codes) runs. Application of verification testing revealed numerous restart and backup issues in both standalone and couple modes. This document reports the resolution of these issues.« less

LAURA Users Manual: 5.3-48528

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Chirstopher O.; Kleb, Bil

2010-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

LAURA Users Manual: 5.5-64987

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, William L.

2013-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintain ability by eliminating the requirement for problem dependent recompilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

LAURA Users Manual: 5.4-54166

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2011-01-01

This users manual provides in-depth information concerning installation and execution of Laura, version 5. Laura is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 Laura code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, Laura now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

LAURA Users Manual: 5.2-43231

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2009-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multiphysics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

Laura Users Manual: 5.1-41601

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2009-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multiphysics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

Modeling the Volcanic Source at Long Valley, CA, Using a Genetic Algorithm Technique

NASA Technical Reports Server (NTRS)

Tiampo, Kristy F.

1999-01-01

In this project, we attempted to model the deformation pattern due to the magmatic source at Long Valley caldera using a real-value coded genetic algorithm (GA) inversion similar to that found in Michalewicz, 1992. The project has been both successful and rewarding. The genetic algorithm, coded in the C programming language, performs stable inversions over repeated trials, with varying initial and boundary conditions. The original model used a GA in which the geophysical information was coded into the fitness function through the computation of surface displacements for a Mogi point source in an elastic half-space. The program was designed to invert for a spherical magmatic source - its depth, horizontal location and volume - using the known surface deformations. It also included the capability of inverting for multiple sources.

POM.gpu-v1.0: a GPU-based Princeton Ocean Model

NASA Astrophysics Data System (ADS)

Xu, S.; Huang, X.; Oey, L.-Y.; Xu, F.; Fu, H.; Zhang, Y.; Yang, G.

2015-09-01

Graphics processing units (GPUs) are an attractive solution in many scientific applications due to their high performance. However, most existing GPU conversions of climate models use GPUs for only a few computationally intensive regions. In the present study, we redesign the mpiPOM (a parallel version of the Princeton Ocean Model) with GPUs. Specifically, we first convert the model from its original Fortran form to a new Compute Unified Device Architecture C (CUDA-C) code, then we optimize the code on each of the GPUs, the communications between the GPUs, and the I / O between the GPUs and the central processing units (CPUs). We show that the performance of the new model on a workstation containing four GPUs is comparable to that on a powerful cluster with 408 standard CPU cores, and it reduces the energy consumption by a factor of 6.8.

Perspectives in numerical astrophysics:

NASA Astrophysics Data System (ADS)

Reverdy, V.

2016-12-01

In this discussion paper, we investigate the current and future status of numerical astrophysics and highlight key questions concerning the transition to the exascale era. We first discuss the fact that one of the main motivation behind high performance simulations should not be the reproduction of observational or experimental data, but the understanding of the emergence of complexity from fundamental laws. This motivation is put into perspective regarding the quest for more computational power and we argue that extra computational resources can be used to gain in abstraction. Then, the readiness level of present-day simulation codes in regard to upcoming exascale architecture is examined and two major challenges are raised concerning both the central role of data movement for performances and the growing complexity of codes. Software architecture is finally presented as a key component to make the most of upcoming architectures while solving original physics problems.

Parallel Unsteady Turbopump Simulations for Liquid Rocket Engines

NASA Technical Reports Server (NTRS)

Kiris, Cetin C.; Kwak, Dochan; Chan, William

2000-01-01

This paper reports the progress being made towards complete turbo-pump simulation capability for liquid rocket engines. Space Shuttle Main Engine (SSME) turbo-pump impeller is used as a test case for the performance evaluation of the MPI and hybrid MPI/Open-MP versions of the INS3D code. Then, a computational model of a turbo-pump has been developed for the shuttle upgrade program. Relative motion of the grid system for rotor-stator interaction was obtained by employing overset grid techniques. Time-accuracy of the scheme has been evaluated by using simple test cases. Unsteady computations for SSME turbo-pump, which contains 136 zones with 35 Million grid points, are currently underway on Origin 2000 systems at NASA Ames Research Center. Results from time-accurate simulations with moving boundary capability, and the performance of the parallel versions of the code will be presented in the final paper.

Tough2{_}MP: A parallel version of TOUGH2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Keni; Wu, Yu-Shu; Ding, Chris

2003-04-09

TOUGH2{_}MP is a massively parallel version of TOUGH2. It was developed for running on distributed-memory parallel computers to simulate large simulation problems that may not be solved by the standard, single-CPU TOUGH2 code. The new code implements an efficient massively parallel scheme, while preserving the full capacity and flexibility of the original TOUGH2 code. The new software uses the METIS software package for grid partitioning and AZTEC software package for linear-equation solving. The standard message-passing interface is adopted for communication among processors. Numerical performance of the current version code has been tested on CRAY-T3E and IBM RS/6000 SP platforms. Inmore » addition, the parallel code has been successfully applied to real field problems of multi-million-cell simulations for three-dimensional multiphase and multicomponent fluid and heat flow, as well as solute transport. In this paper, we will review the development of the TOUGH2{_}MP, and discuss the basic features, modules, and their applications.« less

Natural pixel decomposition for computational tomographic reconstruction from interferometric projection: algorithms and comparison

NASA Astrophysics Data System (ADS)

Cha, Don J.; Cha, Soyoung S.

1995-09-01

A computational tomographic technique, termed the variable grid method (VGM), has been developed for improving interferometric reconstruction of flow fields under ill-posed data conditions of restricted scanning and incomplete projection. The technique is based on natural pixel decomposition, that is, division of a field into variable grid elements. The performances of two algorithms, that is, original and revised versions, are compared to investigate the effects of the data redundancy criteria and seed element forming schemes. Tests of the VGMs are conducted through computer simulation of experiments and reconstruction of fields with a limited view angel of 90 degree(s). The temperature fields at two horizontal sections of a thermal plume of two interacting isothermal cubes, produced by a finite numerical code, are analyzed as test fields. The computer simulation demonstrates the superiority of the revised VGM to either the conventional fixed grid method or the original VGM. Both the maximum and average reconstruction errors are reduced appreciably. The reconstruction shows substantial improvement in the regions with dense scanning by probing rays. These regions are usually of interest in engineering applications.

Parallel computing techniques for rotorcraft aerodynamics

NASA Astrophysics Data System (ADS)

Ekici, Kivanc

The modification of unsteady three-dimensional Navier-Stokes codes for application on massively parallel and distributed computing environments is investigated. The Euler/Navier-Stokes code TURNS (Transonic Unsteady Rotor Navier-Stokes) was chosen as a test bed because of its wide use by universities and industry. For the efficient implementation of TURNS on parallel computing systems, two algorithmic changes are developed. First, main modifications to the implicit operator, Lower-Upper Symmetric Gauss Seidel (LU-SGS) originally used in TURNS, is performed. Second, application of an inexact Newton method, coupled with a Krylov subspace iterative method (Newton-Krylov method) is carried out. Both techniques have been tried previously for the Euler equations mode of the code. In this work, we have extended the methods to the Navier-Stokes mode. Several new implicit operators were tried because of convergence problems of traditional operators with the high cell aspect ratio (CAR) grids needed for viscous calculations on structured grids. Promising results for both Euler and Navier-Stokes cases are presented for these operators. For the efficient implementation of Newton-Krylov methods to the Navier-Stokes mode of TURNS, efficient preconditioners must be used. The parallel implicit operators used in the previous step are employed as preconditioners and the results are compared. The Message Passing Interface (MPI) protocol has been used because of its portability to various parallel architectures. It should be noted that the proposed methodology is general and can be applied to several other CFD codes (e.g. OVERFLOW).

MEMOPS: data modelling and automatic code generation.

PubMed

Fogh, Rasmus H; Boucher, Wayne; Ionides, John M C; Vranken, Wim F; Stevens, Tim J; Laue, Ernest D

2010-03-25

In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces--APIs--currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology.

Near-Body Grid Adaption for Overset Grids

NASA Technical Reports Server (NTRS)

Buning, Pieter G.; Pulliam, Thomas H.

2016-01-01

A solution adaption capability for curvilinear near-body grids has been implemented in the OVERFLOW overset grid computational fluid dynamics code. The approach follows closely that used for the Cartesian off-body grids, but inserts refined grids in the computational space of original near-body grids. Refined curvilinear grids are generated using parametric cubic interpolation, with one-sided biasing based on curvature and stretching ratio of the original grid. Sensor functions, grid marking, and solution interpolation tasks are implemented in the same fashion as for off-body grids. A goal-oriented procedure, based on largest error first, is included for controlling growth rate and maximum size of the adapted grid system. The adaption process is almost entirely parallelized using MPI, resulting in a capability suitable for viscous, moving body simulations. Two- and three-dimensional examples are presented.

Efficient Parallelization of a Dynamic Unstructured Application on the Tera MTA

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak

1999-01-01

The success of parallel computing in solving real-life computationally-intensive problems relies on their efficient mapping and execution on large-scale multiprocessor architectures. Many important applications are both unstructured and dynamic in nature, making their efficient parallel implementation a daunting task. This paper presents the parallelization of a dynamic unstructured mesh adaptation algorithm using three popular programming paradigms on three leading supercomputers. We examine an MPI message-passing implementation on the Cray T3E and the SGI Origin2OOO, a shared-memory implementation using cache coherent nonuniform memory access (CC-NUMA) of the Origin2OOO, and a multi-threaded version on the newly-released Tera Multi-threaded Architecture (MTA). We compare several critical factors of this parallel code development, including runtime, scalability, programmability, and memory overhead. Our overall results demonstrate that multi-threaded systems offer tremendous potential for quickly and efficiently solving some of the most challenging real-life problems on parallel computers.

The "Wow! signal" of the terrestrial genetic code

NASA Astrophysics Data System (ADS)

shCherbak, Vladimir I.; Makukov, Maxim A.

2013-05-01

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like "signal" in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10-13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

The high hall ventilation with the simplified simulation of the fan

NASA Astrophysics Data System (ADS)

Kyncl, Martin; Pelant, Jaroslav

2018-06-01

Here we work with the system of equations describing the non-stationary compressible turbulent multi-component flow in the gravitational field. We focus on the numerical simulation of the fan situated inside the high hall. The RANS equations are discretized with the use of the finite volume method. The original modification of the Riemann problem and its solution is used at the boundaries. The combination of specific boundary conditions is used for the simulation of the fan. The presented computational results are computed with own-developed code (C, FORTRAN, multiprocessor, unstructured meshes in general).

Fractal Viscous Fingering in Fracture Networks

NASA Astrophysics Data System (ADS)

Boyle, E.; Sams, W.; Ferer, M.; Smith, D. H.

2007-12-01

We have used two very different physical models and computer codes to study miscible injection of a low- viscosity fluid into a simple fracture network, where it displaces a much-more viscous "defending" fluid through "rock" that is otherwise impermeable. The one code (NETfLow) is a standard pore level model, originally intended to treat laboratory-scale experiments; it assumes negligible mixing of the two fluids. The other code (NFFLOW) was written to treat reservoir-scale engineering problems; It explicitly treats the flow through the fractures and allows for significant mixing of the fluids at the interface. Both codes treat the fractures as parallel plates, of different effective apertures. Results are presented for the composition profiles from both codes. Independent of the degree of fluid-mixing, the profiles from both models have a functional form identical to that for fractal viscous fingering (i.e., diffusion limited aggregation, DLA). The two codes that solve the equations for different models gave similar results; together they suggest that the injection of a low-viscosity fluid into large- scale fracture networks may be much more significantly affected by fractal fingering than previously illustrated.

Implementation of a Message Passing Interface into a Cloud-Resolving Model for Massively Parallel Computing

NASA Technical Reports Server (NTRS)

Juang, Hann-Ming Henry; Tao, Wei-Kuo; Zeng, Xi-Ping; Shie, Chung-Lin; Simpson, Joanne; Lang, Steve

2004-01-01

The capability for massively parallel programming (MPP) using a message passing interface (MPI) has been implemented into a three-dimensional version of the Goddard Cumulus Ensemble (GCE) model. The design for the MPP with MPI uses the concept of maintaining similar code structure between the whole domain as well as the portions after decomposition. Hence the model follows the same integration for single and multiple tasks (CPUs). Also, it provides for minimal changes to the original code, so it is easily modified and/or managed by the model developers and users who have little knowledge of MPP. The entire model domain could be sliced into one- or two-dimensional decomposition with a halo regime, which is overlaid on partial domains. The halo regime requires that no data be fetched across tasks during the computational stage, but it must be updated before the next computational stage through data exchange via MPI. For reproducible purposes, transposing data among tasks is required for spectral transform (Fast Fourier Transform, FFT), which is used in the anelastic version of the model for solving the pressure equation. The performance of the MPI-implemented codes (i.e., the compressible and anelastic versions) was tested on three different computing platforms. The major results are: 1) both versions have speedups of about 99% up to 256 tasks but not for 512 tasks; 2) the anelastic version has better speedup and efficiency because it requires more computations than that of the compressible version; 3) equal or approximately-equal numbers of slices between the x- and y- directions provide the fastest integration due to fewer data exchanges; and 4) one-dimensional slices in the x-direction result in the slowest integration due to the need for more memory relocation for computation.

Computation of asymmetric supersonic flows around cones at large incidence

NASA Technical Reports Server (NTRS)

Degani, David

1987-01-01

The Schiff-Steger parabolized Navier-Stokes (PNS) code has been modified to allow computation of conical flowfields around cones at high incidence. The improved algorithm of Degani and Schiff has been incorporated with the PNS code. This algorithm adds the cross derivative and circumferential viscous terms to the original PNS code and modifies the algebraic eddy viscosity turbulence model to take into account regions of so called cross-flow separation. Assuming the flowfield is conical (but not necessarily symmetric) a marching stepback procedure is used: the solution is marched one step downstream using improved PNS code and the flow variables are then scaled to place the solution back to the original station. The process is repeated until no change in the flow variables is observed with further marching. The flow variables are then constant along rays of the flowfield. The experiments obtained by Bannik and Nebbeling were chosen as a test case. In these experiments a cone of 7.5 deg. half angle at Mach number 2.94 and Reynolds number 1.372 x 10(7) was tested up 34 deg. angle of attack. At high angle of attack nonconical asymmetric leeward side vortex patterns were observed. In the first set of computations, using an earlier obtained solution of the above cone for angle of attack of 22.6 deg. and at station x=0.5 as a starting solution, the angle of attack was gradually increased up to 34 deg. During this procedure the grid was carfully adjusted to capture the bow shock. A stable, converged symmetric solution was obtained. Since the numerical code converged to a symmetric solution which is not the physical one, the stability was tested by a random perturbation at each point. The possible effect of surface roughness or non perfect body shape was also investigated. It was concluded that although the assumption of conical viscous flows can be very useful for certain cases, it can not be used for the present case. Thus the second part of the investigation attempted to obtain a marching (in space) solution with the PNS method using the conical solution as initial data. Finally, the solution of the full Navier-Stokes equations was carried out.

Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP

NASA Astrophysics Data System (ADS)

Hofierka, Jaroslav; Lacko, Michal; Zubal, Stanislav

2017-10-01

In this paper, we describe the parallelization of three complex and computationally intensive modules of GRASS GIS using the OpenMP application programming interface for multi-core computers. These include the v.surf.rst module for spatial interpolation, the r.sun module for solar radiation modeling and the r.sim.water module for water flow simulation. We briefly describe the functionality of the modules and parallelization approaches used in the modules. Our approach includes the analysis of the module's functionality, identification of source code segments suitable for parallelization and proper application of OpenMP parallelization code to create efficient threads processing the subtasks. We document the efficiency of the solutions using the airborne laser scanning data representing land surface in the test area and derived high-resolution digital terrain model grids. We discuss the performance speed-up and parallelization efficiency depending on the number of processor threads. The study showed a substantial increase in computation speeds on a standard multi-core computer while maintaining the accuracy of results in comparison to the output from original modules. The presented parallelization approach showed the simplicity and efficiency of the parallelization of open-source GRASS GIS modules using OpenMP, leading to an increased performance of this geospatial software on standard multi-core computers.

When technology became language: the origins of the linguistic conception of computer programming, 1950-1960.

PubMed

Nofre, David; Priestley, Mark; Alberts, Gerard

2014-01-01

Language is one of the central metaphors around which the discipline of computer science has been built. The language metaphor entered modern computing as part of a cybernetic discourse, but during the second half of the 1950s acquired a more abstract meaning, closely related to the formal languages of logic and linguistics. The article argues that this transformation was related to the appearance of the commercial computer in the mid-1950s. Managers of computing installations and specialists on computer programming in academic computer centers, confronted with an increasing variety of machines, called for the creation of "common" or "universal languages" to enable the migration of computer code from machine to machine. Finally, the article shows how the idea of a universal language was a decisive step in the emergence of programming languages, in the recognition of computer programming as a proper field of knowledge, and eventually in the way we think of the computer.

Human performance across decision making, selective attention, and working memory tasks: Experimental data and computer simulations.

PubMed

Stocco, Andrea; Yamasaki, Brianna L; Prat, Chantel S

2018-04-01

This article describes the data analyzed in the paper "Individual differences in the Simon effect are underpinned by differences in the competitive dynamics in the basal ganglia: An experimental verification and a computational model" (Stocco et al., 2017) [1]. The data includes behavioral results from participants performing three cognitive tasks (Probabilistic Stimulus Selection (Frank et al., 2004) [2], Simon task (Craft and Simon, 1970) [3], and Automated Operation Span (Unsworth et al., 2005) [4]), as well as simulationed traces generated by a computational neurocognitive model that accounts for individual variations in human performance across the tasks. The experimental data encompasses individual data files (in both preprocessed and native output format) as well as group-level summary files. The simulation data includes the entire model code, the results of a full-grid search of the model's parameter space, and the code used to partition the model space and parallelize the simulations. Finally, the repository includes the R scripts used to carry out the statistical analyses reported in the original paper.

Fast evolving pair-instability supernovae

DOE PAGES

Kozyreva, Alexandra; Gilmer, Matthew; Hirschi, Raphael; ...

2016-10-06

With an increasing number of superluminous supernovae (SLSNe) discovered the ques- tion of their origin remains open and causes heated debates in the supernova commu- nity. Currently, there are three proposed mechanisms for SLSNe: (1) pair-instability supernovae (PISN), (2) magnetar-driven supernovae, and (3) models in which the su- pernova ejecta interacts with a circumstellar material ejected before the explosion. Based on current observations of SLSNe, the PISN origin has been disfavoured for a number of reasons. Many PISN models provide overly broad light curves and too reddened spectra, because of massive ejecta and a high amount of nickel. In themore » cur- rent study we re-examine PISN properties using progenitor models computed with the GENEC code. We calculate supernova explosions with FLASH and light curve evolu- tion with the radiation hydrodynamics code STELLA. We find that high-mass models (200 M⊙ and 250 M⊙) at relatively high metallicity (Z=0.001) do not retain hydro- gen in the outer layers and produce relatively fast evolving PISNe Type I and might be suitable to explain some SLSNe. We also investigate uncertainties in light curve modelling due to codes, opacities, the nickel-bubble effect and progenitor structure and composition.« less

Scaling Optimization of the SIESTA MHD Code

NASA Astrophysics Data System (ADS)

Seal, Sudip; Hirshman, Steven; Perumalla, Kalyan

2013-10-01

SIESTA is a parallel three-dimensional plasma equilibrium code capable of resolving magnetic islands at high spatial resolutions for toroidal plasmas. Originally designed to exploit small-scale parallelism, SIESTA has now been scaled to execute efficiently over several thousands of processors P. This scaling improvement was accomplished with minimal intrusion to the execution flow of the original version. First, the efficiency of the iterative solutions was improved by integrating the parallel tridiagonal block solver code BCYCLIC. Krylov-space generation in GMRES was then accelerated using a customized parallel matrix-vector multiplication algorithm. Novel parallel Hessian generation algorithms were integrated and memory access latencies were dramatically reduced through loop nest optimizations and data layout rearrangement. These optimizations sped up equilibria calculations by factors of 30-50. It is possible to compute solutions with granularity N/P near unity on extremely fine radial meshes (N > 1024 points). Grid separation in SIESTA, which manifests itself primarily in the resonant components of the pressure far from rational surfaces, is strongly suppressed by finer meshes. Large problem sizes of up to 300 K simultaneous non-linear coupled equations have been solved on the NERSC supercomputers. Work supported by U.S. DOE under Contract DE-AC05-00OR22725 with UT-Battelle, LLC.

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

VENTURE/PC manual: A multidimensional multigroup neutron diffusion code system. Version 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shapiro, A.; Huria, H.C.; Cho, K.W.

1991-12-01

VENTURE/PC is a recompilation of part of the Oak Ridge BOLD VENTURE code system, which will operate on an IBM PC or compatible computer. Neutron diffusion theory solutions are obtained for multidimensional, multigroup problems. This manual contains information associated with operating the code system. The purpose of the various modules used in the code system, and the input for these modules are discussed. The PC code structure is also given. Version 2 included several enhancements not given in the original version of the code. In particular, flux iterations can be done in core rather than by reading and writing tomore » disk, for problems which allow sufficient memory for such in-core iterations. This speeds up the iteration process. Version 3 does not include any of the special processors used in the previous versions. These special processors utilized formatted input for various elements of the code system. All such input data is now entered through the Input Processor, which produces standard interface files for the various modules in the code system. In addition, a Standard Interface File Handbook is included in the documentation which is distributed with the code, to assist in developing the input for the Input Processor.« less

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

PubMed Central

Boerner, Susan; McGinnis, Karen M.

2012-01-01

Background Computational analysis of cDNA sequences from multiple organisms suggests that a large portion of transcribed DNA does not code for a functional protein. In mammals, noncoding transcription is abundant, and often results in functional RNA molecules that do not appear to encode proteins. Many long noncoding RNAs (lncRNAs) appear to have epigenetic regulatory function in humans, including HOTAIR and XIST. While epigenetic gene regulation is clearly an essential mechanism in plants, relatively little is known about the presence or function of lncRNAs in plants. Methodology/Principal Findings To explore the connection between lncRNA and epigenetic regulation of gene expression in plants, a computational pipeline using the programming language Python has been developed and applied to maize full length cDNA sequences to identify, classify, and localize potential lncRNAs. The pipeline was used in parallel with an SVM tool for identifying ncRNAs to identify the maximal number of ncRNAs in the dataset. Although the available library of sequences was small and potentially biased toward protein coding transcripts, 15% of the sequences were predicted to be noncoding. Approximately 60% of these sequences appear to act as precursors for small RNA molecules and may function to regulate gene expression via a small RNA dependent mechanism. ncRNAs were predicted to originate from both genic and intergenic loci. Of the lncRNAs that originated from genic loci, ∼20% were antisense to the host gene loci. Conclusions/Significance Consistent with similar studies in other organisms, noncoding transcription appears to be widespread in the maize genome. Computational predictions indicate that maize lncRNAs may function to regulate expression of other genes through multiple RNA mediated mechanisms. PMID:22916204

Sensitivity analysis of the Gupta and Park chemical models on the heat flux by DSMC and CFD codes

NASA Astrophysics Data System (ADS)

Morsa, Luigi; Festa, Giandomenico; Zuppardi, Gennaro

2012-11-01

The present study is the logical continuation of a former paper by the first author in which the influence of the chemical models by Gupta and by Park on the computation of heat flux on the Orion and EXPERT capsules was evaluated. Tests were carried out by the direct simulation Monte Carlo code DS2V and by the computational fluiddynamic (CFD) code H3NS. DS2V implements the Gupta model, while H3NS implements the Park model. In order to compare the effects of the chemical models, the Park model was implemented also in DS2V. The results showed that DS2V and H3NS compute a different composition both in the flow field and on the surface, even using the same chemical model (Park). Furthermore DS2V computes, by the two chemical models, different compositions in the flow field but the same composition on the surface, therefore the same heat flux. In the present study, in order to evaluate the influence of these chemical models also in a CFD code, the Gupta and the Park models have been implemented in FLUENT. Tests by DS2V and by FLUENT, have been carried out for the EXPERT capsule at the altitude of 70 km and with velocity of 5000 m/s. The capsule experiences a hypersonic, continuum low density regime. Due to the energy level of the flow, the vibration equation, lacking in the original version of FLUENT, has been implemented. The results of the heat flux computation verify that FLUENT is quite sensitive to the Gupta and to the Park chemical models. In fact, at the stagnation point, the percentage difference between the models is about 13%. On the opposite the DS2V results by the two models are practically equivalent.

Portable Parallel Programming for the Dynamic Load Balancing of Unstructured Grid Applications

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Das, Sajal K.; Harvey, Daniel; Oliker, Leonid

1999-01-01

The ability to dynamically adapt an unstructured -rid (or mesh) is a powerful tool for solving computational problems with evolving physical features; however, an efficient parallel implementation is rather difficult, particularly from the view point of portability on various multiprocessor platforms We address this problem by developing PLUM, tin automatic anti architecture-independent framework for adaptive numerical computations in a message-passing environment. Portability is demonstrated by comparing performance on an SP2, an Origin2000, and a T3E, without any code modifications. We also present a general-purpose load balancer that utilizes symmetric broadcast networks (SBN) as the underlying communication pattern, with a goal to providing a global view of system loads across processors. Experiments on, an SP2 and an Origin2000 demonstrate the portability of our approach which achieves superb load balance at the cost of minimal extra overhead.

Erratum: Three-cluster dynamics within an ab initio framework [Phys. Rev. C 88 , 034320 (2013)

DOE PAGES

Quaglioni, Sofia; Romero-Redondo, Carolina; Navrátil, Petr

2016-07-14

In this study, we have discovered a typographical error in the portion of code used in our original article to compute the probability distribution of Figs. 7–9 of Sec. III B 2. The correct results are shown in the figures below. The correct probability distribution now shows the characteristic prominence of the “dineutron” over the “cigar” configuration. In addition, the most-probable distance between the two neutrons in the latter configuration is close to 4 fm (rather than the erroneously reported 5 fm). The other results and conclusion of the original paper remain unaffected.

Results of comparative RBMK neutron computation using VNIIEF codes (cell computation, 3D statics, 3D kinetics). Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grebennikov, A.N.; Zhitnik, A.K.; Zvenigorodskaya, O.A.

1995-12-31

In conformity with the protocol of the Workshop under Contract {open_quotes}Assessment of RBMK reactor safety using modern Western Codes{close_quotes} VNIIEF performed a neutronics computation series to compare western and VNIIEF codes and assess whether VNIIEF codes are suitable for RBMK type reactor safety assessment computation. The work was carried out in close collaboration with M.I. Rozhdestvensky and L.M. Podlazov, NIKIET employees. The effort involved: (1) cell computations with the WIMS, EKRAN codes (improved modification of the LOMA code) and the S-90 code (VNIIEF Monte Carlo). Cell, polycell, burnup computation; (2) 3D computation of static states with the KORAT-3D and NEUmore » codes and comparison with results of computation with the NESTLE code (USA). The computations were performed in the geometry and using the neutron constants presented by the American party; (3) 3D computation of neutron kinetics with the KORAT-3D and NEU codes. These computations were performed in two formulations, both being developed in collaboration with NIKIET. Formulation of the first problem maximally possibly agrees with one of NESTLE problems and imitates gas bubble travel through a core. The second problem is a model of the RBMK as a whole with imitation of control and protection system controls (CPS) movement in a core.« less

An Improved Neutron Transport Algorithm for HZETRN2006

NASA Astrophysics Data System (ADS)

Slaba, Tony

NASA's new space exploration initiative includes plans for long term human presence in space thereby placing new emphasis on space radiation analyses. In particular, a systematic effort of verification, validation and uncertainty quantification of the tools commonly used for radiation analysis for vehicle design and mission planning has begun. In this paper, the numerical error associated with energy discretization in HZETRN2006 is addressed; large errors in the low-energy portion of the neutron fluence spectrum are produced due to a numerical truncation error in the transport algorithm. It is shown that the truncation error results from the narrow energy domain of the neutron elastic spectral distributions, and that an extremely fine energy grid is required in order to adequately resolve the problem under the current formulation. Since adding a sufficient number of energy points will render the code computationally inefficient, we revisit the light-ion transport theory developed for HZETRN2006 and focus on neutron elastic interactions. The new approach that is developed numerically integrates with adequate resolution in the energy domain without affecting the run-time of the code and is easily incorporated into the current code. Efforts were also made to optimize the computational efficiency of the light-ion propagator; a brief discussion of the efforts is given along with run-time comparisons between the original and updated codes. Convergence testing is then completed by running the code for various environments and shielding materials with many different energy grids to ensure stability of the proposed method.

Early MIMD experience on the CRAY X-MP

NASA Astrophysics Data System (ADS)

Rhoades, Clifford E.; Stevens, K. G.

1985-07-01

This paper describes some early experience with converting four physics simulation programs to the CRAY X-MP, a current Multiple Instruction, Multiple Data (MIMD) computer consisting of two processors each with an architecture similar to that of the CRAY-1. As a multi-processor, the CRAY X-MP together with the high speed Solid-state Storage Device (SSD) in an ideal machine upon which to study MIMD algorithms for solving the equations of mathematical physics because it is fast enough to run real problems. The computer programs used in this study are all FORTRAN versions of original production codes. They range in sophistication from a one-dimensional numerical simulation of collisionless plasma to a two-dimensional hydrodynamics code with heat flow to a couple of three-dimensional fluid dynamics codes with varying degrees of viscous modeling. Early research with a dual processor configuration has shown speed-ups ranging from 1.55 to 1.98. It has been observed that a few simple extensions to FORTRAN allow a typical programmer to achieve a remarkable level of efficiency. These extensions involve the concept of memory local to a concurrent subprogram and memory common to all concurrent subprograms.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Advanced Architectures for Astrophysical Supercomputing

NASA Astrophysics Data System (ADS)

Barsdell, B. R.; Barnes, D. G.; Fluke, C. J.

2010-12-01

Astronomers have come to rely on the increasing performance of computers to reduce, analyze, simulate and visualize their data. In this environment, faster computation can mean more science outcomes or the opening up of new parameter spaces for investigation. If we are to avoid major issues when implementing codes on advanced architectures, it is important that we have a solid understanding of our algorithms. A recent addition to the high-performance computing scene that highlights this point is the graphics processing unit (GPU). The hardware originally designed for speeding-up graphics rendering in video games is now achieving speed-ups of O(100×) in general-purpose computation - performance that cannot be ignored. We are using a generalized approach, based on the analysis of astronomy algorithms, to identify the optimal problem-types and techniques for taking advantage of both current GPU hardware and future developments in computing architectures.

Calculus domains modelled using an original bool algebra based on polygons

NASA Astrophysics Data System (ADS)

Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

2016-08-01

Analytical and numerical computer based models require analytical definitions of the calculus domains. The paper presents a method to model a calculus domain based on a bool algebra which uses solid and hollow polygons. The general calculus relations of the geometrical characteristics that are widely used in mechanical engineering are tested using several shapes of the calculus domain in order to draw conclusions regarding the most effective methods to discretize the domain. The paper also tests the results of several CAD commercial software applications which are able to compute the geometrical characteristics, being drawn interesting conclusions. The tests were also targeting the accuracy of the results vs. the number of nodes on the curved boundary of the cross section. The study required the development of an original software consisting of more than 1700 computer code lines. In comparison with other calculus methods, the discretization using convex polygons is a simpler approach. Moreover, this method doesn't lead to large numbers as the spline approximation did, in that case being required special software packages in order to offer multiple, arbitrary precision. The knowledge resulted from this study may be used to develop complex computer based models in engineering.

Development and application of the GIM code for the Cyber 203 computer

NASA Technical Reports Server (NTRS)

Stainaker, J. F.; Robinson, M. A.; Rawlinson, E. G.; Anderson, P. G.; Mayne, A. W.; Spradley, L. W.

1982-01-01

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented.

Hyper-Spectral Synthesis of Active OB Stars Using GLaDoS

NASA Astrophysics Data System (ADS)

Hill, N. R.; Townsend, R. H. D.

2016-11-01

In recent years there has been considerable interest in using graphics processing units (GPUs) to perform scientific computations that have traditionally been handled by central processing units (CPUs). However, there is one area where the scientific potential of GPUs has been overlooked - computer graphics, the task they were originally designed for. Here we introduce GLaDoS, a hyper-spectral code which leverages the graphics capabilities of GPUs to synthesize spatially and spectrally resolved images of complex stellar systems. We demonstrate how GLaDoS can be applied to calculate observables for various classes of stars including systems with inhomogenous surface temperatures and contact binaries.

Studying an Eulerian Computer Model on Different High-performance Computer Platforms and Some Applications

NASA Astrophysics Data System (ADS)

Georgiev, K.; Zlatev, Z.

2010-11-01

The Danish Eulerian Model (DEM) is an Eulerian model for studying the transport of air pollutants on large scale. Originally, the model was developed at the National Environmental Research Institute of Denmark. The model computational domain covers Europe and some neighbour parts belong to the Atlantic Ocean, Asia and Africa. If DEM model is to be applied by using fine grids, then its discretization leads to a huge computational problem. This implies that such a model as DEM must be run only on high-performance computer architectures. The implementation and tuning of such a complex large-scale model on each different computer is a non-trivial task. Here, some comparison results of running of this model on different kind of vector (CRAY C92A, Fujitsu, etc.), parallel computers with distributed memory (IBM SP, CRAY T3E, Beowulf clusters, Macintosh G4 clusters, etc.), parallel computers with shared memory (SGI Origin, SUN, etc.) and parallel computers with two levels of parallelism (IBM SMP, IBM BlueGene/P, clusters of multiprocessor nodes, etc.) will be presented. The main idea in the parallel version of DEM is domain partitioning approach. Discussions according to the effective use of the cache and hierarchical memories of the modern computers as well as the performance, speed-ups and efficiency achieved will be done. The parallel code of DEM, created by using MPI standard library, appears to be highly portable and shows good efficiency and scalability on different kind of vector and parallel computers. Some important applications of the computer model output are presented in short.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carothers, Christopher D.; Meredith, Jeremy S.; Blanco, Marc

Performance modeling of extreme-scale applications on accurate representations of potential architectures is critical for designing next generation supercomputing systems because it is impractical to construct prototype systems at scale with new network hardware in order to explore designs and policies. However, these simulations often rely on static application traces that can be difficult to work with because of their size and lack of flexibility to extend or scale up without rerunning the original application. To address this problem, we have created a new technique for generating scalable, flexible workloads from real applications, we have implemented a prototype, called Durango, thatmore » combines a proven analytical performance modeling language, Aspen, with the massively parallel HPC network modeling capabilities of the CODES framework.Our models are compact, parameterized and representative of real applications with computation events. They are not resource intensive to create and are portable across simulator environments. We demonstrate the utility of Durango by simulating the LULESH application in the CODES simulation environment on several topologies and show that Durango is practical to use for simulation without loss of fidelity, as quantified by simulation metrics. During our validation of Durango's generated communication model of LULESH, we found that the original LULESH miniapp code had a latent bug where the MPI_Waitall operation was used incorrectly. This finding underscores the potential need for a tool such as Durango, beyond its benefits for flexible workload generation and modeling.Additionally, we demonstrate the efficacy of Durango's direct integration approach, which links Aspen into CODES as part of the running network simulation model. Here, Aspen generates the application-level computation timing events, which in turn drive the start of a network communication phase. Results show that Durango's performance scales well when executing both torus and dragonfly network models on up to 4K Blue Gene/Q nodes using 32K MPI ranks, Durango also avoids the overheads and complexities associated with extreme-scale trace files.« less

Conversion and comparison of the mathematical, three-dimensional, finite-difference, ground-water flow model to the modular, three-dimensional, finite-difference, ground-water flow model for the Tesuque aquifer system in northern New Mexico

USGS Publications Warehouse

Umari, A.M.; Szeliga, T.L.

1989-01-01

The three-dimensional finite-difference groundwater model (using a mathematical groundwater flow code) of the Tesuque aquifer system in northern New Mexico was converted to run using the U.S. Geological Survey 's modular groundwater flow code. Results from the final versions of the predevelopment and 1947 to 2080 transient simulations of the two models are compared. A correlation coefficient of 0.9905 was obtained for the match in block-by-block head-dependent fluxes for predevelopment conditions. There are, however, significant differences in at least two specific cases. In the first case, a difference is associated with the net loss from the Pojoaque River and its tributaries to the aquifer. The net loss by the river is given as 1.134 cu ft/sec using the original groundwater model, which is 38.1% less than the net loss by the river of 1.8319 cu ft/sec computed in this study. In the second case, the large difference is computed for the transient decline in the hydraulic head of a model block near Tesuque Pueblo. The hydraulic-head decline by 2080 is, using the original model, 249 ft, which is 14.7% less than the hydraulic head of 292 ft computed by this study. In general, the differences between the two sets of results are not large enough to lead to different conclusions regarding the behavior of the system at steady state or when pumped. (USGS)

Flexible Inhibitor Fluid-Structure Interaction Simulation in RSRM.

NASA Astrophysics Data System (ADS)

Wasistho, Bono

2005-11-01

We employ our tightly coupled fluid/structure/combustion simulation code 'Rocstar-3' for solid propellant rocket motors to study 3D flows past rigid and flexible inhibitors in the Reusable Solid Rocket Motor (RSRM). We perform high resolution simulations of a section of the rocket near the center joint slot at 100 seconds after ignition, using inflow conditions based on less detailed 3D simulations of the full RSRM. Our simulations include both inviscid and turbulent flows (using LES dynamic subgrid-scale model), and explore the interaction between the inhibitor and the resulting fluid flow. The response of the solid components is computed by an implicit finite element solver. The internal mesh motion scheme in our block-structured fluid solver enables our code to handle significant changes in geometry. We compute turbulent statistics and determine the compound instabilities originated from the natural hydrodynamic instabilities and the inhibitor motion. The ultimate goal is to studdy the effect of inhibitor flexing on the turbulent field.

Multidimensional Modeling of Atmospheric Effects and Surface Heterogeneities on Remote Sensing

NASA Technical Reports Server (NTRS)

Gerstl, S. A. W.; Simmer, C.; Zardecki, A. (Principal Investigator)

1985-01-01

The overall goal of this project is to establish a modeling capability that allows a quantitative determination of atmospheric effects on remote sensing including the effects of surface heterogeneities. This includes an improved understanding of aerosol and haze effects in connection with structural, angular, and spatial surface heterogeneities. One important objective of the research is the possible identification of intrinsic surface or canopy characteristics that might be invariant to atmospheric perturbations so that they could be used for scene identification. Conversely, an equally important objective is to find a correction algorithm for atmospheric effects in satellite-sensed surface reflectances. The technical approach is centered around a systematic model and code development effort based on existing, highly advanced computer codes that were originally developed for nuclear radiation shielding applications. Computational techniques for the numerical solution of the radiative transfer equation are adapted on the basis of the discrete-ordinates finite-element method which proved highly successful for one and two-dimensional radiative transfer problems with fully resolved angular representation of the radiation field.

Improvement of the cruise performances of a wing by means of aerodynamic optimization. Validation with a Far-Field method

NASA Astrophysics Data System (ADS)

Jiménez-Varona, J.; Ponsin Roca, J.

2015-06-01

Under a contract with AIRBUS MILITARY (AI-M), an exercise to analyze the potential of optimization techniques to improve the wing performances at cruise conditions has been carried out by using an in-house design code. The original wing was provided by AI-M and several constraints were posed for the redesign. To maximize the aerodynamic efficiency at cruise, optimizations were performed using the design techniques developed internally at INTA under a research program (Programa de Termofluidodinámica). The code is a gradient-based optimizaa tion code, which uses classical finite differences approach for gradient computations. Several techniques for search direction computation are implemented for unconstrained and constrained problems. Techniques for geometry modifications are based on different approaches which include perturbation functions for the thickness and/or mean line distributions and others by Bézier curves fitting of certain degree. It is very e important to afford a real design which involves several constraints that reduce significantly the feasible design space. And the assessment of the code is needed in order to check the capabilities and the possible drawbacks. Lessons learnt will help in the development of future enhancements. In addition, the validation of the results was done using also the well-known TAU flow solver and a far-field drag method in order to determine accurately the improvement in terms of drag counts.

Logical qubit fusion

NASA Astrophysics Data System (ADS)

Moussa, Jonathan; Ryan-Anderson, Ciaran

The canonical modern plan for universal quantum computation is a Clifford+T gate set implemented in a topological error-correcting code. This plan has the basic disparity that logical Clifford gates are natural for codes in two spatial dimensions while logical T gates are natural in three. Recent progress has reduced this disparity by proposing logical T gates in two dimensions with doubled, stacked, or gauge color codes, but these proposals lack an error threshold. An alternative universal gate set is Clifford+F, where a fusion (F) gate converts two logical qubits into a logical qudit. We show that logical F gates can be constructed by identifying compatible pairs of qubit and qudit codes that stabilize the same logical subspace, much like the original Bravyi-Kitaev construction of magic state distillation. The simplest example of high-distance compatible codes results in a proposal that is very similar to the stacked color code with the key improvement of retaining an error threshold. Sandia National Labs is a multi-program laboratory managed and operated by Sandia Corp, a wholly owned subsidiary of Lockheed Martin Corp, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Adding EUNIS and VAULT rocket data to the VSO with Modern Perl frameworks

NASA Astrophysics Data System (ADS)

Mansky, Edmund

2017-08-01

A new Perl code is described, that uses the modern Object-oriented Moose framework, to add EUNIS and VAULT rocket data to the Virtual Solar Observatory website. The code permits the easy fixing of FITS header fields in the case where some FITS fields that are required are missing from the original data files. The code makes novel use of the Moose extensions “before” and “after” to build in dependencies so that database creation of tables occurs before the loading of data, and that the validation of file-dependent tables occurs after the loading is completed. Also described is the computation and loading of the deferred FITS field CHECKSUM into the database following the loading and validation of the file-dependent tables. The loading of the EUNIS 2006 and 2007 flight data, and the VAULT 2.0 flight data is described in detail as illustrative examples.

FPGA acceleration of rigid-molecule docking codes

PubMed Central

Sukhwani, B.; Herbordt, M.C.

2011-01-01

Modelling the interactions of biological molecules, or docking, is critical both to understanding basic life processes and to designing new drugs. The field programmable gate array (FPGA) based acceleration of a recently developed, complex, production docking code is described. The authors found that it is necessary to extend their previous three-dimensional (3D) correlation structure in several ways, most significantly to support simultaneous computation of several correlation functions. The result for small-molecule docking is a 100-fold speed-up of a section of the code that represents over 95% of the original run-time. An additional 2% is accelerated through a previously described method, yielding a total acceleration of 36× over a single core and 10× over a quad-core. This approach is found to be an ideal complement to graphics processing unit (GPU) based docking, which excels in the protein–protein domain. PMID:21857870

A new communications technique for the nonvocal person, using the Apple II Computer.

PubMed

Seamone, W

1982-01-01

The purpose of this paper is to describe a technique for nonvocal personal communication for the severely handicapped person, using the Apple II computer system and standard commercially available software diskettes (Visi-Calc). The user's input in a pseudo-Morse code is generated via minute chin motions or limited finger motions applied to a suitable configured two-switch device, and input via the JHU/APL Morse code interface card. The commands and features of the program's row-column matrix, originally intended and widely used for financial management, are used here to call up and modify a large array of stored sentences which can be useful in personal communication. It is not known at this time if the system is in fact cost-effective for the sole purpose of nonvocal communication, since system tradeoff studies have not been made relative to other techniques. However, in some instances an Apple computer may be already available for other purposes at the institution or in the home, and the system described could simply be another utilization of that personal computer. In any case, the system clearly does not meet the requirement of portability. No special components (except for the JHU/APL Morse interface card) and no special programming experience are required to duplicate the communications technique described.

Modeling of light scattering by icy bodies

NASA Astrophysics Data System (ADS)

Kolokolova, L.; Mackowski, D.; Pitman, K.; Verbiscer, A.; Buratti, B.; Momary, T.

2014-07-01

As a result of ground-based, space-based, and in-situ spacecraft mission observations, a great amount of photometric, polarimetric, and spectroscopic data of icy bodies (satellites of giant planets, Kuiper Belt objects, comet nuclei, and icy particles in cometary comae and rings) has been accumulated. These data have revealed fascinating light-scattering phenomena, such as the opposition surge resulting from coherent backscattering and shadow hiding and the negative polarization associated with them. Near-infrared (NIR) spectra of these bodies are especially informative as the depth, width, and shape of the absorption bands of ice are sensitive not only to the ice abundance but also to the size of icy grains. Numerous NIR spectra obtained by Cassini's Visual and Infrared Mapping Spectrometer (VIMS) have been used to map the microcharacteristics of the icy satellites [1] and rings of Saturn [2]. VIMS data have also permitted a study of the opposition surge for icy satellites of Saturn [3], showing that coherent backscattering affects not only brightness and polarization of icy bodies but also their spectra [4]. To study all of the light-scattering phenomena that affect the photopolarimetric and spectroscopic characteristics of icy bodies, including coherent backscattering, requires computer modeling that rigorously considers light scattering by a large number of densely packed small particles that form either layers (in the case of regolith) or big clusters (ring and comet particles) . Such opportunity has appeared recently with a development of a new version MSTM4 of the Multi-Sphere T-Matrix code [5]. Simulations of reflectance and absorbance spectra of a ''target'' (particle layer or cluster) require that the dimensions of the target be significantly larger than the wavelength, sphere radius, and layer thickness. For wavelength-sized spheres and packing fractions typical of regolith, targets can contain dozens of thousands of spheres that, with the original MSTM code, would require enormous computer RAM and CPU. MSTM4 adopts a discrete Fourier convolution (DFC), implemented using a fast Fourier transform (FFT), for the evaluation of the exciting field. This approach is very similar to that used in the discrete-dipole approximation (DDA) codes, with the difference that it considers multipole nature of the translation operators, and does not require that the sphere origins be located on a regular lattice. The MSTM4 code not only allows us to consider a larger number of constituent particles but also is about 100 times faster in wall-clock time than the original version of the MSTM code. Example of MSTM4 modeling is shown in the Figure.

Methodology for sensitivity analysis, approximate analysis, and design optimization in CFD for multidisciplinary applications

NASA Technical Reports Server (NTRS)

Taylor, Arthur C., III; Hou, Gene W.

1994-01-01

The straightforward automatic-differentiation and the hand-differentiated incremental iterative methods are interwoven to produce a hybrid scheme that captures some of the strengths of each strategy. With this compromise, discrete aerodynamic sensitivity derivatives are calculated with the efficient incremental iterative solution algorithm of the original flow code. Moreover, the principal advantage of automatic differentiation is retained (i.e., all complicated source code for the derivative calculations is constructed quickly with accuracy). The basic equations for second-order sensitivity derivatives are presented; four methods are compared. Each scheme requires that large systems are solved first for the first-order derivatives and, in all but one method, for the first-order adjoint variables. Of these latter three schemes, two require no solutions of large systems thereafter. For the other two for which additional systems are solved, the equations and solution procedures are analogous to those for the first order derivatives. From a practical viewpoint, implementation of the second-order methods is feasible only with software tools such as automatic differentiation, because of the extreme complexity and large number of terms. First- and second-order sensitivities are calculated accurately for two airfoil problems, including a turbulent flow example; both geometric-shape and flow-condition design variables are considered. Several methods are tested; results are compared on the basis of accuracy, computational time, and computer memory. For first-order derivatives, the hybrid incremental iterative scheme obtained with automatic differentiation is competitive with the best hand-differentiated method; for six independent variables, it is at least two to four times faster than central finite differences and requires only 60 percent more memory than the original code; the performance is expected to improve further in the future.

DEC/SOL: solution of dense systems of linear algebraic equations. [In Fortran IV and compass for CDC 7600; DECST and SOLST for CDC STAR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hindmarsh, A.C.; Sloan, L.J.; Dubois, P.F.

1978-12-01

This report supersedes the original version, dated June 1976. It describes four versions of a pair of subroutines for solving N x N systems of linear algebraic equations. In each case, the first routine, DEC, performs an LU decomposition of the matrix with partial pivoting, and the second, SOL, computes the solution vector by back-substitution. The first version is in Fortran IV, and is derived from routines DECOMP and SOLVE written by C.B. Moler. The second is a version for the CDC 7600 computer using STACKLIB. The third is a hand-coded (Compass) version for the 7600. The fourth is amore » vectorized version for the CDC STAR, renamed DECST and SOLST. Comparative tests on these routines are also described. The Compass version is faster than the others on the 7600 by factors of up to 5. The major revisions to the original report, and to the subroutines described, are an updated description of the availability of each version of DEC/SOL; correction of some errors in the Compass version, as altered so as to be compatible with FTN; and a new STAR version, which runs much faster than the earlier one. The standard Fortran version, the Fortran/STACKLIB version, and the object code generated from the Compass version and available in STACKLIB have not been changed.« less

Uniform rovibrational collisional N2 bin model for DSMC, with application to atmospheric entry flows

NASA Astrophysics Data System (ADS)

Torres, E.; Bondar, Ye. A.; Magin, T. E.

2016-11-01

A state-to-state model for internal energy exchange and molecular dissociation allows for high-fidelity DSMC simulations. Elementary reaction cross sections for the N2 (v, J)+ N system were previously extracted from a quantum-chemical database, originally compiled at NASA Ames Research Center. Due to the high computational cost of simulating the full range of inelastic collision processes (approx. 23 million reactions), a coarse-grain model, called the Uniform RoVibrational Collisional (URVC) bin model can be used instead. This allows to reduce the original 9390 rovibrational levels of N2 to 10 energy bins. In the present work, this reduced model is used to simulate a 2D flow configuration, which more closely reproduces the conditions of high-speed entry into Earth's atmosphere. For this purpose, the URVC bin model had to be adapted for integration into the "Rarefied Gas Dynamics Analysis System" (RGDAS), a separate high-performance DSMC code capable of handling complex geometries and parallel computations. RGDAS was developed at the Institute of Theoretical and Applied Mechanics in Novosibirsk, Russia for use by the European Space Agency (ESA) and shares many features with the well-known SMILE code developed by the same group. We show that the reduced mechanism developed previously can be implemented in RGDAS, and the results exhibit nonequilibrium effects consistent with those observed in previous 1D-simulations.

Simulation of the energy spectra of original versus recombined H{sub 2}{sup +} molecular ions transmitted through thin foils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

2004-09-01

This work presents the results of computer simulations for the energy spectra of original versus recombined H{sub 2}{sup +} molecular ions transmitted through thin amorphous carbon foils, for a broad range of incident energies. A detailed description of the projectile motion through the target has been done, including nuclear scattering and Coulomb repulsion as well as electronic self-retarding and wake forces; the two latter are calculated in the dielectric formalism framework. Differences in the energy spectra of recombined and original transmitted H{sub 2}{sup +} molecular ions clearly appear in the simulations, in agreement with the available experimental data. Our simulationmore » code also differentiates the contributions due to original and to recombined H{sub 2}{sup +} molecular ions when the energy spectra contain both contributions, a feature that could be used for experimental purposes in estimating the ratio between the number of original and recombined H{sub 2}{sup +} molecular ions transmitted through thin foils.« less

Mal-Xtract: Hidden Code Extraction using Memory Analysis

NASA Astrophysics Data System (ADS)

Lim, Charles; Syailendra Kotualubun, Yohanes; Suryadi; Ramli, Kalamullah

2017-01-01

Software packer has been used effectively to hide the original code inside a binary executable, making it more difficult for existing signature based anti malware software to detect malicious code inside the executable. A new method of written and rewritten memory section is introduced to to detect the exact end time of unpacking routine and extract original code from packed binary executable using Memory Analysis running in an software emulated environment. Our experiment results show that at least 97% of the original code from the various binary executable packed with different software packers could be extracted. The proposed method has also been successfully extracted hidden code from recent malware family samples.

Mobile code security

NASA Astrophysics Data System (ADS)

Ramalingam, Srikumar

2001-11-01

A highly secure mobile agent system is very important for a mobile computing environment. The security issues in mobile agent system comprise protecting mobile hosts from malicious agents, protecting agents from other malicious agents, protecting hosts from other malicious hosts and protecting agents from malicious hosts. Using traditional security mechanisms the first three security problems can be solved. Apart from using trusted hardware, very few approaches exist to protect mobile code from malicious hosts. Some of the approaches to solve this problem are the use of trusted computing, computing with encrypted function, steganography, cryptographic traces, Seal Calculas, etc. This paper focuses on the simulation of some of these existing techniques in the designed mobile language. Some new approaches to solve malicious network problem and agent tampering problem are developed using public key encryption system and steganographic concepts. The approaches are based on encrypting and hiding the partial solutions of the mobile agents. The partial results are stored and the address of the storage is destroyed as the agent moves from one host to another host. This allows only the originator to make use of the partial results. Through these approaches some of the existing problems are solved.

Implementation of a 3D mixing layer code on parallel computers

NASA Technical Reports Server (NTRS)

Roe, K.; Thakur, R.; Dang, T.; Bogucz, E.

1995-01-01

This paper summarizes our progress and experience in the development of a Computational-Fluid-Dynamics code on parallel computers to simulate three-dimensional spatially-developing mixing layers. In this initial study, the three-dimensional time-dependent Euler equations are solved using a finite-volume explicit time-marching algorithm. The code was first programmed in Fortran 77 for sequential computers. The code was then converted for use on parallel computers using the conventional message-passing technique, while we have not been able to compile the code with the present version of HPF compilers.

Automatic detection of white-light flare kernels in SDO/HMI intensitygrams

NASA Astrophysics Data System (ADS)

Mravcová, Lucia; Švanda, Michal

2017-11-01

Solar flares with a broadband emission in the white-light range of the electromagnetic spectrum belong to most enigmatic phenomena on the Sun. The origin of the white-light emission is not entirely understood. We aim to systematically study the visible-light emission connected to solar flares in SDO/HMI observations. We developed a code for automatic detection of kernels of flares with HMI intensity brightenings and study properties of detected candidates. The code was tuned and tested and with a little effort, it could be applied to any suitable data set. By studying a few flare examples, we found indication that HMI intensity brightening might be an artefact of the simplified procedure used to compute HMI observables.

Automatic Between-Pulse Analysis of DIII-D Experimental Data Performed Remotely on a Supercomputer at Argonne Leadership Computing Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostuk, M.; Uram, T. D.; Evans, T.

For the first time, an automatically triggered, between-pulse fusion science analysis code was run on-demand at a remotely located supercomputer at Argonne Leadership Computing Facility (ALCF, Lemont, IL) in support of in-process experiments being performed at DIII-D (San Diego, CA). This represents a new paradigm for combining geographically distant experimental and high performance computing (HPC) facilities to provide enhanced data analysis that is quickly available to researchers. Enhanced analysis improves the understanding of the current pulse, translating into a more efficient use of experimental resources, and to the quality of the resultant science. The analysis code used here, called SURFMN,more » calculates the magnetic structure of the plasma using Fourier transform. Increasing the number of Fourier components provides a more accurate determination of the stochastic boundary layer near the plasma edge by better resolving magnetic islands, but requires 26 minutes to complete using local DIII-D resources, putting it well outside the useful time range for between pulse analysis. These islands relate to confinement and edge localized mode (ELM) suppression, and may be controlled by adjusting coil currents for the next pulse. Argonne has ensured on-demand execution of SURFMN by providing a reserved queue, a specialized service that launches the code after receiving an automatic trigger, and with network access from the worker nodes for data transfer. Runs are executed on 252 cores of ALCF’s Cooley cluster and the data is available locally at DIII-D within three minutes of triggering. The original SURFMN design limits additional improvements with more cores, however our work shows a path forward where codes that benefit from thousands of processors can run between pulses.« less

Automatic Between-Pulse Analysis of DIII-D Experimental Data Performed Remotely on a Supercomputer at Argonne Leadership Computing Facility

DOE PAGES

Kostuk, M.; Uram, T. D.; Evans, T.; ...

2018-02-01

For the first time, an automatically triggered, between-pulse fusion science analysis code was run on-demand at a remotely located supercomputer at Argonne Leadership Computing Facility (ALCF, Lemont, IL) in support of in-process experiments being performed at DIII-D (San Diego, CA). This represents a new paradigm for combining geographically distant experimental and high performance computing (HPC) facilities to provide enhanced data analysis that is quickly available to researchers. Enhanced analysis improves the understanding of the current pulse, translating into a more efficient use of experimental resources, and to the quality of the resultant science. The analysis code used here, called SURFMN,more » calculates the magnetic structure of the plasma using Fourier transform. Increasing the number of Fourier components provides a more accurate determination of the stochastic boundary layer near the plasma edge by better resolving magnetic islands, but requires 26 minutes to complete using local DIII-D resources, putting it well outside the useful time range for between pulse analysis. These islands relate to confinement and edge localized mode (ELM) suppression, and may be controlled by adjusting coil currents for the next pulse. Argonne has ensured on-demand execution of SURFMN by providing a reserved queue, a specialized service that launches the code after receiving an automatic trigger, and with network access from the worker nodes for data transfer. Runs are executed on 252 cores of ALCF’s Cooley cluster and the data is available locally at DIII-D within three minutes of triggering. The original SURFMN design limits additional improvements with more cores, however our work shows a path forward where codes that benefit from thousands of processors can run between pulses.« less

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.

PubMed

Pang, Chao; Sollie, Annet; Sijtsma, Anna; Hendriksen, Dennis; Charbon, Bart; de Haan, Mark; de Boer, Tommy; Kelpin, Fleur; Jetten, Jonathan; van der Velde, Joeri K; Smidt, Nynke; Sijmons, Rolf; Hillege, Hans; Swertz, Morris A

2015-01-01

There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA's applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90 000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from http://www.molgenis.org/wiki/SORTA. © The Author(s) 2015. Published by Oxford University Press.

SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data

PubMed Central

Pang, Chao; Sollie, Annet; Sijtsma, Anna; Hendriksen, Dennis; Charbon, Bart; de Haan, Mark; de Boer, Tommy; Kelpin, Fleur; Jetten, Jonathan; van der Velde, Joeri K.; Smidt, Nynke; Sijmons, Rolf; Hillege, Hans; Swertz, Morris A.

2015-01-01

There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA’s applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90 000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from http://www.molgenis.org/wiki/SORTA PMID:26385205

Optimization of Car Body under Constraints of Noise, Vibration, and Harshness (NVH), and Crash

NASA Technical Reports Server (NTRS)

Kodiyalam, Srinivas; Yang, Ren-Jye; Sobieszczanski-Sobieski, Jaroslaw (Editor)

2000-01-01

To be competitive on the today's market, cars have to be as light as possible while meeting the Noise, Vibration, and Harshness (NVH) requirements and conforming to Government-man dated crash survival regulations. The latter are difficult to meet because they involve very compute-intensive, nonlinear analysis, e.g., the code RADIOSS capable of simulation of the dynamics, and the geometrical and material nonlinearities of a thin-walled car structure in crash, would require over 12 days of elapsed time for a single design of a 390K elastic degrees of freedom model, if executed on a single processor of the state-of-the-art SGI Origin2000 computer. Of course, in optimization that crash analysis would have to be invoked many times. Needless to say, that has rendered such optimization intractable until now. The car finite element model is shown. The advent of computers that comprise large numbers of concurrently operating processors has created a new environment wherein the above optimization, and other engineering problems heretofore regarded as intractable may be solved. The procedure, shown, is a piecewise approximation based method and involves using a sensitivity based Taylor series approximation model for NVH and a polynomial response surface model for Crash. In that method the NVH constraints are evaluated using a finite element code (MSC/NASTRAN) that yields the constraint values and their derivatives with respect to design variables. The crash constraints are evaluated using the explicit code RADIOSS on the Origin 2000 operating on 256 processors simultaneously to generate data for a polynomial response surface in the design variable domain. The NVH constraints and their derivatives combined with the response surface for the crash constraints form an approximation to the system analysis (surrogate analysis) that enables a cycle of multidisciplinary optimization within move limits. In the inner loop, the NVH sensitivities are recomputed to update the NVH approximation model while keeping the Crash response surface constant. In every outer loop, the Crash response surface approximation is updated, including a gradual increase in the order of the response surface and the response surface extension in the direction of the search. In this optimization task, the NVH discipline has 30 design variables while the crash discipline has 20 design variables. A subset of these design variables (10) are common to both the NVH and crash disciplines. In order to construct a linear response surface for the Crash discipline constraints, a minimum of 21 design points would have to be analyzed using the RADIOSS code. On a single processor in Origin 2000 that amount of computing would require over 9 months! In this work, these runs were carried out concurrently on the Origin 2000 using multiple processors, ranging from 8 to 16, for each crash (RADIOSS) analysis. Another figure shows the wall time required for a single RADIOSS analysis using varying number of processors, as well as provides a comparison of 2 different common data placement procedures within the allotted memories for each analysis. The initial design is an infeasible design with NVH discipline Static Torsion constraint violations of over 10%. The final optimized design is a feasible design with a weight reduction of 15 kg compared to the initial design. This work demonstrates how advanced methodology for optimization combined with the technology of concurrent processing enables applications that until now were out of reach because of very long time-to-solution.

LTSS compendium: an introduction to the CDC 7600 and the Livermore Timesharing System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fong, K. W.

1977-08-15

This report is an introduction to the CDC 7600 computer and to the Livermore Timesharing System (LTSS) used by the National Magnetic Fusion Energy Computer Center (NMFECC) and the Lawrence Livermore Laboratory Computer Center (LLLCC or Octopus network) on their 7600's. This report is based on a document originally written specifically about the system as it is implemented at NMFECC but has been broadened to point out differences in implementation at LLLCC. It also contains information about LLLCC not relevant to NMFECC. This report is written for computational physicists who want to prepare large production codes to run under LTSSmore » on the 7600's. The generalized discussion of the operating system focuses on creating and executing controllees. This document and its companion, UCID-17557, CDC 7600 LTSS Programming Stratagems, provide a basis for understanding more specialized documents about individual parts of the system.« less

A distributed version of the NASA Engine Performance Program

NASA Technical Reports Server (NTRS)

Cours, Jeffrey T.; Curlett, Brian P.

1993-01-01

Distributed NEPP, a version of the NASA Engine Performance Program, uses the original NEPP code but executes it in a distributed computer environment. Multiple workstations connected by a network increase the program's speed and, more importantly, the complexity of the cases it can handle in a reasonable time. Distributed NEPP uses the public domain software package, called Parallel Virtual Machine, allowing it to execute on clusters of machines containing many different architectures. It includes the capability to link with other computers, allowing them to process NEPP jobs in parallel. This paper discusses the design issues and granularity considerations that entered into programming Distributed NEPP and presents the results of timing runs.

Computer Description of Black Hawk Helicopter

DTIC Science & Technology

1979-06-01

Model Combinatorial Geometry Models Black Hawk Helicopter Helicopter GIFT Computer Code Geometric Description of Targets 20. ABSTRACT...description was made using the technique of combinatorial geometry (COM-GEOM) and will be used as input to the GIFT computer code which generates Tliic...rnHp The data used bv the COVART comtmter code was eenerated bv the Geometric Information for Targets ( GIFT )Z computer code. This report documents

csa2sac—A program for computing discharge from continuous slope-area stage data

USGS Publications Warehouse

Wiele, Stephen M.

2015-12-17

In addition to csa2sac, the SAC7 program is required. It is the same as the original SAC program, except that it is compiled for 64-bit Windows operating systems and has a slightly different command line input. It is available online (http://water.usgs.gov/software/SAC/) as part of the SACGUI installation program. The program name, “SAC7.exe,” is coded into csa2sac, and must not be changed.

Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment.

PubMed

Meng, Bowen; Pratx, Guillem; Xing, Lei

2011-12-01

Four-dimensional CT (4DCT) and cone beam CT (CBCT) are widely used in radiation therapy for accurate tumor target definition and localization. However, high-resolution and dynamic image reconstruction is computationally demanding because of the large amount of data processed. Efficient use of these imaging techniques in the clinic requires high-performance computing. The purpose of this work is to develop a novel ultrafast, scalable and reliable image reconstruction technique for 4D CBCT∕CT using a parallel computing framework called MapReduce. We show the utility of MapReduce for solving large-scale medical physics problems in a cloud computing environment. In this work, we accelerated the Feldcamp-Davis-Kress (FDK) algorithm by porting it to Hadoop, an open-source MapReduce implementation. Gated phases from a 4DCT scans were reconstructed independently. Following the MapReduce formalism, Map functions were used to filter and backproject subsets of projections, and Reduce function to aggregate those partial backprojection into the whole volume. MapReduce automatically parallelized the reconstruction process on a large cluster of computer nodes. As a validation, reconstruction of a digital phantom and an acquired CatPhan 600 phantom was performed on a commercial cloud computing environment using the proposed 4D CBCT∕CT reconstruction algorithm. Speedup of reconstruction time is found to be roughly linear with the number of nodes employed. For instance, greater than 10 times speedup was achieved using 200 nodes for all cases, compared to the same code executed on a single machine. Without modifying the code, faster reconstruction is readily achievable by allocating more nodes in the cloud computing environment. Root mean square error between the images obtained using MapReduce and a single-threaded reference implementation was on the order of 10(-7). Our study also proved that cloud computing with MapReduce is fault tolerant: the reconstruction completed successfully with identical results even when half of the nodes were manually terminated in the middle of the process. An ultrafast, reliable and scalable 4D CBCT∕CT reconstruction method was developed using the MapReduce framework. Unlike other parallel computing approaches, the parallelization and speedup required little modification of the original reconstruction code. MapReduce provides an efficient and fault tolerant means of solving large-scale computing problems in a cloud computing environment.

Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment

PubMed Central

Meng, Bowen; Pratx, Guillem; Xing, Lei

2011-01-01

Purpose: Four-dimensional CT (4DCT) and cone beam CT (CBCT) are widely used in radiation therapy for accurate tumor target definition and localization. However, high-resolution and dynamic image reconstruction is computationally demanding because of the large amount of data processed. Efficient use of these imaging techniques in the clinic requires high-performance computing. The purpose of this work is to develop a novel ultrafast, scalable and reliable image reconstruction technique for 4D CBCT/CT using a parallel computing framework called MapReduce. We show the utility of MapReduce for solving large-scale medical physics problems in a cloud computing environment. Methods: In this work, we accelerated the Feldcamp–Davis–Kress (FDK) algorithm by porting it to Hadoop, an open-source MapReduce implementation. Gated phases from a 4DCT scans were reconstructed independently. Following the MapReduce formalism, Map functions were used to filter and backproject subsets of projections, and Reduce function to aggregate those partial backprojection into the whole volume. MapReduce automatically parallelized the reconstruction process on a large cluster of computer nodes. As a validation, reconstruction of a digital phantom and an acquired CatPhan 600 phantom was performed on a commercial cloud computing environment using the proposed 4D CBCT/CT reconstruction algorithm. Results: Speedup of reconstruction time is found to be roughly linear with the number of nodes employed. For instance, greater than 10 times speedup was achieved using 200 nodes for all cases, compared to the same code executed on a single machine. Without modifying the code, faster reconstruction is readily achievable by allocating more nodes in the cloud computing environment. Root mean square error between the images obtained using MapReduce and a single-threaded reference implementation was on the order of 10−7. Our study also proved that cloud computing with MapReduce is fault tolerant: the reconstruction completed successfully with identical results even when half of the nodes were manually terminated in the middle of the process. Conclusions: An ultrafast, reliable and scalable 4D CBCT/CT reconstruction method was developed using the MapReduce framework. Unlike other parallel computing approaches, the parallelization and speedup required little modification of the original reconstruction code. MapReduce provides an efficient and fault tolerant means of solving large-scale computing problems in a cloud computing environment. PMID:22149842

SWRT: A package for semi-analytical solutions of surface wave propagation, including mode conversion, across transversely aligned vertical discontinuities

NASA Astrophysics Data System (ADS)

Datta, Arjun

2018-03-01

We present a suite of programs that implement decades-old algorithms for computation of seismic surface wave reflection and transmission coefficients at a welded contact between two laterally homogeneous quarter-spaces. For Love as well as Rayleigh waves, the algorithms are shown to be capable of modelling multiple mode conversions at a lateral discontinuity, which was not shown in the original publications or in the subsequent literature. Only normal incidence at a lateral boundary is considered so there is no Love-Rayleigh coupling, but incidence of any mode and coupling to any (other) mode can be handled. The code is written in Python and makes use of SciPy's Simpson's rule integrator and NumPy's linear algebra solver for its core functionality. Transmission-side results from this code are found to be in good agreement with those from finite-difference simulations. In today's research environment of extensive computing power, the coded algorithms are arguably redundant but SWRT can be used as a valuable testing tool for the ever evolving numerical solvers of seismic wave propagation. SWRT is available via GitHub (https://github.com/arjundatta23/SWRT.git).

Satellite Image Mosaic Engine

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2006-01-01

A computer program automatically builds large, full-resolution mosaics of multispectral images of Earth landmasses from images acquired by Landsat 7, complete with matching of colors and blending between adjacent scenes. While the code has been used extensively for Landsat, it could also be used for other data sources. A single mosaic of as many as 8,000 scenes, represented by more than 5 terabytes of data and the largest set produced in this work, demonstrated what the code could do to provide global coverage. The program first statistically analyzes input images to determine areas of coverage and data-value distributions. It then transforms the input images from their original universal transverse Mercator coordinates to other geographical coordinates, with scaling. It applies a first-order polynomial brightness correction to each band in each scene. It uses a data-mask image for selecting data and blending of input scenes. Under control by a user, the program can be made to operate on small parts of the output image space, with check-point and restart capabilities. The program runs on SGI IRIX computers. It is capable of parallel processing using shared-memory code, large memories, and tens of central processing units. It can retrieve input data and store output data at locations remote from the processors on which it is executed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Xiaoying; Rybarcyk, Larry

HPSim is a GPU-accelerated online multi-particle beam dynamics simulation tool for ion linacs. It was originally developed for use on the Los Alamos 800-MeV proton linac. It is a “z-code” that contains typical linac beam transport elements. The linac RF-gap transformation utilizes transit-time-factors to calculate the beam acceleration therein. The space-charge effects are computed using the 2D SCHEFF (Space CHarge EFFect) algorithm, which calculates the radial and longitudinal space charge forces for cylindrically symmetric beam distributions. Other space- charge routines to be incorporated include the 3D PICNIC and a 3D Poisson solver. HPSim can simulate beam dynamics in drift tubemore » linacs (DTLs) and coupled cavity linacs (CCLs). Elliptical superconducting cavity (SC) structures will also be incorporated into the code. The computational core of the code is written in C++ and accelerated using the NVIDIA CUDA technology. Users access the core code, which is wrapped in Python/C APIs, via Pythons scripts that enable ease-of-use and automation of the simulations. The overall linac description including the EPICS PV machine control parameters is kept in an SQLite database that also contains calibration and conversion factors required to transform the machine set points into model values used in the simulation.« less

Grid2: A Program for Rapid Estimation of the Jovian Radiation Environment

NASA Technical Reports Server (NTRS)

Evans, R. W.; Brinza, D. E.

2014-01-01

Grid2 is a program that utilizes the Galileo Interim Radiation Electron model 2 (GIRE2) Jovian radiation model to compute fluences and doses for Jupiter missions. (Note: The iterations of these two softwares have been GIRE and GIRE2; likewise Grid and Grid2.) While GIRE2 is an important improvement over the original GIRE radiation model, the GIRE2 model can take as long as a day or more to compute these quantities for a complete mission. Grid2 fits the results of the detailed GIRE2 code with a set of grids in local time and position thereby greatly speeding up the execution of the model-minutes as opposed to days. The Grid2 model covers the time period from 1971 to 2050 and distances of 1.03 to 30 Jovian diameters (Rj). It is available as a direct-access database through a FORTRAN interface program. The new database is only slightly larger than the original grid version: 1.5 gigabytes (GB) versus 1.2 GB.

User manual for semi-circular compact range reflector code: Version 2

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1987-01-01

A computer code has been developed at the Ohio State University ElectroScience Laboratory to analyze a semi-circular paraboloidal reflector with or without a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the reflector or its individual components at a given distance from the center of the paraboloid. The code computes the fields along a radial, horizontal, vertical or axial cut at that distance. Thus, it is very effective in computing the size of the sweet spot for a semi-circular compact range reflector. This report describes the operation of the code. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

On the Origin of Protein Superfamilies and Superfolds

NASA Astrophysics Data System (ADS)

Magner, Abram; Szpankowski, Wojciech; Kihara, Daisuke

2015-02-01

Distributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to the skewed distributions. We consider that protein sequences and folds constitute an information theoretic channel and computed the most efficient distribution of sequences that code all protein folds. The identified distributions of sequences and folds are found to follow a power law, consistent with those observed for proteins in nature. Importantly, the skewed distributions of sequences and folds are suggested to have different origins: the skewed distribution of sequences is due to evolutionary pressure to achieve efficient coding of necessary folds, whereas that of folds is based on the thermodynamic stability of folds. The current study provides a new information theoretic framework for proteins that could be widely applied for understanding protein sequences, structures, functions, and interactions.

High-Performance Java Codes for Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

Hanford meteorological station computer codes: Volume 9, The quality assurance computer codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burk, K.W.; Andrews, G.L.

1989-02-01

The Hanford Meteorological Station (HMS) was established in 1944 on the Hanford Site to collect and archive meteorological data and provide weather forecasts and related services for Hanford Site approximately 1/2 mile east of the 200 West Area and is operated by PNL for the US Department of Energy. Meteorological data are collected from various sensors and equipment located on and off the Hanford Site. These data are stored in data bases on the Digital Equipment Corporation (DEC) VAX 11/750 at the HMS (hereafter referred to as the HMS computer). Files from those data bases are routinely transferred to themore » Emergency Management System (EMS) computer at the Unified Dose Assessment Center (UDAC). To ensure the quality and integrity of the HMS data, a set of Quality Assurance (QA) computer codes has been written. The codes will be routinely used by the HMS system manager or the data base custodian. The QA codes provide detailed output files that will be used in correcting erroneous data. The following sections in this volume describe the implementation and operation of QA computer codes. The appendices contain detailed descriptions, flow charts, and source code listings of each computer code. 2 refs.« less

Overcoming Challenges in Kinetic Modeling of Magnetized Plasmas and Vacuum Electronic Devices

NASA Astrophysics Data System (ADS)

Omelchenko, Yuri; Na, Dong-Yeop; Teixeira, Fernando

2017-10-01

We transform the state-of-the art of plasma modeling by taking advantage of novel computational techniques for fast and robust integration of multiscale hybrid (full particle ions, fluid electrons, no displacement current) and full-PIC models. These models are implemented in 3D HYPERS and axisymmetric full-PIC CONPIC codes. HYPERS is a massively parallel, asynchronous code. The HYPERS solver does not step fields and particles synchronously in time but instead executes local variable updates (events) at their self-adaptive rates while preserving fundamental conservation laws. The charge-conserving CONPIC code has a matrix-free explicit finite-element (FE) solver based on a sparse-approximate inverse (SPAI) algorithm. This explicit solver approximates the inverse FE system matrix (``mass'' matrix) using successive sparsity pattern orders of the original matrix. It does not reduce the set of Maxwell's equations to a vector-wave (curl-curl) equation of second order but instead utilizes the standard coupled first-order Maxwell's system. We discuss the ability of our codes to accurately and efficiently account for multiscale physical phenomena in 3D magnetized space and laboratory plasmas and axisymmetric vacuum electronic devices.

User's Guide for MSAP2D: A Program for Unsteady Aerodynamic and Aeroelastic (Flutter and Forced Response) Analysis of Multistage Compressors and Turbines. 1.0

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Srivastava, R.

1996-01-01

This guide describes the input data required for using MSAP2D (Multi Stage Aeroelastic analysis Program - Two Dimensional) computer code. MSAP2D can be used for steady, unsteady aerodynamic, and aeroelastic (flutter and forced response) analysis of bladed disks arranged in multiple blade rows such as those found in compressors, turbines, counter rotating propellers or propfans. The code can also be run for single blade row. MSAP2D code is an extension of the original NPHASE code for multiblade row aerodynamic and aeroelastic analysis. Euler equations are used to obtain aerodynamic forces. The structural dynamic equations are written for a rigid typical section undergoing pitching (torsion) and plunging (bending) motion. The aeroelastic equations are solved in time domain. For single blade row analysis, frequency domain analysis is also provided to obtain unsteady aerodynamic coefficients required in an eigen analysis for flutter. In this manual, sample input and output are provided for a single blade row example, two blade row example with equal and unequal number of blades in the blade rows.

Transonic Navier-Stokes wing solution using a zonal approach. Part 1: Solution methodology and code validation

NASA Technical Reports Server (NTRS)

Flores, J.; Gundy, K.; Gundy, K.; Gundy, K.; Gundy, K.; Gundy, K.

1986-01-01

A fast diagonalized Beam-Warming algorithm is coupled with a zonal approach to solve the three-dimensional Euler/Navier-Stokes equations. The computer code, called Transonic Navier-Stokes (TNS), uses a total of four zones for wing configurations (or can be extended to complete aircraft configurations by adding zones). In the inner blocks near the wing surface, the thin-layer Navier-Stokes equations are solved, while in the outer two blocks the Euler equations are solved. The diagonal algorithm yields a speedup of as much as a factor of 40 over the original algorithm/zonal method code. The TNS code, in addition, has the capability to model wind tunnel walls. Transonic viscous solutions are obtained on a 150,000-point mesh for a NACA 0012 wing. A three-order-of-magnitude drop in the L2-norm of the residual requires approximately 500 iterations, which takes about 45 min of CPU time on a Cray-XMP processor. Simulations are also conducted for a different geometrical wing called WING C. All cases show good agreement with experimental data.

De Novo Origin of Human Protein-Coding Genes

PubMed Central

Wu, Dong-Dong; Irwin, David M.; Zhang, Ya-Ping

2011-01-01

The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA–seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes. PMID:22102831

PARMELA_B: a new version of PARMELA with coherent synchrotron radiation effects and a finite difference space charge routine

NASA Astrophysics Data System (ADS)

Koltenbah, Benjamin E. C.; Parazzoli, Claudio G.; Greegor, Robert B.; Dowell, David H.

2002-07-01

Recent interest in advanced laser light sources has stimulated development of accelerator systems of intermediate beam energy, 100-200 MeV, and high charge, 1-10 nC, for high power FEL applications and high energy, 1-2 GeV, high charge, SASE-FEL applications. The current generation of beam transport codes which were developed for high-energy, low-charge beams with low self-fields are inadequate to address this energy and charge regime, and better computational tools are required to accurately calculate self-fields. To that end, we have developed a new version of PARMELA, named PARMELA_B and written in Fortran 95, which includes a coherent synchrotron radiation (CSR) routine and an improved, generalized space charge (SC) routine. An electron bunch is simulated by a collection of macro-particles, which traverses a series of beam line elements. At each time step through the calculation, the momentum of each particle is updated due to the presence of external and self-fields. The self-fields are due to CSR and SC. For the CSR calculations, the macro-particles are further combined into macro-particle-bins that follow the central trajectory of the bend. The energy change through the time step is calculated from expressions derived from the Liénard-Wiechart formulae, and from this energy change the particle's momentum is updated. For the SC calculations, we maintain the same rest-frame-electrostatic approach of the original PARMELA; however, we employ a finite difference Poisson equation solver instead of the symmetrical ring algorithm of the original code. In this way, we relax the symmetry assumptions in the original code. This method is based upon standard numerical procedures and conserves momentum to first order. The SC computational grid is adaptive and conforms to the size of the pulse as it evolves through the calculation. We provide descriptions of these two algorithms, validation comparisons with other CSR and SC methods, and a limited comparison with experimental results.

Semantic Interoperability for Computational Mineralogy: Experiences of the eMinerals Consortium

NASA Astrophysics Data System (ADS)

Walker, A. M.; White, T. O.; Dove, M. T.; Bruin, R. P.; Couch, P. A.; Tyer, R. P.

2006-12-01

The use of atomic scale computer simulation of minerals to obtain information for geophysics and environmental science has grown enormously over the past couple of decades. It is now routine to probe mineral behavior in the Earth's deep interior and in the surface environment by borrowing methods and simulation codes from computational chemistry and physics. It is becoming increasingly important to use methods embodied in more than one of these codes to solve any single scientific problem. However, scientific codes are rarely designed for easy interoperability and data exchange; data formats are often code-specific, poorly documented and fragile, liable to frequent change between software versions, and even compiler versions. This means that the scientist's simple desire to use the methodological approaches offered by multiple codes is frustrated, and even the sharing of data between collaborators becomes fraught with difficulties. The eMinerals consortium was formed in the early stages of the UK eScience program with the aim of developing the tools needed to apply atomic scale simulation to environmental problems in a grid-enabled world, and to harness the computational power offered by grid technologies to address some outstanding mineralogical problems. One example of the kind of problem we can tackle is the origin of the compressibility anomaly in silica glass. By passing data directly between simulation and analysis tools we were able to probe this effect in more detail than has previously been possible and have shown how the anomaly is related to the details of the amorphous structure. In order to approach this kind of problem we have constructed a mini-grid, a small scale and extensible combined compute- and data-grid that allows the execution of many calculations in parallel, and the transparent storage of semantically-rich marked-up result data. Importantly, we automatically capture multiple kinds of metadata and key results from each calculation. We believe that the lessons learned and tools developed will be useful in many areas of science beyond the computational mineralogy. Key tools that will be described include: a pure Fortran XML library (FoX) that presents XPath, SAX and DOM interfaces as well as permitting the easy production of valid XML from legacy Fortran programs; a job submission framework that automatically schedules calculations to remote grid resources, handles data staging and metadata capture; and a tool (AgentX) that map concepts from an ontology onto locations in documents of various formats that we use to enable data exchange.

User's manual for semi-circular compact range reflector code

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1986-01-01

A computer code was developed to analyze a semi-circular paraboloidal reflector antenna with a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the antenna or its individual components at a given distance from the center of the paraboloid. Thus, it is very effective in computing the size of the sweet spot for RCS or antenna measurement. The operation of the code is described. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

Highly fault-tolerant parallel computation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spielman, D.A.

We re-introduce the coded model of fault-tolerant computation in which the input and output of a computational device are treated as words in an error-correcting code. A computational device correctly computes a function in the coded model if its input and output, once decoded, are a valid input and output of the function. In the coded model, it is reasonable to hope to simulate all computational devices by devices whose size is greater by a constant factor but which are exponentially reliable even if each of their components can fail with some constant probability. We consider fine-grained parallel computations inmore » which each processor has a constant probability of producing the wrong output at each time step. We show that any parallel computation that runs for time t on w processors can be performed reliably on a faulty machine in the coded model using w log{sup O(l)} w processors and time t log{sup O(l)} w. The failure probability of the computation will be at most t {center_dot} exp(-w{sup 1/4}). The codes used to communicate with our fault-tolerant machines are generalized Reed-Solomon codes and can thus be encoded and decoded in O(n log{sup O(1)} n) sequential time and are independent of the machine they are used to communicate with. We also show how coded computation can be used to self-correct many linear functions in parallel with arbitrarily small overhead.« less

An emulator for minimizing computer resources for finite element analysis

NASA Technical Reports Server (NTRS)

Melosh, R.; Utku, S.; Islam, M.; Salama, M.

1984-01-01

A computer code, SCOPE, has been developed for predicting the computer resources required for a given analysis code, computer hardware, and structural problem. The cost of running the code is a small fraction (about 3 percent) of the cost of performing the actual analysis. However, its accuracy in predicting the CPU and I/O resources depends intrinsically on the accuracy of calibration data that must be developed once for the computer hardware and the finite element analysis code of interest. Testing of the SCOPE code on the AMDAHL 470 V/8 computer and the ELAS finite element analysis program indicated small I/O errors (3.2 percent), larger CPU errors (17.8 percent), and negligible total errors (1.5 percent).

A generalized one-dimensional computer code for turbomachinery cooling passage flow calculations

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Roelke, Richard J.; Meitner, Peter L.

1989-01-01

A generalized one-dimensional computer code for analyzing the flow and heat transfer in the turbomachinery cooling passages was developed. This code is capable of handling rotating cooling passages with turbulators, 180 degree turns, pin fins, finned passages, by-pass flows, tip cap impingement flows, and flow branching. The code is an extension of a one-dimensional code developed by P. Meitner. In the subject code, correlations for both heat transfer coefficient and pressure loss computations were developed to model each of the above mentioned type of coolant passages. The code has the capability of independently computing the friction factor and heat transfer coefficient on each side of a rectangular passage. Either the mass flow at the inlet to the channel or the exit plane pressure can be specified. For a specified inlet total temperature, inlet total pressure, and exit static pressure, the code computers the flow rates through the main branch and the subbranches, flow through tip cap for impingement cooling, in addition to computing the coolant pressure, temperature, and heat transfer coefficient distribution in each coolant flow branch. Predictions from the subject code for both nonrotating and rotating passages agree well with experimental data. The code was used to analyze the cooling passage of a research cooled radial rotor.

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †

PubMed Central

Murdani, Muhammad Harist; Hong, Bonghee

2018-01-01

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes (Ad-Hoc) and neighborhood proximity (Top-K). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space. PMID:29587366

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †.

PubMed

Murdani, Muhammad Harist; Kwon, Joonho; Choi, Yoon-Ho; Hong, Bonghee

2018-03-24

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes ( Ad-Hoc ) and neighborhood proximity ( Top-K ). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space.

CDC 7600 LTSS programming stratagens: preparing your first production code for the Livermore Timesharing System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fong, K. W.

1977-08-15

This report deals with some techniques in applied programming using the Livermore Timesharing System (LTSS) on the CDC 7600 computers at the National Magnetic Fusion Energy Computer Center (NMFECC) and the Lawrence Livermore Laboratory Computer Center (LLLCC or Octopus network). This report is based on a document originally written specifically about the system as it is implemented at NMFECC but has been revised to accommodate differences between LLLCC and NMFECC implementations. Topics include: maintaining programs, debugging, recovering from system crashes, and using the central processing unit, memory, and input/output devices efficiently and economically. Routines that aid in these procedures aremore » mentioned. The companion report, UCID-17556, An LTSS Compendium, discusses the hardware and operating system and should be read before reading this report.« less

AERO2S - SUBSONIC AERODYNAMIC ANALYSIS OF WINGS WITH LEADING- AND TRAILING-EDGE FLAPS IN COMBINATION WITH CANARD OR HORIZONTAL TAIL SURFACES (IBM PC VERSION)

NASA Technical Reports Server (NTRS)

Carlson, H. W.

1994-01-01

This code was developed to aid design engineers in the selection and evaluation of aerodynamically efficient wing-canard and wing-horizontal-tail configurations that may employ simple hinged-flap systems. Rapid estimates of the longitudinal aerodynamic characteristics of conceptual airplane lifting surface arrangements are provided. The method is particularly well suited to configurations which, because of high speed flight requirements, must employ thin wings with highly swept leading edges. The code is applicable to wings with either sharp or rounded leading edges. The code provides theoretical pressure distributions over the wing, the canard or horizontal tail, and the deflected flap surfaces as well as estimates of the wing lift, drag, and pitching moments which account for attainable leading edge thrust and leading edge separation vortex forces. The wing planform information is specified by a series of leading edge and trailing edge breakpoints for a right hand wing panel. Up to 21 pairs of coordinates may be used to describe both the leading edge and the trailing edge. The code has been written to accommodate 2000 right hand panel elements, but can easily be modified to accommodate a larger or smaller number of elements depending on the capacity of the target computer platform. The code provides solutions for wing surfaces composed of all possible combinations of leading edge and trailing edge flap settings provided by the original deflection multipliers and by the flap deflection multipliers. Up to 25 pairs of leading edge and trailing edge flap deflection schedules may thus be treated simultaneously. The code also provides for an improved accounting of hinge-line singularities in determination of wing forces and moments. To determine lifting surface perturbation velocity distributions, the code provides for a maximum of 70 iterations. The program is constructed so that successive runs may be made with a given code entry. To make additional runs, it is necessary only to add an identification record and the namelist data that are to be changed from the previous run. This code was originally developed in 1989 in FORTRAN V on a CDC 6000 computer system, and was later ported to an MS-DOS environment. Both versions are available from COSMIC. There are only a few differences between the PC version (LAR-14458) and CDC version (LAR-14178) of AERO2S distributed by COSMIC. The CDC version has one main source code file while the PC version has two files which are easier to edit and compile on a PC. The PC version does not require a FORTRAN compiler which supports NAMELIST because a special INPUT subroutine has been added. The CDC version includes two MODIFY decks which can be used to improve the code and prevent the possibility of some infrequently occurring errors while PC-version users will have to make these code changes manually. The PC version includes an executable which was generated with the Ryan McFarland/FORTRAN compiler and requires 253K RAM and an 80x87 math co-processor. Using this executable, the sample case requires about four hours to execute on an 8MHz AT-class microcomputer with a co-processor. The source code conforms to the FORTRAN 77 standard except that it uses variables longer than six characters. With two minor modifications, the PC version should be portable to any computer with a FORTRAN compiler and sufficient memory. The CDC version of AERO2S is available in CDC NOS Internal format on a 9-track 1600 BPI magnetic tape. The PC version is available on a set of two 5.25 inch 360K MS-DOS format diskettes. IBM AT is a registered trademark of International Business Machines. MS-DOS is a registered trademark of Microsoft Corporation. CDC is a registered trademark of Control Data Corporation. NOS is a trademark of Control Data Corporation.

AERO2S - SUBSONIC AERODYNAMIC ANALYSIS OF WINGS WITH LEADING- AND TRAILING-EDGE FLAPS IN COMBINATION WITH CANARD OR HORIZONTAL TAIL SURFACES (CDC VERSION)

NASA Technical Reports Server (NTRS)

Darden, C. M.

1994-01-01

This code was developed to aid design engineers in the selection and evaluation of aerodynamically efficient wing-canard and wing-horizontal-tail configurations that may employ simple hinged-flap systems. Rapid estimates of the longitudinal aerodynamic characteristics of conceptual airplane lifting surface arrangements are provided. The method is particularly well suited to configurations which, because of high speed flight requirements, must employ thin wings with highly swept leading edges. The code is applicable to wings with either sharp or rounded leading edges. The code provides theoretical pressure distributions over the wing, the canard or horizontal tail, and the deflected flap surfaces as well as estimates of the wing lift, drag, and pitching moments which account for attainable leading edge thrust and leading edge separation vortex forces. The wing planform information is specified by a series of leading edge and trailing edge breakpoints for a right hand wing panel. Up to 21 pairs of coordinates may be used to describe both the leading edge and the trailing edge. The code has been written to accommodate 2000 right hand panel elements, but can easily be modified to accommodate a larger or smaller number of elements depending on the capacity of the target computer platform. The code provides solutions for wing surfaces composed of all possible combinations of leading edge and trailing edge flap settings provided by the original deflection multipliers and by the flap deflection multipliers. Up to 25 pairs of leading edge and trailing edge flap deflection schedules may thus be treated simultaneously. The code also provides for an improved accounting of hinge-line singularities in determination of wing forces and moments. To determine lifting surface perturbation velocity distributions, the code provides for a maximum of 70 iterations. The program is constructed so that successive runs may be made with a given code entry. To make additional runs, it is necessary only to add an identification record and the namelist data that are to be changed from the previous run. This code was originally developed in 1989 in FORTRAN V on a CDC 6000 computer system, and was later ported to an MS-DOS environment. Both versions are available from COSMIC. There are only a few differences between the PC version (LAR-14458) and CDC version (LAR-14178) of AERO2S distributed by COSMIC. The CDC version has one main source code file while the PC version has two files which are easier to edit and compile on a PC. The PC version does not require a FORTRAN compiler which supports NAMELIST because a special INPUT subroutine has been added. The CDC version includes two MODIFY decks which can be used to improve the code and prevent the possibility of some infrequently occurring errors while PC-version users will have to make these code changes manually. The PC version includes an executable which was generated with the Ryan McFarland/FORTRAN compiler and requires 253K RAM and an 80x87 math co-processor. Using this executable, the sample case requires about four hours to execute on an 8MHz AT-class microcomputer with a co-processor. The source code conforms to the FORTRAN 77 standard except that it uses variables longer than six characters. With two minor modifications, the PC version should be portable to any computer with a FORTRAN compiler and sufficient memory. The CDC version of AERO2S is available in CDC NOS Internal format on a 9-track 1600 BPI magnetic tape. The PC version is available on a set of two 5.25 inch 360K MS-DOS format diskettes. IBM AT is a registered trademark of International Business Machines. MS-DOS is a registered trademark of Microsoft Corporation. CDC is a registered trademark of Control Data Corporation. NOS is a trademark of Control Data Corporation.

The hacker ethic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Granger, S.

The hacker ethic can be a peculiar concept to those unfamiliar with hacking and what really is. In fact, the entire definition of hacking is somewhat obscure. Hacking originated as a challenge between programmers. Programmers at MIT are known for coining the term. Individuals would hack at code meaning that they would work at programming problems until they could maniuplate their computers into doing exactly what they wanted. The MIT hackers began with simple programs and moved on to fidding with UNIX machines, especially those on the Arpanet. Hackers started freely distributing their code to their friends and eventually tomore » their friends across the network. This gave rise to a notion that software should be free. Eventually this was taken to the extreme information and network access should also be free.« less

Multitasking the three-dimensional transport code TORT on CRAY platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azmy, Y.Y.; Barnett, D.A.; Burre, C.A.

1996-04-01

The multitasking options in the three-dimensional neutral particle transport code TORT originally implemented for Cray`s CTSS operating system are revived and extended to run on Cray Y/MP and C90 computers using the UNICOS operating system. These include two coarse-grained domain decompositions; across octants, and across directions within an octant, termed Octant Parallel (OP), and Direction Parallel (DP), respectively. Parallel performance of the DP is significantly enhanced by increasing the task grain size and reducing load imbalance via dynamic scheduling of the discrete angles among the participating tasks. Substantial Wall Clock speedup factors, approaching 4.5 using 8 tasks, have been measuredmore » in a time-sharing environment, and generally depend on the test problem specifications, number of tasks, and machine loading during execution.« less

Comparison of the Computational Efficiency of the Original Versus Reformulated High-Fidelity Generalized Method of Cells

NASA Technical Reports Server (NTRS)

Arnold, Steven M; Bednarcyk, Brett; Aboydi, Jacob

2004-01-01

The High-Fidelity Generalized Method of Cells (HFGMC) micromechanics model has recently been reformulated by Bansal and Pindera (in the context of elastic phases with perfect bonding) to maximize its computational efficiency. This reformulated version of HFGMC has now been extended to include both inelastic phases and imperfect fiber-matrix bonding. The present paper presents an overview of the HFGMC theory in both its original and reformulated forms and a comparison of the results of the two implementations. The objective is to establish the correlation between the two HFGMC formulations and document the improved efficiency offered by the reformulation. The results compare the macro and micro scale predictions of the continuous reinforcement (doubly-periodic) and discontinuous reinforcement (triply-periodic) versions of both formulations into the inelastic regime, and, in the case of the discontinuous reinforcement version, with both perfect and weak interfacial bonding. The results demonstrate that identical predictions are obtained using either the original or reformulated implementations of HFGMC aside from small numerical differences in the inelastic regime due to the different implementation schemes used for the inelastic terms present in the two formulations. Finally, a direct comparison of execution times is presented for the original formulation and reformulation code implementations. It is shown that as the discretization employed in representing the composite repeating unit cell becomes increasingly refined (requiring a larger number of sub-volumes), the reformulated implementation becomes significantly (approximately an order of magnitude at best) more computationally efficient in both the continuous reinforcement (doubly-periodic) and discontinuous reinforcement (triply-periodic) cases.

Volume accumulator design analysis computer codes

NASA Technical Reports Server (NTRS)

Whitaker, W. D.; Shimazaki, T. T.

1973-01-01

The computer codes, VANEP and VANES, were written and used to aid in the design and performance calculation of the volume accumulator units (VAU) for the 5-kwe reactor thermoelectric system. VANEP computes the VAU design which meets the primary coolant loop VAU volume and pressure performance requirements. VANES computes the performance of the VAU design, determined from the VANEP code, at the conditions of the secondary coolant loop. The codes can also compute the performance characteristics of the VAU's under conditions of possible modes of failure which still permit continued system operation.

"Hour of Code": Can It Change Students' Attitudes toward Programming?

ERIC Educational Resources Information Center

Du, Jie; Wimmer, Hayden; Rada, Roy

2016-01-01

The Hour of Code is a one-hour introduction to computer science organized by Code.org, a non-profit dedicated to expanding participation in computer science. This study investigated the impact of the Hour of Code on students' attitudes towards computer programming and their knowledge of programming. A sample of undergraduate students from two…

Talking about Code: Integrating Pedagogical Code Reviews into Early Computing Courses

ERIC Educational Resources Information Center

Hundhausen, Christopher D.; Agrawal, Anukrati; Agarwal, Pawan

2013-01-01

Given the increasing importance of soft skills in the computing profession, there is good reason to provide students withmore opportunities to learn and practice those skills in undergraduate computing courses. Toward that end, we have developed an active learning approach for computing education called the "Pedagogical Code Review"…

Authorship attribution of source code by using back propagation neural network based on particle swarm optimization

PubMed Central

Xu, Guoai; Li, Qi; Guo, Yanhui; Zhang, Miao

2017-01-01

Authorship attribution is to identify the most likely author of a given sample among a set of candidate known authors. It can be not only applied to discover the original author of plain text, such as novels, blogs, emails, posts etc., but also used to identify source code programmers. Authorship attribution of source code is required in diverse applications, ranging from malicious code tracking to solving authorship dispute or software plagiarism detection. This paper aims to propose a new method to identify the programmer of Java source code samples with a higher accuracy. To this end, it first introduces back propagation (BP) neural network based on particle swarm optimization (PSO) into authorship attribution of source code. It begins by computing a set of defined feature metrics, including lexical and layout metrics, structure and syntax metrics, totally 19 dimensions. Then these metrics are input to neural network for supervised learning, the weights of which are output by PSO and BP hybrid algorithm. The effectiveness of the proposed method is evaluated on a collected dataset with 3,022 Java files belong to 40 authors. Experiment results show that the proposed method achieves 91.060% accuracy. And a comparison with previous work on authorship attribution of source code for Java language illustrates that this proposed method outperforms others overall, also with an acceptable overhead. PMID:29095934

NavP: Structured and Multithreaded Distributed Parallel Programming

NASA Technical Reports Server (NTRS)

Pan, Lei

2007-01-01

We present Navigational Programming (NavP) -- a distributed parallel programming methodology based on the principles of migrating computations and multithreading. The four major steps of NavP are: (1) Distribute the data using the data communication pattern in a given algorithm; (2) Insert navigational commands for the computation to migrate and follow large-sized distributed data; (3) Cut the sequential migrating thread and construct a mobile pipeline; and (4) Loop back for refinement. NavP is significantly different from the current prevailing Message Passing (MP) approach. The advantages of NavP include: (1) NavP is structured distributed programming and it does not change the code structure of an original algorithm. This is in sharp contrast to MP as MP implementations in general do not resemble the original sequential code; (2) NavP implementations are always competitive with the best MPI implementations in terms of performance. Approaches such as DSM or HPF have failed to deliver satisfying performance as of today in contrast, even if they are relatively easy to use compared to MP; (3) NavP provides incremental parallelization, which is beyond the reach of MP; and (4) NavP is a unifying approach that allows us to exploit both fine- (multithreading on shared memory) and coarse- (pipelined tasks on distributed memory) grained parallelism. This is in contrast to the currently popular hybrid use of MP+OpenMP, which is known to be complex to use. We present experimental results that demonstrate the effectiveness of NavP.

Efficient Unstructured Grid Adaptation Methods for Sonic Boom Prediction

NASA Technical Reports Server (NTRS)

Campbell, Richard L.; Carter, Melissa B.; Deere, Karen A.; Waithe, Kenrick A.

2008-01-01

This paper examines the use of two grid adaptation methods to improve the accuracy of the near-to-mid field pressure signature prediction of supersonic aircraft computed using the USM3D unstructured grid flow solver. The first method (ADV) is an interactive adaptation process that uses grid movement rather than enrichment to more accurately resolve the expansion and compression waves. The second method (SSGRID) uses an a priori adaptation approach to stretch and shear the original unstructured grid to align the grid with the pressure waves and reduce the cell count required to achieve an accurate signature prediction at a given distance from the vehicle. Both methods initially create negative volume cells that are repaired in a module in the ADV code. While both approaches provide significant improvements in the near field signature (< 3 body lengths) relative to a baseline grid without increasing the number of grid points, only the SSGRID approach allows the details of the signature to be accurately computed at mid-field distances (3-10 body lengths) for direct use with mid-field-to-ground boom propagation codes.

Guidelines for developing vectorizable computer programs

NASA Technical Reports Server (NTRS)

Miner, E. W.

1982-01-01

Some fundamental principles for developing computer programs which are compatible with array-oriented computers are presented. The emphasis is on basic techniques for structuring computer codes which are applicable in FORTRAN and do not require a special programming language or exact a significant penalty on a scalar computer. Researchers who are using numerical techniques to solve problems in engineering can apply these basic principles and thus develop transportable computer programs (in FORTRAN) which contain much vectorizable code. The vector architecture of the ASC is discussed so that the requirements of array processing can be better appreciated. The "vectorization" of a finite-difference viscous shock-layer code is used as an example to illustrate the benefits and some of the difficulties involved. Increases in computing speed with vectorization are illustrated with results from the viscous shock-layer code and from a finite-element shock tube code. The applicability of these principles was substantiated through running programs on other computers with array-associated computing characteristics, such as the Hewlett-Packard (H-P) 1000-F.

Exploration of ICD-9-CM Coding of Chronic Disease within the Elixhauser Comorbidity Measure in Patients with Chronic Heart Failure

PubMed Central

Garvin, Jennifer Hornung; Redd, Andrew; Bolton, Dan; Graham, Pauline; Roche, Dominic; Groeneveld, Peter; Leecaster, Molly; Shen, Shuying; Weiner, Mark G.

2013-01-01

Introduction International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes capture comorbidities that can be used to risk adjust nonrandom patient groups. We explored the accuracy of capturing comorbidities associated with one risk adjustment method, the Elixhauser Comorbidity Measure (ECM), in patients with chronic heart failure (CHF) at one Veterans Affairs (VA) medical center. We explored potential reasons for the differences found between the original codes assigned and conditions found through retrospective review. Methods This descriptive, retrospective study used a cohort of patients discharged with a principal diagnosis coded as CHF from one VA medical center in 2003. One admission per patient was used in the study; with multiple admissions, only the first admission was analyzed. We compared the assignment of original codes assigned to conditions found in a retrospective, manual review of the medical record conducted by an investigator with coding expertise as well as by physicians. Members of the team experienced with assigning ICD-9-CM codes and VA coding processes developed themes related to systemic reasons why chronic conditions were not coded in VA records using applied thematic techniques. Results In the 181-patient cohort, 388 comorbid conditions were identified; 305 of these were chronic conditions, originally coded at the time of discharge with an average of 1.7 comorbidities related to the ECM per patient. The review by an investigator with coding expertise revealed a total of 937 comorbidities resulting in 618 chronic comorbid conditions with an average of 3.4 per patient; physician review found 872 total comorbidities with 562 chronic conditions (average 3.1 per patient). The agreement between the original and the retrospective coding review was 88 percent. The kappa statistic for the original and the retrospective coding review was 0.375 with a 95 percent confidence interval (CI) of 0.352 to 0.398. The kappa statistic for the retrospective coding review and physician review was 0.849 (CI, 0.823–0.875). The kappa statistic for the original coding and the physician review was 0.340 (CI, 0.316–0.364). Several systemic factors were identified, including familiarity with inpatient VA and non-VA guidelines, the quality of documentation, and operational requirements to complete the coding process within short time frames and to identify the reasons for movement within a given facility. Conclusion Comorbidities within the ECM representing chronic conditions were significantly underrepresented in the original code assignment. Contributing factors potentially include prioritization of codes related to acute conditions over chronic conditions; coders’ professional training, educational level, and experience; and the limited number of codes allowed in initial coding software. This study highlights the need to evaluate systemic causes of underrepresentation of chronic conditions to improve the accuracy of risk adjustment used for health services research, resource allocation, and performance measurement. PMID:24159270

The Helicopter Antenna Radiation Prediction Code (HARP)

NASA Technical Reports Server (NTRS)

Klevenow, F. T.; Lynch, B. G.; Newman, E. H.; Rojas, R. G.; Scheick, J. T.; Shamansky, H. T.; Sze, K. Y.

1990-01-01

The first nine months effort in the development of a user oriented computer code, referred to as the HARP code, for analyzing the radiation from helicopter antennas is described. The HARP code uses modern computer graphics to aid in the description and display of the helicopter geometry. At low frequencies the helicopter is modeled by polygonal plates, and the method of moments is used to compute the desired patterns. At high frequencies the helicopter is modeled by a composite ellipsoid and flat plates, and computations are made using the geometrical theory of diffraction. The HARP code will provide a user friendly interface, employing modern computer graphics, to aid the user to describe the helicopter geometry, select the method of computation, construct the desired high or low frequency model, and display the results.

Enhanced fault-tolerant quantum computing in d-level systems.

PubMed

Campbell, Earl T

2014-12-05

Error-correcting codes protect quantum information and form the basis of fault-tolerant quantum computing. Leading proposals for fault-tolerant quantum computation require codes with an exceedingly rare property, a transversal non-Clifford gate. Codes with the desired property are presented for d-level qudit systems with prime d. The codes use n=d-1 qudits and can detect up to ∼d/3 errors. We quantify the performance of these codes for one approach to quantum computation known as magic-state distillation. Unlike prior work, we find performance is always enhanced by increasing d.

Convergence acceleration of the Proteus computer code with multigrid methods

NASA Technical Reports Server (NTRS)

Demuren, A. O.; Ibraheem, S. O.

1992-01-01

Presented here is the first part of a study to implement convergence acceleration techniques based on the multigrid concept in the Proteus computer code. A review is given of previous studies on the implementation of multigrid methods in computer codes for compressible flow analysis. Also presented is a detailed stability analysis of upwind and central-difference based numerical schemes for solving the Euler and Navier-Stokes equations. Results are given of a convergence study of the Proteus code on computational grids of different sizes. The results presented here form the foundation for the implementation of multigrid methods in the Proteus code.

Implementation of radiation shielding calculation methods. Volume 1: Synopsis of methods and summary of results

NASA Technical Reports Server (NTRS)

Capo, M. A.; Disney, R. K.

1971-01-01

The work performed in the following areas is summarized: (1) Analysis of Realistic nuclear-propelled vehicle was analyzed using the Marshall Space Flight Center computer code package. This code package includes one and two dimensional discrete ordinate transport, point kernel, and single scatter techniques, as well as cross section preparation and data processing codes, (2) Techniques were developed to improve the automated data transfer in the coupled computation method of the computer code package and improve the utilization of this code package on the Univac-1108 computer system. (3) The MSFC master data libraries were updated.

Nonuniform code concatenation for universal fault-tolerant quantum computing

NASA Astrophysics Data System (ADS)

Nikahd, Eesa; Sedighi, Mehdi; Saheb Zamani, Morteza

2017-09-01

Using transversal gates is a straightforward and efficient technique for fault-tolerant quantum computing. Since transversal gates alone cannot be computationally universal, they must be combined with other approaches such as magic state distillation, code switching, or code concatenation to achieve universality. In this paper we propose an alternative approach for universal fault-tolerant quantum computing, mainly based on the code concatenation approach proposed in [T. Jochym-O'Connor and R. Laflamme, Phys. Rev. Lett. 112, 010505 (2014), 10.1103/PhysRevLett.112.010505], but in a nonuniform fashion. The proposed approach is described based on nonuniform concatenation of the 7-qubit Steane code with the 15-qubit Reed-Muller code, as well as the 5-qubit code with the 15-qubit Reed-Muller code, which lead to two 49-qubit and 47-qubit codes, respectively. These codes can correct any arbitrary single physical error with the ability to perform a universal set of fault-tolerant gates, without using magic state distillation.

An emergentist perspective on the origin of number sense

PubMed Central

2018-01-01

The finding that human infants and many other animal species are sensitive to numerical quantity has been widely interpreted as evidence for evolved, biologically determined numerical capacities across unrelated species, thereby supporting a ‘nativist’ stance on the origin of number sense. Here, we tackle this issue within the ‘emergentist’ perspective provided by artificial neural network models, and we build on computer simulations to discuss two different approaches to think about the innateness of number sense. The first, illustrated by artificial life simulations, shows that numerical abilities can be supported by domain-specific representations emerging from evolutionary pressure. The second assumes that numerical representations need not be genetically pre-determined but can emerge from the interplay between innate architectural constraints and domain-general learning mechanisms, instantiated in deep learning simulations. We show that deep neural networks endowed with basic visuospatial processing exhibit a remarkable performance in numerosity discrimination before any experience-dependent learning, whereas unsupervised sensory experience with visual sets leads to subsequent improvement of number acuity and reduces the influence of continuous visual cues. The emergent neuronal code for numbers in the model includes both numerosity-sensitive (summation coding) and numerosity-selective response profiles, closely mirroring those found in monkey intraparietal neurons. We conclude that a form of innatism based on architectural and learning biases is a fruitful approach to understanding the origin and development of number sense. This article is part of a discussion meeting issue ‘The origins of numerical abilities'. PMID:29292348

Hybrid-view programming of nuclear fusion simulation code in the PGAS parallel programming language XcalableMP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsugane, Keisuke; Boku, Taisuke; Murai, Hitoshi

Recently, the Partitioned Global Address Space (PGAS) parallel programming model has emerged as a usable distributed memory programming model. XcalableMP (XMP) is a PGAS parallel programming language that extends base languages such as C and Fortran with directives in OpenMP-like style. XMP supports a global-view model that allows programmers to define global data and to map them to a set of processors, which execute the distributed global data as a single thread. In XMP, the concept of a coarray is also employed for local-view programming. In this study, we port Gyrokinetic Toroidal Code - Princeton (GTC-P), which is a three-dimensionalmore » gyrokinetic PIC code developed at Princeton University to study the microturbulence phenomenon in magnetically confined fusion plasmas, to XMP as an example of hybrid memory model coding with the global-view and local-view programming models. In local-view programming, the coarray notation is simple and intuitive compared with Message Passing Interface (MPI) programming while the performance is comparable to that of the MPI version. Thus, because the global-view programming model is suitable for expressing the data parallelism for a field of grid space data, we implement a hybrid-view version using a global-view programming model to compute the field and a local-view programming model to compute the movement of particles. Finally, the performance is degraded by 20% compared with the original MPI version, but the hybrid-view version facilitates more natural data expression for static grid space data (in the global-view model) and dynamic particle data (in the local-view model), and it also increases the readability of the code for higher productivity.« less

Hybrid-view programming of nuclear fusion simulation code in the PGAS parallel programming language XcalableMP

DOE PAGES

Tsugane, Keisuke; Boku, Taisuke; Murai, Hitoshi; ...

2016-06-01

Recently, the Partitioned Global Address Space (PGAS) parallel programming model has emerged as a usable distributed memory programming model. XcalableMP (XMP) is a PGAS parallel programming language that extends base languages such as C and Fortran with directives in OpenMP-like style. XMP supports a global-view model that allows programmers to define global data and to map them to a set of processors, which execute the distributed global data as a single thread. In XMP, the concept of a coarray is also employed for local-view programming. In this study, we port Gyrokinetic Toroidal Code - Princeton (GTC-P), which is a three-dimensionalmore » gyrokinetic PIC code developed at Princeton University to study the microturbulence phenomenon in magnetically confined fusion plasmas, to XMP as an example of hybrid memory model coding with the global-view and local-view programming models. In local-view programming, the coarray notation is simple and intuitive compared with Message Passing Interface (MPI) programming while the performance is comparable to that of the MPI version. Thus, because the global-view programming model is suitable for expressing the data parallelism for a field of grid space data, we implement a hybrid-view version using a global-view programming model to compute the field and a local-view programming model to compute the movement of particles. Finally, the performance is degraded by 20% compared with the original MPI version, but the hybrid-view version facilitates more natural data expression for static grid space data (in the global-view model) and dynamic particle data (in the local-view model), and it also increases the readability of the code for higher productivity.« less

TOPAZ2D heat transfer code users manual and thermal property data base

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shapiro, A.B.; Edwards, A.L.

1990-05-01

TOPAZ2D is a two dimensional implicit finite element computer code for heat transfer analysis. This user's manual provides information on the structure of a TOPAZ2D input file. Also included is a material thermal property data base. This manual is supplemented with The TOPAZ2D Theoretical Manual and the TOPAZ2D Verification Manual. TOPAZ2D has been implemented on the CRAY, SUN, and VAX computers. TOPAZ2D can be used to solve for the steady state or transient temperature field on two dimensional planar or axisymmetric geometries. Material properties may be temperature dependent and either isotropic or orthotropic. A variety of time and temperature dependentmore » boundary conditions can be specified including temperature, flux, convection, and radiation. Time or temperature dependent internal heat generation can be defined locally be element or globally by material. TOPAZ2D can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in material surrounding the enclosure. Additional features include thermally controlled reactive chemical mixtures, thermal contact resistance across an interface, bulk fluid flow, phase change, and energy balances. Thermal stresses can be calculated using the solid mechanics code NIKE2D which reads the temperature state data calculated by TOPAZ2D. A three dimensional version of the code, TOPAZ3D is available. The material thermal property data base, Chapter 4, included in this manual was originally published in 1969 by Art Edwards for use with his TRUMP finite difference heat transfer code. The format of the data has been altered to be compatible with TOPAZ2D. Bob Bailey is responsible for adding the high explosive thermal property data.« less

Green's function methods in heavy ion shielding

NASA Technical Reports Server (NTRS)

Wilson, John W.; Costen, Robert C.; Shinn, Judy L.; Badavi, Francis F.

1993-01-01

An analytic solution to the heavy ion transport in terms of Green's function is used to generate a highly efficient computer code for space applications. The efficiency of the computer code is accomplished by a nonperturbative technique extending Green's function over the solution domain. The computer code can also be applied to accelerator boundary conditions to allow code validation in laboratory experiments.

Analytical modeling of operating characteristics of premixing-prevaporizing fuel-air mixing passages. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Anderson, O. L.; Chiappetta, L. M.; Edwards, D. E.; Mcvey, J. B.

1982-01-01

A user's manual describing the operation of three computer codes (ADD code, PTRAK code, and VAPDIF code) is presented. The general features of the computer codes, the input/output formats, run streams, and sample input cases are described.

Assessing primary care data quality.

PubMed

Lim, Yvonne Mei Fong; Yusof, Maryati; Sivasampu, Sheamini

2018-04-16

Purpose The purpose of this paper is to assess National Medical Care Survey data quality. Design/methodology/approach Data completeness and representativeness were computed for all observations while other data quality measures were assessed using a 10 per cent sample from the National Medical Care Survey database; i.e., 12,569 primary care records from 189 public and private practices were included in the analysis. Findings Data field completion ranged from 69 to 100 per cent. Error rates for data transfer from paper to web-based application varied between 0.5 and 6.1 per cent. Error rates arising from diagnosis and clinical process coding were higher than medication coding. Data fields that involved free text entry were more prone to errors than those involving selection from menus. The authors found that completeness, accuracy, coding reliability and representativeness were generally good, while data timeliness needs to be improved. Research limitations/implications Only data entered into a web-based application were examined. Data omissions and errors in the original questionnaires were not covered. Practical implications Results from this study provided informative and practicable approaches to improve primary health care data completeness and accuracy especially in developing nations where resources are limited. Originality/value Primary care data quality studies in developing nations are limited. Understanding errors and missing data enables researchers and health service administrators to prevent quality-related problems in primary care data.

Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory.

PubMed

Di Giulio, Massimo

2017-02-07

Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code". And, given that in the genetic code table are mirrored both the biosynthetic relationships between amino acids and their physico-chemical properties, all this would be a test that would falsify the physico-chemical theories of the origin of the genetic code. That is to say, if the physico-chemical properties of amino acids had a fundamental role in organizing the genetic code, then we would not have duly revealed the presence - in the genetic code - of the biosynthetic relationships between amino acids, and on the contrary this has been observed. Therefore, this falsifies the physico-chemical theories of genetic code origin. Whereas, the coevolution theory of the origin of the genetic code would be corroborated by this analysis, because it would be able to give a description of evolution of the genetic code more coherent with the indisputable empirical observations that link both the biosynthetic relationships of amino acids and their physico-chemical properties to the evolutionary organization of the genetic code. Copyright © 2016 Elsevier Ltd. All rights reserved.

Automated apparatus and method of generating native code for a stitching machine

NASA Technical Reports Server (NTRS)

Miller, Jeffrey L. (Inventor)

2000-01-01

A computer system automatically generates CNC code for a stitching machine. The computer determines the locations of a present stitching point and a next stitching point. If a constraint is not found between the present stitching point and the next stitching point, the computer generates code for making a stitch at the next stitching point. If a constraint is found, the computer generates code for changing a condition (e.g., direction) of the stitching machine's stitching head.

Computer codes developed and under development at Lewis

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1992-01-01

The objective of this summary is to provide a brief description of: (1) codes developed or under development at LeRC; and (2) the development status of IPACS with some typical early results. The computer codes that have been developed and/or are under development at LeRC are listed in the accompanying charts. This list includes: (1) the code acronym; (2) select physics descriptors; (3) current enhancements; and (4) present (9/91) code status with respect to its availability and documentation. The computer codes list is grouped by related functions such as: (1) composite mechanics; (2) composite structures; (3) integrated and 3-D analysis; (4) structural tailoring; and (5) probabilistic structural analysis. These codes provide a broad computational simulation infrastructure (technology base-readiness) for assessing the structural integrity/durability/reliability of propulsion systems. These codes serve two other very important functions: they provide an effective means of technology transfer; and they constitute a depository of corporate memory.

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

PubMed Central

2014-01-01

Background Non-coding sequences such as microRNAs have important roles in disease processes. Computational microRNA target identification (CMTI) is becoming increasingly important since traditional experimental methods for target identification pose many difficulties. These methods are time-consuming, costly, and often need guidance from computational methods to narrow down candidate genes anyway. However, most CMTI methods are computationally demanding, since they need to handle not only several million query microRNA and reference RNA pairs, but also several million nucleotide comparisons within each given pair. Thus, the need to perform microRNA identification at such large scale has increased the demand for parallel computing. Methods Although most CMTI programs (e.g., the miRanda algorithm) are based on a modified Smith-Waterman (SW) algorithm, the existing parallel SW implementations (e.g., CUDASW++ 2.0/3.0, SWIPE) are unable to meet this demand in CMTI tasks. We present CUDA-miRanda, a fast microRNA target identification algorithm that takes advantage of massively parallel computing on Graphics Processing Units (GPU) using NVIDIA's Compute Unified Device Architecture (CUDA). CUDA-miRanda specifically focuses on the local alignment of short (i.e., ≤ 32 nucleotides) sequences against longer reference sequences (e.g., 20K nucleotides). Moreover, the proposed algorithm is able to report multiple alignments (up to 191 top scores) and the corresponding traceback sequences for any given (query sequence, reference sequence) pair. Results Speeds over 5.36 Giga Cell Updates Per Second (GCUPs) are achieved on a server with 4 NVIDIA Tesla M2090 GPUs. Compared to the original miRanda algorithm, which is evaluated on an Intel Xeon E5620@2.4 GHz CPU, the experimental results show up to 166 times performance gains in terms of execution time. In addition, we have verified that the exact same targets were predicted in both CUDA-miRanda and the original miRanda implementations through multiple test datasets. Conclusions We offer a GPU-based alternative to high performance compute (HPC) that can be developed locally at a relatively small cost. The community of GPU developers in the biomedical research community, particularly for genome analysis, is still growing. With increasing shared resources, this community will be able to advance CMTI in a very significant manner. Our source code is available at https://sourceforge.net/projects/cudamiranda/. PMID:25077821

Performance Bounds on Two Concatenated, Interleaved Codes

NASA Technical Reports Server (NTRS)

Moision, Bruce; Dolinar, Samuel

2010-01-01

A method has been developed of computing bounds on the performance of a code comprised of two linear binary codes generated by two encoders serially concatenated through an interleaver. Originally intended for use in evaluating the performances of some codes proposed for deep-space communication links, the method can also be used in evaluating the performances of short-block-length codes in other applications. The method applies, more specifically, to a communication system in which following processes take place: At the transmitter, the original binary information that one seeks to transmit is first processed by an encoder into an outer code (Co) characterized by, among other things, a pair of numbers (n,k), where n (n > k)is the total number of code bits associated with k information bits and n k bits are used for correcting or at least detecting errors. Next, the outer code is processed through either a block or a convolutional interleaver. In the block interleaver, the words of the outer code are processed in blocks of I words. In the convolutional interleaver, the interleaving operation is performed bit-wise in N rows with delays that are multiples of B bits. The output of the interleaver is processed through a second encoder to obtain an inner code (Ci) characterized by (ni,ki). The output of the inner code is transmitted over an additive-white-Gaussian- noise channel characterized by a symbol signal-to-noise ratio (SNR) Es/No and a bit SNR Eb/No. At the receiver, an inner decoder generates estimates of bits. Depending on whether a block or a convolutional interleaver is used at the transmitter, the sequence of estimated bits is processed through a block or a convolutional de-interleaver, respectively, to obtain estimates of code words. Then the estimates of the code words are processed through an outer decoder, which generates estimates of the original information along with flags indicating which estimates are presumed to be correct and which are found to be erroneous. From the perspective of the present method, the topic of major interest is the performance of the communication system as quantified in the word-error rate and the undetected-error rate as functions of the SNRs and the total latency of the interleaver and inner code. The method is embodied in equations that describe bounds on these functions. Throughout the derivation of the equations that embody the method, it is assumed that the decoder for the outer code corrects any error pattern of t or fewer errors, detects any error pattern of s or fewer errors, may detect some error patterns of more than s errors, and does not correct any patterns of more than t errors. Because a mathematically complete description of the equations that embody the method and of the derivation of the equations would greatly exceed the space available for this article, it must suffice to summarize by reporting that the derivation includes consideration of several complex issues, including relationships between latency and memory requirements for block and convolutional codes, burst error statistics, enumeration of error-event intersections, and effects of different interleaving depths. In a demonstration, the method was used to calculate bounds on the performances of several communication systems, each based on serial concatenation of a (63,56) expurgated Hamming code with a convolutional inner code through a convolutional interleaver. The bounds calculated by use of the method were compared with results of numerical simulations of performances of the systems to show the regions where the bounds are tight (see figure).

Using virtualization to protect the proprietary material science applications in volunteer computing

NASA Astrophysics Data System (ADS)

Khrapov, Nikolay P.; Rozen, Valery V.; Samtsevich, Artem I.; Posypkin, Mikhail A.; Sukhomlin, Vladimir A.; Oganov, Artem R.

2018-04-01

USPEX is a world-leading software for computational material design. In essence, USPEX splits simulation into a large number of workunits that can be processed independently. This scheme ideally fits the desktop grid architecture. Workunit processing is done by a simulation package aimed at energy minimization. Many of such packages are proprietary and should be protected from unauthorized access when running on a volunteer PC. In this paper we present an original approach based on virtualization. In a nutshell, the proprietary code and input files are stored in an encrypted folder and run inside a virtual machine image that is also password protected. The paper describes this approach in detail and discusses its application in USPEX@home volunteer project.

Keys to a successful project: Associated data and planning: Data standards. Chapter 5 in Measuring and monitoring biological diversity: Standard methods for amphibians

USGS Publications Warehouse

McDiarmid, Roy W.; Heyer, W. Ronald; Donnelly, Maureen A.; McDiarmid, Roy W.; Hayek, Lee-Ann C.; Foster, Mercedes S.

1994-01-01

The many individual salamanders, frogs, caecilians, and their larvae encountered during the course of an inventory or monitoring project will have to be identified to species. Depending on the goals and sampling method(s) used, some individuals will be identified from a distance by their calls, others will be handled. At the same time, some will be marked for recapture, and others will be sampled as vouchers. For each, certain minimum data should be recorded. In this section, data pertaining to locality and sampling methodology are considered, information on microhabitats and specimen vouchers is covered in sections that follow. I feel strongly that the data outlined here should be the minimum for any project. Investigators with specific goals may require additional types of data as well.Standardized, printed sheets containing the required data categories provide a convenient, inexpensive, and effective way to ensure that all the desired information is recorded in a consistent format, Data sheets should be well organized, printed on good-quality paper (75%-100% cotton content) and include extra space (e.g., other side of sheet) for notes that do not fit preestablished categoriesData should be recorded in the field with permanent (waterproof) ink as simply and directly as possible. I strongly recommend against the use of data codes in the field; it is too easy to forget codes or to enter the wrong code. Original data sheets can be photocopied for security, but they should not be copied by hand. If data are to be coded for computer analysis, the original or photocopied sheets should be used for data entry to minimize transcription errors. Some workers prefer recording information on small tape recorders; this also works well if a list of the standard data categories is checked during taping to ensure that all required information is recorded. Information recorded on tapes should be transcribed to data sheets or into a computer within 24 hours of the sample.

Modularized seismic full waveform inversion based on waveform sensitivity kernels - The software package ASKI

NASA Astrophysics Data System (ADS)

Schumacher, Florian; Friederich, Wolfgang; Lamara, Samir; Gutt, Phillip; Paffrath, Marcel

2015-04-01

We present a seismic full waveform inversion concept for applications ranging from seismological to enineering contexts, based on sensitivity kernels for full waveforms. The kernels are derived from Born scattering theory as the Fréchet derivatives of linearized frequency-domain full waveform data functionals, quantifying the influence of elastic earth model parameters and density on the data values. For a specific source-receiver combination, the kernel is computed from the displacement and strain field spectrum originating from the source evaluated throughout the inversion domain, as well as the Green function spectrum and its strains originating from the receiver. By storing the wavefield spectra of specific sources/receivers, they can be re-used for kernel computation for different specific source-receiver combinations, optimizing the total number of required forward simulations. In the iterative inversion procedure, the solution of the forward problem, the computation of sensitivity kernels and the derivation of a model update is held completely separate. In particular, the model description for the forward problem and the description of the inverted model update are kept independent. Hence, the resolution of the inverted model as well as the complexity of solving the forward problem can be iteratively increased (with increasing frequency content of the inverted data subset). This may regularize the overall inverse problem and optimizes the computational effort of both, solving the forward problem and computing the model update. The required interconnection of arbitrary unstructured volume and point grids is realized by generalized high-order integration rules and 3D-unstructured interpolation methods. The model update is inferred solving a minimization problem in a least-squares sense, resulting in Gauss-Newton convergence of the overall inversion process. The inversion method was implemented in the modularized software package ASKI (Analysis of Sensitivity and Kernel Inversion), which provides a generalized interface to arbitrary external forward modelling codes. So far, the 3D spectral-element code SPECFEM3D (Tromp, Komatitsch and Liu, 2008) and the 1D semi-analytical code GEMINI (Friederich and Dalkolmo, 1995) in both, Cartesian and spherical framework are supported. The creation of interfaces to further forward codes is planned in the near future. ASKI is freely available under the terms of the GPL at www.rub.de/aski . Since the independent modules of ASKI must communicate via file output/input, large storage capacities need to be accessible conveniently. Storing the complete sensitivity matrix to file, however, permits the scientist full manual control over each step in a customized procedure of sensitivity/resolution analysis and full waveform inversion. In the presentation, we will show some aspects of the theory behind the full waveform inversion method and its practical realization by the software package ASKI, as well as synthetic and real-data applications from different scales and geometries.

Reactivity effects in VVER-1000 of the third unit of the kalinin nuclear power plant at physical start-up. Computations in ShIPR intellectual code system with library of two-group cross sections generated by UNK code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zizin, M. N.; Zimin, V. G.; Zizina, S. N., E-mail: zizin@adis.vver.kiae.ru

2010-12-15

The ShIPR intellectual code system for mathematical simulation of nuclear reactors includes a set of computing modules implementing the preparation of macro cross sections on the basis of the two-group library of neutron-physics cross sections obtained for the SKETCH-N nodal code. This library is created by using the UNK code for 3D diffusion computation of first VVER-1000 fuel loadings. Computation of neutron fields in the ShIPR system is performed using the DP3 code in the two-group diffusion approximation in 3D triangular geometry. The efficiency of all groups of control rods for the first fuel loading of the third unit ofmore » the Kalinin Nuclear Power Plant is computed. The temperature, barometric, and density effects of reactivity as well as the reactivity coefficient due to the concentration of boric acid in the reactor were computed additionally. Results of computations are compared with the experiment.« less

Reactivity effects in VVER-1000 of the third unit of the kalinin nuclear power plant at physical start-up. Computations in ShIPR intellectual code system with library of two-group cross sections generated by UNK code

NASA Astrophysics Data System (ADS)

Zizin, M. N.; Zimin, V. G.; Zizina, S. N.; Kryakvin, L. V.; Pitilimov, V. A.; Tereshonok, V. A.

2010-12-01

The ShIPR intellectual code system for mathematical simulation of nuclear reactors includes a set of computing modules implementing the preparation of macro cross sections on the basis of the two-group library of neutron-physics cross sections obtained for the SKETCH-N nodal code. This library is created by using the UNK code for 3D diffusion computation of first VVER-1000 fuel loadings. Computation of neutron fields in the ShIPR system is performed using the DP3 code in the two-group diffusion approximation in 3D triangular geometry. The efficiency of all groups of control rods for the first fuel loading of the third unit of the Kalinin Nuclear Power Plant is computed. The temperature, barometric, and density effects of reactivity as well as the reactivity coefficient due to the concentration of boric acid in the reactor were computed additionally. Results of computations are compared with the experiment.

Users manual and modeling improvements for axial turbine design and performance computer code TD2-2

NASA Technical Reports Server (NTRS)

Glassman, Arthur J.

1992-01-01

Computer code TD2 computes design point velocity diagrams and performance for multistage, multishaft, cooled or uncooled, axial flow turbines. This streamline analysis code was recently modified to upgrade modeling related to turbine cooling and to the internal loss correlation. These modifications are presented in this report along with descriptions of the code's expanded input and output. This report serves as the users manual for the upgraded code, which is named TD2-2.

An Object-Oriented Approach to Writing Computational Electromagnetics Codes

NASA Technical Reports Server (NTRS)

Zimmerman, Martin; Mallasch, Paul G.

1996-01-01

Presently, most computer software development in the Computational Electromagnetics (CEM) community employs the structured programming paradigm, particularly using the Fortran language. Other segments of the software community began switching to an Object-Oriented Programming (OOP) paradigm in recent years to help ease design and development of highly complex codes. This paper examines design of a time-domain numerical analysis CEM code using the OOP paradigm, comparing OOP code and structured programming code in terms of software maintenance, portability, flexibility, and speed.

Summary of evidence for an anticodonic basis for the origin of the genetic code

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1981-01-01

This article summarizes data supporting the hypothesis that the genetic code origin was based on relationships (probably affinities) between amino acids and their anticodon nucleotides. Selective activation seems to follow from selective affinity and consequently, incorporation of amino acids into peptides can also be selective. It is suggested that these selectivities in affinity and activation, coupled with the base pairing specificities, allowed the origin of the code and the process of translation.

Computer Description of the Field Artillery Ammunition Supply Vehicle

DTIC Science & Technology

1983-04-01

Combinatorial Geometry (COM-GEOM) GIFT Computer Code Computer Target Description 2& AfTNACT (Cmne M feerve shb N ,neemssalyan ify by block number) A...input to the GIFT computer code to generate target vulnerability data. F.a- 4 ono OF I NOV 5S OLETE UNCLASSIFIED SECUOITY CLASSIFICATION OF THIS PAGE...Combinatorial Geometry (COM-GEOM) desrription. The "Geometric Information for Tarqets" ( GIFT ) computer code accepts the CO!-GEOM description and

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2011 CFR

2011-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2012 CFR

2012-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2014 CFR

2014-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2010 CFR

2010-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar data produced for...

Antenna pattern study, task 2

NASA Technical Reports Server (NTRS)

Harper, Warren

1989-01-01

Two electromagnetic scattering codes, NEC-BSC and ESP3, were delivered and installed on a NASA VAX computer for use by Marshall Space Flight Center antenna design personnel. The existing codes and certain supplementary software were updated, the codes installed on a computer that will be delivered to the customer, to provide capability for graphic display of the data to be computed by the use of the codes and to assist the customer in the solution of specific problems that demonstrate the use of the codes. With the exception of one code revision, all of these tasks were performed.

Conference Proceedings on Validation of Computational Fluid Dynamics. Volume 1. Symposium Papers and Round Table Discussion Held in Lisbon, Portugal on 2-5 May 1988

DTIC Science & Technology

1988-05-01

the representation of the shock, the non -conservative difference scheme in the original method being replaced by a ’ quasi - conservative’ operator 3...domain. In order to simulate the experimentally observed pressure distribution at the exit a formulation of the non -reflecting pressure condition Is used...and Experimental Aero- dynamics: Wing Surface Generator Code, Control Surface and Boundary Conditions". DFVLR IB 221-87 A 01, 1987. [11] Kordulla, W.(ed

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

PubMed

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal significance is measurable. These two codes codify roughly for the two ARS classes, in particular, the CAG code for the class II while the UNN/NUN code for the class I. Furthermore, the subclasses of ARSs show a statistical significance of their distribution in the genetic code table. Nevertheless, the more sensible explanation for these observations would be the following. The observation that would link the two classes of ARSs to the CAG and UNN/NUN codes, and the statistical significance of the distribution of the subclasses of ARSs in the genetic code table, would be only a secondary effect due to the highly significant distribution of the polarity of amino acids and their biosynthetic relationships in the genetic code. That is to say, the polarity of amino acids and their biosynthetic relationships would have conditioned the evolution of ARSs so that their presence in the genetic code would have been detectable. Even if the ARSs would not have-on their own-influenced directly the evolutionary organization of the genetic code. In other words, the role that ARSs had in the origin of the genetic code would have been entirely marginal. This conclusion would be in perfect accord with the predictions of the coevolution theory. Conversely, this conclusion would be in contrast-at least partially-with the physicochemical theories of the origin of the genetic code because they would foresee an absolutely more active role of ARSs in the origin of the organization of the genetic code. Copyright © 2017 Elsevier Ltd. All rights reserved.

SolCalc: A Suite for the Calculation and the Display of Magnetic Fields Generated by Solenoid Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopes, M. L.

2014-07-01

SolCalc is a software suite that computes and displays magnetic fields generated by a three dimensional (3D) solenoid system. Examples of such systems are the Mu2e magnet system and Helical Solenoids for muon cooling systems. SolCalc was originally coded in Matlab, and later upgraded to a compiled version (called MEX) to improve solving speed. Matlab was chosen because its graphical capabilities represent an attractive feature over other computer languages. Solenoid geometries can be created using any text editor or spread sheets and can be displayed dynamically in 3D. Fields are computed from any given list of coordinates. The field distributionmore » on the surfaces of the coils can be displayed as well. SolCalc was benchmarked against a well-known commercial software for speed and accuracy and the results compared favorably.« less

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2013 CFR

2013-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... funds; (ii) Studies, analyses, test data, or similar data produced for this contract, when the study...

Nonlinear Modeling of Radial Stellar Pulsations

NASA Astrophysics Data System (ADS)

Smolec, R.

2009-09-01

In this thesis, I present the results of my work concerning the nonlinear modeling of radial stellar pulsations. I will focus on classical Cepheids, particularly on the double-mode phenomenon. History of nonlinear modeling of radial stellar pulsations begins in the sixties of the previous century. At the beginning convection was disregarded in model equations. Qualitatively, almost all features of the radial pulsators were successfully modeled with purely radiative hydrocodes. Among problems that remained, the most disturbing was modeling of the double-mode phenomenon. This long-standing problem seemed to be finally solved with the inclusion of turbulent convection into the model equations (Kollath et al. 1998, Feuchtinger 1998). Although dynamical aspects of the double-mode behaviour were extensively studied, its origin, particularly the specific role played by convection, remained obscure. To study this and other problems of radial stellar pulsations, I implemented the convection into pulsation hydrocodes. The codes adopt the Kuhfuss (1986) convection model. In other codes, particularly in the Florida-Budapest hydrocode (e.g. Kollath et al. 2002), used in comput! ation of most of the published double-mode models, different approximations concerning e.g. eddy-viscous terms or treatment of convectively stable regions are adopted. Particularly the neglect of negative buoyancy effects in the Florida-Budapest code and its consequences, were never discussed in the literature. These consequences are severe. Concerning the single-mode pulsators, neglect of negative buoyancy leads to smaller pulsation amplitudes, in comparison to amplitudes computed with code including these effects. Particularly, neglect of negative buoyancy reduces the amplitude of the fundamental mode very strong. This property of the Florida-Budapest models is crucial in bringing up the stable non-resonant double-mode Cepheid pulsation involving fundamental and first overtone modes (F/1O). Such pulsation is not observed in models computed including negative buoyancy. As the neglect of negative buoyancy is physically not correct, so are the double-mode Cepheid models computed with the Florida-Budapest hydrocode. Extensive search for F/1O double-mode Cepheid pulsation with the codes including negative buoyancy effects yielded null result. Some resonant double-mode F/1O Cepheid models were found, but their occurrence was restricted to a very narrow domain in the Hertzsprung-Russel diagram. Model computations intended to model the double-overtone (1O/2O) Cepheids in the Large Magellanic Cloud, also revealed some stable double-mode pulsations, however, restricted to a narrow period range. Resonances are most likely conductive in bringing up the double-mode behaviour observed in these models. However, majority of the double-overtone LMC Cepheids cannot be reproduced with our codes. Hence, the modeling of double-overtone Cepheids with convective hydrocodes is not satisfactory, either. Double-mode pulsation still lacks satisfactory explanation, and problem of its modeling remains open.

A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support.

PubMed

Giulio, Massimo Di

2018-05-19

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. The comparison between these two χ values showed that the coevolution theory is able to explain - in this strictly empirical analysis - the origin of the genetic code better than that of the physicochemical theory. Copyright © 2018 Elsevier B.V. All rights reserved.

Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

NASA Technical Reports Server (NTRS)

Rose, Geoffrey K.; Nguyen, Duc T.; Newman, Brett A.

2017-01-01

Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

User Instructions for the Systems Assessment Capability, Rev. 1, Computer Codes Volume 3: Utility Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eslinger, Paul W.; Aaberg, Rosanne L.; Lopresti, Charles A.

2004-09-14

This document contains detailed user instructions for a suite of utility codes developed for Rev. 1 of the Systems Assessment Capability. The suite of computer codes for Rev. 1 of Systems Assessment Capability performs many functions.

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection.

PubMed

Mendes-Junior, C T; Castelli, E C; Meyer, D; Simões, A L; Donadi, E A

2013-12-01

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3'UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.

Aeras: A next generation global atmosphere model

DOE PAGES

Spotz, William F.; Smith, Thomas M.; Demeshko, Irina P.; ...

2015-06-01

Sandia National Laboratories is developing a new global atmosphere model named Aeras that is performance portable and supports the quantification of uncertainties. These next-generation capabilities are enabled by building Aeras on top of Albany, a code base that supports the rapid development of scientific application codes while leveraging Sandia's foundational mathematics and computer science packages in Trilinos and Dakota. Embedded uncertainty quantification (UQ) is an original design capability of Albany, and performance portability is a recent upgrade. Other required features, such as shell-type elements, spectral elements, efficient explicit and semi-implicit time-stepping, transient sensitivity analysis, and concurrent ensembles, were not componentsmore » of Albany as the project began, and have been (or are being) added by the Aeras team. We present early UQ and performance portability results for the shallow water equations.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivanov, A. A., E-mail: aai@a5.kiam.ru; Martynov, A. A., E-mail: martynov@a5.kiam.ru; Medvedev, S. Yu., E-mail: medvedev@a5.kiam.ru

In the MHD tokamak plasma theory, the plasma pressure is usually assumed to be isotropic. However, plasma heating by neutral beam injection and RF heating can lead to a strong anisotropy of plasma parameters and rotation of the plasma. The development of MHD equilibrium theory taking into account the plasma inertia and anisotropic pressure began a long time ago, but until now it has not been consistently applied in computational codes for engineering calculations of the plasma equilibrium and evolution in tokamak. This paper contains a detailed derivation of the axisymmetric plasma equilibrium equation in the most general form (withmore » arbitrary rotation and anisotropic pressure) and description of the specialized version of the SPIDER code. The original method of calculation of the equilibrium with an anisotropic pressure and a prescribed rotational transform profile is proposed. Examples of calculations and discussion of the results are also presented.« less

LINE: a code which simulates spectral line shapes for fusion reaction products generated by various speed distributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slaughter, D.

1985-03-01

A computer code is described which estimates the energy spectrum or ''line-shape'' for the charged particles and ..gamma..-rays produced by the fusion of low-z ions in a hot plasma. The simulation has several ''built-in'' ion velocity distributions characteristic of heated plasmas and it also accepts arbitrary speed and angular distributions although they must all be symmetric about the z-axis. An energy spectrum of one of the reaction products (ion, neutron, or ..gamma..-ray) is calculated at one angle with respect to the symmetry axis. The results are shown in tabular form, they are plotted graphically, and the moments of the spectrummore » to order ten are calculated both with respect to the origin and with respect to the mean.« less

COSMOABC: Likelihood-free inference via Population Monte Carlo Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Ishida, E. E. O.; Vitenti, S. D. P.; Penna-Lima, M.; Cisewski, J.; de Souza, R. S.; Trindade, A. M. M.; Cameron, E.; Busti, V. C.; COIN Collaboration

2015-11-01

Approximate Bayesian Computation (ABC) enables parameter inference for complex physical systems in cases where the true likelihood function is unknown, unavailable, or computationally too expensive. It relies on the forward simulation of mock data and comparison between observed and synthetic catalogues. Here we present COSMOABC, a Python ABC sampler featuring a Population Monte Carlo variation of the original ABC algorithm, which uses an adaptive importance sampling scheme. The code is very flexible and can be easily coupled to an external simulator, while allowing to incorporate arbitrary distance and prior functions. As an example of practical application, we coupled COSMOABC with the NUMCOSMO library and demonstrate how it can be used to estimate posterior probability distributions over cosmological parameters based on measurements of galaxy clusters number counts without computing the likelihood function. COSMOABC is published under the GPLv3 license on PyPI and GitHub and documentation is available at http://goo.gl/SmB8EX.

Automated Generation of Message-Passing Programs: An Evaluation Using CAPTools

NASA Technical Reports Server (NTRS)

Hribar, Michelle R.; Jin, Haoqiang; Yan, Jerry C.; Saini, Subhash (Technical Monitor)

1998-01-01

Scientists at NASA Ames Research Center have been developing computational aeroscience applications on highly parallel architectures over the past ten years. During that same time period, a steady transition of hardware and system software also occurred, forcing us to expend great efforts into migrating and re-coding our applications. As applications and machine architectures become increasingly complex, the cost and time required for this process will become prohibitive. In this paper, we present the first set of results in our evaluation of interactive parallelization tools. In particular, we evaluate CAPTool's ability to parallelize computational aeroscience applications. CAPTools was tested on serial versions of the NAS Parallel Benchmarks and ARC3D, a computational fluid dynamics application, on two platforms: the SGI Origin 2000 and the Cray T3E. This evaluation includes performance, amount of user interaction required, limitations and portability. Based on these results, a discussion on the feasibility of computer aided parallelization of aerospace applications is presented along with suggestions for future work.

DOE Office of Scientific and Technical Information (OSTI.GOV)

The Analysis of Search Results for the Clarification and Identification of Technology Emergence (AR-CITE) computer code examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e. scholarly publications and citation, world patents, news archives, and on-line mapping networks) are assembled to become one collective networkmore » (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the subject domain to be clarified and identified.« less

Learning Compact Binary Face Descriptor for Face Recognition.

PubMed

Lu, Jiwen; Liong, Venice Erin; Zhou, Xiuzhuang; Zhou, Jie

2015-10-01

Binary feature descriptors such as local binary patterns (LBP) and its variations have been widely used in many face recognition systems due to their excellent robustness and strong discriminative power. However, most existing binary face descriptors are hand-crafted, which require strong prior knowledge to engineer them by hand. In this paper, we propose a compact binary face descriptor (CBFD) feature learning method for face representation and recognition. Given each face image, we first extract pixel difference vectors (PDVs) in local patches by computing the difference between each pixel and its neighboring pixels. Then, we learn a feature mapping to project these pixel difference vectors into low-dimensional binary vectors in an unsupervised manner, where 1) the variance of all binary codes in the training set is maximized, 2) the loss between the original real-valued codes and the learned binary codes is minimized, and 3) binary codes evenly distribute at each learned bin, so that the redundancy information in PDVs is removed and compact binary codes are obtained. Lastly, we cluster and pool these binary codes into a histogram feature as the final representation for each face image. Moreover, we propose a coupled CBFD (C-CBFD) method by reducing the modality gap of heterogeneous faces at the feature level to make our method applicable to heterogeneous face recognition. Extensive experimental results on five widely used face datasets show that our methods outperform state-of-the-art face descriptors.

Development of a model and computer code to describe solar grade silicon production processes

NASA Technical Reports Server (NTRS)

Gould, R. K.; Srivastava, R.

1979-01-01

Two computer codes were developed for describing flow reactors in which high purity, solar grade silicon is produced via reduction of gaseous silicon halides. The first is the CHEMPART code, an axisymmetric, marching code which treats two phase flows with models describing detailed gas-phase chemical kinetics, particle formation, and particle growth. It can be used to described flow reactors in which reactants, mix, react, and form a particulate phase. Detailed radial gas-phase composition, temperature, velocity, and particle size distribution profiles are computed. Also, deposition of heat, momentum, and mass (either particulate or vapor) on reactor walls is described. The second code is a modified version of the GENMIX boundary layer code which is used to compute rates of heat, momentum, and mass transfer to the reactor walls. This code lacks the detailed chemical kinetics and particle handling features of the CHEMPART code but has the virtue of running much more rapidly than CHEMPART, while treating the phenomena occurring in the boundary layer in more detail.

Biometrics encryption combining palmprint with two-layer error correction codes

NASA Astrophysics Data System (ADS)

Li, Hengjian; Qiu, Jian; Dong, Jiwen; Feng, Guang

2017-07-01

To bridge the gap between the fuzziness of biometrics and the exactitude of cryptography, based on combining palmprint with two-layer error correction codes, a novel biometrics encryption method is proposed. Firstly, the randomly generated original keys are encoded by convolutional and cyclic two-layer coding. The first layer uses a convolution code to correct burst errors. The second layer uses cyclic code to correct random errors. Then, the palmprint features are extracted from the palmprint images. Next, they are fused together by XORing operation. The information is stored in a smart card. Finally, the original keys extraction process is the information in the smart card XOR the user's palmprint features and then decoded with convolutional and cyclic two-layer code. The experimental results and security analysis show that it can recover the original keys completely. The proposed method is more secure than a single password factor, and has higher accuracy than a single biometric factor.

Preface.

PubMed

Ditlevsen, Susanne; Lansky, Petr

2016-06-01

This Special Issue of Mathematical Biosciences and Engineering contains 11 selected papers presented at the Neural Coding 2014 workshop. The workshop was held in the royal city of Versailles in France, October 6-10, 2014. This was the 11th of a series of international workshops on this subject, the first held in Prague (1995), then Versailles (1997), Osaka (1999), Plymouth (2001), Aulla (2003), Marburg (2005), Montevideo (2007), Tainan (2009), Limassol (2010), and again in Prague (2012). Also selected papers from Prague were published as a special issue of Mathematical Biosciences and Engineering and in this way a tradition was started. Similarly to the previous workshops, this was a single track multidisciplinary event bringing together experimental and computational neuroscientists. The Neural Coding Workshops are traditionally biennial symposia. They are relatively small in size, interdisciplinary with major emphasis on the search for common principles in neural coding. The workshop was conceived to bring together scientists from different disciplines for an in-depth discussion of mathematical model-building and computational strategies. Further information on the meeting can be found at the NC2014 website at https://colloque6.inra.fr/neural_coding_2014. The meeting was supported by French National Institute for Agricultural Research, the world's leading institution in this field. This Special Issue of Mathematical Biosciences and Engineering contains 11 selected papers presented at the Neural Coding 2014 workshop. The workshop was held in the royal city of Versailles in France, October 6-10, 2014. This was the 11th of a series of international workshops on this subject, the first held in Prague (1995), then Versailles (1997), Osaka (1999), Plymouth (2001), Aulla (2003), Marburg (2005), Montevideo (2007), Tainan (2009), Limassol (2010), and again in Prague (2012). Also selected papers from Prague were published as a special issue of Mathematical Biosciences and Engineering and in this way a tradition was started. Similarly to the previous workshops, this was a single track multidisciplinary event bringing together experimental and computational neuroscientists. The Neural Coding Workshops are traditionally biennial symposia. They are relatively small in size, interdisciplinary with major emphasis on the search for common principles in neural coding. The workshop was conceived to bring together scientists from different disciplines for an in-depth discussion of mathematical model-building and computational strategies. Further information on the meeting can be found at the NC2014 website at https://colloque6.inra.fr/neural_coding_2014. The meeting was supported by French National Institute for Agricultural Research, the world's leading institution in this field. Understanding how the brain processes information is one of the most challenging subjects in neuroscience. The papers presented in this special issue show a small corner of the huge diversity of this field, and illustrate how scientists with different backgrounds approach this vast subject. The diversity of disciplines engaged in these investigations is remarkable: biologists, mathematicians, physicists, psychologists, computer scientists, and statisticians, all have original tools and ideas by which to try to elucidate the underlying mechanisms. In this issue, emphasis is put on mathematical modeling of single neurons. A variety of problems in computational neuroscience accompanied with a rich diversity of mathematical tools and approaches are presented. We hope it will inspire and challenge the readers in their own research. We would like to thank the authors for their valuable contributions and the referees for their priceless effort of reviewing the manuscripts. Finally, we would like to thank Yang Kuang for supporting us and making this publication possible.

Comparison of two computer codes for crack growth analysis: NASCRAC Versus NASA/FLAGRO

NASA Technical Reports Server (NTRS)

Stallworth, R.; Meyers, C. A.; Stinson, H. C.

1989-01-01

Results are presented from the comparison study of two computer codes for crack growth analysis - NASCRAC and NASA/FLAGRO. The two computer codes gave compatible conservative results when the part through crack analysis solutions were analyzed versus experimental test data. Results showed good correlation between the codes for the through crack at a lug solution. For the through crack at a lug solution, NASA/FLAGRO gave the most conservative results.

Reaction path of energetic materials using THOR code

NASA Astrophysics Data System (ADS)

Duraes, L.; Campos, J.; Portugal, A.

1997-07-01

The method of predicting reaction path, using a thermochemical computer code, named THOR, allows for isobar and isochor adiabatic combustion and CJ detonation regimes, the calculation of the composition and thermodynamic properties of reaction products of energetic materials. THOR code assumes the thermodynamic equilibria of all possible products, for the minimum Gibbs free energy, using a thermal equation of state (EoS). The used HL EoS is a new EoS developed in previous works. HL EoS is supported by a Boltzmann EoS, taking α =13.5 to the exponent of the intermolecular potential and θ=1.4 to the adimensional temperature. This code allows now the possibility of estimating various sets of reaction products, obtained successively by the decomposition of the original reacting compound, as a function of the released energy. Two case studies of thermal decomposition procedure were selected, described, calculated and discussed - Ammonium Nitrate based explosives and Nitromethane - because they are very known explosives and their equivalence ratio is respectively near and greater than the stoicheiometry. Predictions of detonation properties of other condensed explosives, as a function of energy release, present results in good correlation with experimental values.

THR-TH: a high-temperature gas-cooled nuclear reactor core thermal hydraulics code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondy, D.R.

1984-07-01

The ORNL version of PEBBLE, the (RZ) pebble bed thermal hydraulics code, has been extended for application to a prismatic gas cooled reactor core. The supplemental treatment is of one-dimensional coolant flow in up to a three-dimensional core description. Power density data from a neutronics and exposure calculation are used as the basic information for the thermal hydraulics calculation of heat removal. Two-dimensional neutronics results may be expanded for a three-dimensional hydraulics calculation. The geometric description for the hydraulics problem is the same as used by the neutronics code. A two-dimensional thermal cell model is used to predict temperatures inmore » the fuel channel. The capability is available in the local BOLD VENTURE computation system for reactor core analysis with capability to account for the effect of temperature feedback by nuclear cross section correlation. Some enhancements have also been added to the original code to add pebble bed modeling flexibility and to generate useful auxiliary results. For example, an estimate is made of the distribution of fuel temperatures based on average and extreme conditions regularly calculated at a number of locations.« less

Performance of a Light-Weight Ablative Thermal Protection Material for the Stardust Mission Sample Return Capsule

NASA Technical Reports Server (NTRS)

Covington, M. A.

2005-01-01

New tests and analyses are reported that were carried out to resolve testing uncertainties in the original development and qualification of a lightweight ablative material used for the Stardust spacecraft forebody heat shield. These additional arcjet tests and analyses confirmed the ablative and thermal performance of low density Phenolic Impregnated Carbon Ablator (PICA) material used for the Stardust design. Testing was done under conditions that simulate the peak convective heating conditions (1200 W/cm2 and 0.5 atm) expected during Earth entry of the Stardust Sample Return Capsule. Test data and predictions from an ablative material response computer code for the in-depth temperatures were compared to guide iterative adjustment of material thermophysical properties used in the code so that the measured and predicted temperatures agreed. The PICA recession rates and maximum internal temperatures were satisfactorily predicted by the computer code with the revised properties. Predicted recession rates were also in acceptable agreement with measured rates for heating conditions 37% greater than the nominal peak heating rate of 1200 W/sq cm. The measured in-depth temperature response data show consistent temperature rise deviations that may be caused by an undocumented endothermic process within the PICA material that is not accurately modeled by the computer code. Predictions of the Stardust heat shield performance based on the present evaluation provide evidence that the maximum adhesive bondline temperature will be much lower than the maximum allowable of 250 C and an earlier design prediction. The re-evaluation also suggests that even with a 25 percent increase in peak heating rates, the total recession of the heat shield would be a small fraction of the as-designed thickness. These results give confidence in the Stardust heat shield design and confirm the potential of PICA material for use in new planetary probe and sample return applications.

Computational Predictions of the Performance Wright 'Bent End' Propellers

NASA Technical Reports Server (NTRS)

Wang, Xiang-Yu; Ash, Robert L.; Bobbitt, Percy J.; Prior, Edwin (Technical Monitor)

2002-01-01

Computational analysis of two 1911 Wright brothers 'Bent End' wooden propeller reproductions have been performed and compared with experimental test results from the Langley Full Scale Wind Tunnel. The purpose of the analysis was to check the consistency of the experimental results and to validate the reliability of the tests. This report is one part of the project on the propeller performance research of the Wright 'Bent End' propellers, intend to document the Wright brothers' pioneering propeller design contributions. Two computer codes were used in the computational predictions. The FLO-MG Navier-Stokes code is a CFD (Computational Fluid Dynamics) code based on the Navier-Stokes Equations. It is mainly used to compute the lift coefficient and the drag coefficient at specified angles of attack at different radii. Those calculated data are the intermediate results of the computation and a part of the necessary input for the Propeller Design Analysis Code (based on Adkins and Libeck method), which is a propeller design code used to compute the propeller thrust coefficient, the propeller power coefficient and the propeller propulsive efficiency.

The Computational Infrastructure for Geodynamics as a Community of Practice

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2016-12-01

Computational Infrastructure for Geodynamics (CIG), geodynamics.org, originated in 2005 out of community recognition that the efforts of individual or small groups of researchers to develop scientifically-sound software is impossible to sustain, duplicates effort, and makes it difficult for scientists to adopt state-of-the art computational methods that promote new discovery. As a community of practice, participants in CIG share an interest in computational modeling in geodynamics and work together on open source software to build the capacity to support complex, extensible, scalable, interoperable, reliable, and reusable software in an effort to increase the return on investment in scientific software development and increase the quality of the resulting software. The group interacts regularly to learn from each other and better their practices formally through webinar series, workshops, and tutorials and informally through listservs and hackathons. Over the past decade, we have learned that successful scientific software development requires at a minimum: collaboration between domain-expert researchers, software developers and computational scientists; clearly identified and committed lead developer(s); well-defined scientific and computational goals that are regularly evaluated and updated; well-defined benchmarks and testing throughout development; attention throughout development to usability and extensibility; understanding and evaluation of the complexity of dependent libraries; and managed user expectations through education, training, and support. CIG's code donation standards provide the basis for recently formalized best practices in software development (geodynamics.org/cig/dev/best-practices/). Best practices include use of version control; widely used, open source software libraries; extensive test suites; portable configuration and build systems; extensive documentation internal and external to the code; and structured, human readable input formats.

Highly Scalable Asynchronous Computing Method for Partial Differential Equations: A Path Towards Exascale

NASA Astrophysics Data System (ADS)

Konduri, Aditya

Many natural and engineering systems are governed by nonlinear partial differential equations (PDEs) which result in a multiscale phenomena, e.g. turbulent flows. Numerical simulations of these problems are computationally very expensive and demand for extreme levels of parallelism. At realistic conditions, simulations are being carried out on massively parallel computers with hundreds of thousands of processing elements (PEs). It has been observed that communication between PEs as well as their synchronization at these extreme scales take up a significant portion of the total simulation time and result in poor scalability of codes. This issue is likely to pose a bottleneck in scalability of codes on future Exascale systems. In this work, we propose an asynchronous computing algorithm based on widely used finite difference methods to solve PDEs in which synchronization between PEs due to communication is relaxed at a mathematical level. We show that while stability is conserved when schemes are used asynchronously, accuracy is greatly degraded. Since message arrivals at PEs are random processes, so is the behavior of the error. We propose a new statistical framework in which we show that average errors drop always to first-order regardless of the original scheme. We propose new asynchrony-tolerant schemes that maintain accuracy when synchronization is relaxed. The quality of the solution is shown to depend, not only on the physical phenomena and numerical schemes, but also on the characteristics of the computing machine. A novel algorithm using remote memory access communications has been developed to demonstrate excellent scalability of the method for large-scale computing. Finally, we present a path to extend this method in solving complex multi-scale problems on Exascale machines.

Proceduracy: Computer Code Writing in the Continuum of Literacy

ERIC Educational Resources Information Center

Vee, Annette

2010-01-01

This dissertation looks at computer programming through the lens of literacy studies, building from the concept of code as a written text with expressive and rhetorical power. I focus on the intersecting technological and social factors of computer code writing as a literacy--a practice I call "proceduracy". Like literacy, proceduracy is a human…

Computer Code Aids Design Of Wings

NASA Technical Reports Server (NTRS)

Carlson, Harry W.; Darden, Christine M.

1993-01-01

AERO2S computer code developed to aid design engineers in selection and evaluation of aerodynamically efficient wing/canard and wing/horizontal-tail configurations that includes simple hinged-flap systems. Code rapidly estimates longitudinal aerodynamic characteristics of conceptual airplane lifting-surface arrangements. Developed in FORTRAN V on CDC 6000 computer system, and ported to MS-DOS environment.

Grid2: A Program for Rapid Estimation of the Jovian Radiation Environment: A Numeric Implementation of the GIRE2 Jovian Radiation Model for Estimating Trapped Radiation for Mission Concept Studies

NASA Technical Reports Server (NTRS)

Evans, R. W.; Brinza, D. E.

2014-01-01

Grid2 is a program that utilizes the Galileo Interim Radiation Electron model 2 (GIRE2) Jovian radiation model to compute fluences and doses for Jupiter missions. (Note: The iterations of these two softwares have been GIRE and GIRE2; likewise Grid and Grid2.) While GIRE2 is an important improvement over the original GIRE radiation model, the GIRE2 model can take as long as a day or more to compute these quantities for a complete mission. Grid2 fits the results of the detailed GIRE2 code with a set of grids in local time and position thereby greatly speeding up the execution of the model--minutes as opposed to days. The Grid2 model covers the time period from 1971 to 2050and distances of 1.03 to 30 Jovian diameters (Rj). It is available as a direct-access database through a FORTRAN interface program. The new database is only slightly larger than the original grid version: 1.5 gigabytes (GB) versus 1.2 GB.

Cloud Computing for Complex Performance Codes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Appel, Gordon John; Hadgu, Teklu; Klein, Brandon Thorin

This report describes the use of cloud computing services for running complex public domain performance assessment problems. The work consisted of two phases: Phase 1 was to demonstrate complex codes, on several differently configured servers, could run and compute trivial small scale problems in a commercial cloud infrastructure. Phase 2 focused on proving non-trivial large scale problems could be computed in the commercial cloud environment. The cloud computing effort was successfully applied using codes of interest to the geohydrology and nuclear waste disposal modeling community.

APC: A New Code for Atmospheric Polarization Computations

NASA Technical Reports Server (NTRS)

Korkin, Sergey V.; Lyapustin, Alexei I.; Rozanov, Vladimir V.

2014-01-01

A new polarized radiative transfer code Atmospheric Polarization Computations (APC) is described. The code is based on separation of the diffuse light field into anisotropic and smooth (regular) parts. The anisotropic part is computed analytically. The smooth regular part is computed numerically using the discrete ordinates method. Vertical stratification of the atmosphere, common types of bidirectional surface reflection and scattering by spherical particles or spheroids are included. A particular consideration is given to computation of the bidirectional polarization distribution function (BPDF) of the waved ocean surface.

Installed F/A-18 inlet flow calculations at 30 degrees angle-of-attack: A comparative study

NASA Technical Reports Server (NTRS)

Smith, C. Frederic; Podleski, Steve D.

1994-01-01

NASA Lewis is currently engaged in a research effort as a team member of the High Alpha Technology Program (HATP) within NASA. This program utilizes a specially equipped F/A-18, the High Alpha Research Vehicle (HARV), in an ambitious effort to improve the maneuverability of high-performance military aircraft at low subsonic speed, high angle of attack conditions. The overall objective of the Lewis effort is to develop inlet technology that will ensure efficient airflow delivery to the engine during these maneuvers. One part of the Lewis approach utilizes computational fluid dynamics codes to predict the installed performance of inlets for these highly maneuverable aircraft. Full Navier-Stokes (FNS) calculations on the installed F/A-18 inlet at 30 degrees angle of attack, 0 degrees yaw, and a freestream Mach number of 0.2 have been obtained in this study using an algebraic turbulence model with two grids (original and revised). Results obtained with the original grid were used to determine where further grid refinements and additional geometry were needed. In order to account properly for the external effects, the forebody, leading edge extension (LEX), ramp, and wing were included with inlet geometry. In the original grid, the diverter, LEX slot, and leading edge flap were not included due to insufficient geometry definition, but were included in a revised grid. In addition, a thin-layer Navier-Stokes (TLNS) code is used with the revised grid and the numerical results are compared to those obtained with the FNS code. The TLNS code was used to evaluate the effects on the solution using a code with more recent CFD developments such as upwinding with TVD schemes versus central differencing with artificial dissipation. The calculations are compared to a limited amount of available experimental data. The predicted forebody/fuselage surface static pressures compared well with data of all solutions. The predicted trajectory of the vortex generated under the LEX was different for each solution. These discrepancies are attributed to differences in the grid resolution and turbulence modeling. All solutions predict that this vortex is ingested by the inlet. The predicted inlet total pressure recoveries are lower than data and the distortions are higher than data. The results obtained with the revised grid were significantly improved from the original grid results. The original grid results indicated the ingested vortex migrated to the engine face and caused additional distortions to those already present due to secondary flow development. The revised grid results indicate that the ingested vortex is dissipated along the inlet duct inboard wall. The TLNS results indicate the flow at the engine face was much more distorted than the FNS results and is attributed to the pole boundary condition introducing numerical distortions into the flow field.

Hypercube matrix computation task

NASA Technical Reports Server (NTRS)

Calalo, Ruel H.; Imbriale, William A.; Jacobi, Nathan; Liewer, Paulett C.; Lockhart, Thomas G.; Lyzenga, Gregory A.; Lyons, James R.; Manshadi, Farzin; Patterson, Jean E.

1988-01-01

A major objective of the Hypercube Matrix Computation effort at the Jet Propulsion Laboratory (JPL) is to investigate the applicability of a parallel computing architecture to the solution of large-scale electromagnetic scattering problems. Three scattering analysis codes are being implemented and assessed on a JPL/California Institute of Technology (Caltech) Mark 3 Hypercube. The codes, which utilize different underlying algorithms, give a means of evaluating the general applicability of this parallel architecture. The three analysis codes being implemented are a frequency domain method of moments code, a time domain finite difference code, and a frequency domain finite elements code. These analysis capabilities are being integrated into an electromagnetics interactive analysis workstation which can serve as a design tool for the construction of antennas and other radiating or scattering structures. The first two years of work on the Hypercube Matrix Computation effort is summarized. It includes both new developments and results as well as work previously reported in the Hypercube Matrix Computation Task: Final Report for 1986 to 1987 (JPL Publication 87-18).

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

PubMed Central

José, Marco V.; Govezensky, Tzipe; García, José A.; Bobadilla, Juan R.

2009-01-01

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC. PMID:19183813

Calculation of Water Drop Trajectories to and About Arbitrary Three-Dimensional Bodies in Potential Airflow

NASA Technical Reports Server (NTRS)

Norment, H. G.

1980-01-01

Calculations can be performed for any atmospheric conditions and for all water drop sizes, from the smallest cloud droplet to large raindrops. Any subsonic, external, non-lifting flow can be accommodated; flow into, but not through, inlets also can be simulated. Experimental water drop drag relations are used in the water drop equations of motion and effects of gravity settling are included. Seven codes are described: (1) a code used to debug and plot body surface description data; (2) a code that processes the body surface data to yield the potential flow field; (3) a code that computes flow velocities at arrays of points in space; (4) a code that computes water drop trajectories from an array of points in space; (5) a code that computes water drop trajectories and fluxes to arbitrary target points; (6) a code that computes water drop trajectories tangent to the body; and (7) a code that produces stereo pair plots which include both the body and trajectories. Code descriptions include operating instructions, card inputs and printouts for example problems, and listing of the FORTRAN codes. Accuracy of the calculations is discussed, and trajectory calculation results are compared with prior calculations and with experimental data.

Utilizing GPUs to Accelerate Turbomachinery CFD Codes

NASA Technical Reports Server (NTRS)

MacCalla, Weylin; Kulkarni, Sameer

2016-01-01

GPU computing has established itself as a way to accelerate parallel codes in the high performance computing world. This work focuses on speeding up APNASA, a legacy CFD code used at NASA Glenn Research Center, while also drawing conclusions about the nature of GPU computing and the requirements to make GPGPU worthwhile on legacy codes. Rewriting and restructuring of the source code was avoided to limit the introduction of new bugs. The code was profiled and investigated for parallelization potential, then OpenACC directives were used to indicate parallel parts of the code. The use of OpenACC directives was not able to reduce the runtime of APNASA on either the NVIDIA Tesla discrete graphics card, or the AMD accelerated processing unit. Additionally, it was found that in order to justify the use of GPGPU, the amount of parallel work being done within a kernel would have to greatly exceed the work being done by any one portion of the APNASA code. It was determined that in order for an application like APNASA to be accelerated on the GPU, it should not be modular in nature, and the parallel portions of the code must contain a large portion of the code's computation time.

PASCO: Structural panel analysis and sizing code: Users manual - Revised

NASA Technical Reports Server (NTRS)

Anderson, M. S.; Stroud, W. J.; Durling, B. J.; Hennessy, K. W.

1981-01-01

A computer code denoted PASCO is described for analyzing and sizing uniaxially stiffened composite panels. Buckling and vibration analyses are carried out with a linked plate analysis computer code denoted VIPASA, which is included in PASCO. Sizing is based on nonlinear mathematical programming techniques and employs a computer code denoted CONMIN, also included in PASCO. Design requirements considered are initial buckling, material strength, stiffness and vibration frequency. A user's manual for PASCO is presented.

Computation of Reacting Flows in Combustion Processes

NASA Technical Reports Server (NTRS)

Keith, Theo G., Jr.; Chen, Kuo-Huey

1997-01-01

The main objective of this research was to develop an efficient three-dimensional computer code for chemically reacting flows. The main computer code developed is ALLSPD-3D. The ALLSPD-3D computer program is developed for the calculation of three-dimensional, chemically reacting flows with sprays. The ALL-SPD code employs a coupled, strongly implicit solution procedure for turbulent spray combustion flows. A stochastic droplet model and an efficient method for treatment of the spray source terms in the gas-phase equations are used to calculate the evaporating liquid sprays. The chemistry treatment in the code is general enough that an arbitrary number of reaction and species can be defined by the users. Also, it is written in generalized curvilinear coordinates with both multi-block and flexible internal blockage capabilities to handle complex geometries. In addition, for general industrial combustion applications, the code provides both dilution and transpiration cooling capabilities. The ALLSPD algorithm, which employs the preconditioning and eigenvalue rescaling techniques, is capable of providing efficient solution for flows with a wide range of Mach numbers. Although written for three-dimensional flows in general, the code can be used for two-dimensional and axisymmetric flow computations as well. The code is written in such a way that it can be run in various computer platforms (supercomputers, workstations and parallel processors) and the GUI (Graphical User Interface) should provide a user-friendly tool in setting up and running the code.

The discounting model selector: Statistical software for delay discounting applications.

PubMed

Gilroy, Shawn P; Franck, Christopher T; Hantula, Donald A

2017-05-01

Original, open-source computer software was developed and validated against established delay discounting methods in the literature. The software executed approximate Bayesian model selection methods from user-supplied temporal discounting data and computed the effective delay 50 (ED50) from the best performing model. Software was custom-designed to enable behavior analysts to conveniently apply recent statistical methods to temporal discounting data with the aid of a graphical user interface (GUI). The results of independent validation of the approximate Bayesian model selection methods indicated that the program provided results identical to that of the original source paper and its methods. Monte Carlo simulation (n = 50,000) confirmed that true model was selected most often in each setting. Simulation code and data for this study were posted to an online repository for use by other researchers. The model selection approach was applied to three existing delay discounting data sets from the literature in addition to the data from the source paper. Comparisons of model selected ED50 were consistent with traditional indices of discounting. Conceptual issues related to the development and use of computer software by behavior analysts and the opportunities afforded by free and open-sourced software are discussed and a review of possible expansions of this software are provided. © 2017 Society for the Experimental Analysis of Behavior.

NASA Rotor 37 CFD Code Validation: Glenn-HT Code

NASA Technical Reports Server (NTRS)

Ameri, Ali A.

2010-01-01

In order to advance the goals of NASA aeronautics programs, it is necessary to continuously evaluate and improve the computational tools used for research and design at NASA. One such code is the Glenn-HT code which is used at NASA Glenn Research Center (GRC) for turbomachinery computations. Although the code has been thoroughly validated for turbine heat transfer computations, it has not been utilized for compressors. In this work, Glenn-HT was used to compute the flow in a transonic compressor and comparisons were made to experimental data. The results presented here are in good agreement with this data. Most of the measures of performance are well within the measurement uncertainties and the exit profiles of interest agree with the experimental measurements.

Final report for the Tera Computer TTI CRADA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davidson, G.S.; Pavlakos, C.; Silva, C.

1997-01-01

Tera Computer and Sandia National Laboratories have completed a CRADA, which examined the Tera Multi-Threaded Architecture (MTA) for use with large codes of importance to industry and DOE. The MTA is an innovative architecture that uses parallelism to mask latency between memories and processors. The physical implementation is a parallel computer with high cross-section bandwidth and GaAs processors designed by Tera, which support many small computation threads and fast, lightweight context switches between them. When any thread blocks while waiting for memory accesses to complete, another thread immediately begins execution so that high CPU utilization is maintained. The Tera MTAmore » parallel computer has a single, global address space, which is appealing when porting existing applications to a parallel computer. This ease of porting is further enabled by compiler technology that helps break computations into parallel threads. DOE and Sandia National Laboratories were interested in working with Tera to further develop this computing concept. While Tera Computer would continue the hardware development and compiler research, Sandia National Laboratories would work with Tera to ensure that their compilers worked well with important Sandia codes, most particularly CTH, a shock physics code used for weapon safety computations. In addition to that important code, Sandia National Laboratories would complete research on a robotic path planning code, SANDROS, which is important in manufacturing applications, and would evaluate the MTA performance on this code. Finally, Sandia would work directly with Tera to develop 3D visualization codes, which would be appropriate for use with the MTA. Each of these tasks has been completed to the extent possible, given that Tera has just completed the MTA hardware. All of the CRADA work had to be done on simulators.« less

Analysis of selected data from the triservice missile data base

NASA Technical Reports Server (NTRS)

Allen, Jerry M.; Shaw, David S.; Sawyer, Wallace C.

1989-01-01

An extremely large, systematic, axisymmetric-body/tail-fin data base has been gathered through tests of an innovative missile model design which is described herein. These data were originally obtained for incorporation into a missile aerodynamics code based on engineering methods (Program MISSILE3), but these data are also valuable as diagnostic test cases for developing computational methods because of the individual-fin data included in the data base. Detailed analyses of four sample cases from these data are presented to illustrate interesting individual-fin force and moment trends. These samples quantitatively show how bow shock, fin orientation, fin deflection, and body vortices can produce strong, unusual, and computationally challenging effects on individual fin loads. Flow-visualization photographs are examined to provide physical insight into the cause of these effects.

Neural classification of the selected family of butterflies

NASA Astrophysics Data System (ADS)

Zaborowicz, M.; Boniecki, P.; Piekarska-Boniecka, H.; Koszela, K.; Mueller, W.; Górna, K.; Okoń, P.

2017-07-01

There have been noticed growing explorers' interest in drawing conclusions based on information of data coded in a graphic form. The neuronal identification of pictorial data, with special emphasis on both quantitative and qualitative analysis, is more frequently utilized to gain and deepen the empirical data knowledge. Extraction and then classification of selected picture features, such as color or surface structure, enables one to create computer tools in order to identify these objects presented as, for example, digital pictures. The work presents original computer system "Processing the image v.1.0" designed to digitalize pictures on the basis of color criterion. The system has been applied to generate a reference learning file for generating the Artificial Neural Network (ANN) to identify selected kinds of butterflies from the Papilionidae family.

Operations analysis (study 2.1). Program listing for the LOVES computer code

NASA Technical Reports Server (NTRS)

Wray, S. T., Jr.

1974-01-01

A listing of the LOVES computer program is presented. The program is coded partially in SIMSCRIPT and FORTRAN. This version of LOVES is compatible with both the CDC 7600 and the UNIVAC 1108 computers. The code has been compiled, loaded, and executed successfully on the EXEC 8 system for the UNIVAC 1108.

Analysis of the Length of Braille Texts in English Braille American Edition, the Nemeth Code, and Computer Braille Code versus the Unified English Braille Code

ERIC Educational Resources Information Center

Knowlton, Marie; Wetzel, Robin

2006-01-01

This study compared the length of text in English Braille American Edition, the Nemeth code, and the computer braille code with the Unified English Braille Code (UEBC)--also known as Unified English Braille (UEB). The findings indicate that differences in the length of text are dependent on the type of material that is transcribed and the grade…

A MATLAB based 3D modeling and inversion code for MT data

NASA Astrophysics Data System (ADS)

Singh, Arun; Dehiya, Rahul; Gupta, Pravin K.; Israil, M.

2017-07-01

The development of a MATLAB based computer code, AP3DMT, for modeling and inversion of 3D Magnetotelluric (MT) data is presented. The code comprises two independent components: grid generator code and modeling/inversion code. The grid generator code performs model discretization and acts as an interface by generating various I/O files. The inversion code performs core computations in modular form - forward modeling, data functionals, sensitivity computations and regularization. These modules can be readily extended to other similar inverse problems like Controlled-Source EM (CSEM). The modular structure of the code provides a framework useful for implementation of new applications and inversion algorithms. The use of MATLAB and its libraries makes it more compact and user friendly. The code has been validated on several published models. To demonstrate its versatility and capabilities the results of inversion for two complex models are presented.

The role of the PIRT process in identifying code improvements and executing code development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, G.E.; Boyack, B.E.

1997-07-01

In September 1988, the USNRC issued a revised ECCS rule for light water reactors that allows, as an option, the use of best estimate (BE) plus uncertainty methods in safety analysis. The key feature of this licensing option relates to quantification of the uncertainty in the determination that an NPP has a {open_quotes}low{close_quotes} probability of violating the safety criteria specified in 10 CFR 50. To support the 1988 licensing revision, the USNRC and its contractors developed the CSAU evaluation methodology to demonstrate the feasibility of the BE plus uncertainty approach. The PIRT process, Step 3 in the CSAU methodology, wasmore » originally formulated to support the BE plus uncertainty licensing option as executed in the CSAU approach to safety analysis. Subsequent work has shown the PIRT process to be a much more powerful tool than conceived in its original form. Through further development and application, the PIRT process has shown itself to be a robust means to establish safety analysis computer code phenomenological requirements in their order of importance to such analyses. Used early in research directed toward these objectives, PIRT results also provide the technical basis and cost effective organization for new experimental programs needed to improve the safety analysis codes for new applications. The primary purpose of this paper is to describe the generic PIRT process, including typical and common illustrations from prior applications. The secondary objective is to provide guidance to future applications of the process to help them focus, in a graded approach, on systems, components, processes and phenomena that have been common in several prior applications.« less

Applications of automatic differentiation in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Carle, A.; Bischof, C.; Haigler, Kara J.; Newman, Perry A.

1994-01-01

Automatic differentiation (AD) is a powerful computational method that provides for computing exact sensitivity derivatives (SD) from existing computer programs for multidisciplinary design optimization (MDO) or in sensitivity analysis. A pre-compiler AD tool for FORTRAN programs called ADIFOR has been developed. The ADIFOR tool has been easily and quickly applied by NASA Langley researchers to assess the feasibility and computational impact of AD in MDO with several different FORTRAN programs. These include a state-of-the-art three dimensional multigrid Navier-Stokes flow solver for wings or aircraft configurations in transonic turbulent flow. With ADIFOR the user specifies sets of independent and dependent variables with an existing computer code. ADIFOR then traces the dependency path throughout the code, applies the chain rule to formulate derivative expressions, and generates new code to compute the required SD matrix. The resulting codes have been verified to compute exact non-geometric and geometric SD for a variety of cases. in less time than is required to compute the SD matrix using centered divided differences.

Fundamentals, current state of the development of, and prospects for further improvement of the new-generation thermal-hydraulic computational HYDRA-IBRAE/LM code for simulation of fast reactor systems

NASA Astrophysics Data System (ADS)

Alipchenkov, V. M.; Anfimov, A. M.; Afremov, D. A.; Gorbunov, V. S.; Zeigarnik, Yu. A.; Kudryavtsev, A. V.; Osipov, S. L.; Mosunova, N. A.; Strizhov, V. F.; Usov, E. V.

2016-02-01

The conceptual fundamentals of the development of the new-generation system thermal-hydraulic computational HYDRA-IBRAE/LM code are presented. The code is intended to simulate the thermalhydraulic processes that take place in the loops and the heat-exchange equipment of liquid-metal cooled fast reactor systems under normal operation and anticipated operational occurrences and during accidents. The paper provides a brief overview of Russian and foreign system thermal-hydraulic codes for modeling liquid-metal coolants and gives grounds for the necessity of development of a new-generation HYDRA-IBRAE/LM code. Considering the specific engineering features of the nuclear power plants (NPPs) equipped with the BN-1200 and the BREST-OD-300 reactors, the processes and the phenomena are singled out that require a detailed analysis and development of the models to be correctly described by the system thermal-hydraulic code in question. Information on the functionality of the computational code is provided, viz., the thermalhydraulic two-phase model, the properties of the sodium and the lead coolants, the closing equations for simulation of the heat-mass exchange processes, the models to describe the processes that take place during the steam-generator tube rupture, etc. The article gives a brief overview of the usability of the computational code, including a description of the support documentation and the supply package, as well as possibilities of taking advantages of the modern computer technologies, such as parallel computations. The paper shows the current state of verification and validation of the computational code; it also presents information on the principles of constructing of and populating the verification matrices for the BREST-OD-300 and the BN-1200 reactor systems. The prospects are outlined for further development of the HYDRA-IBRAE/LM code, introduction of new models into it, and enhancement of its usability. It is shown that the program of development and practical application of the code will allow carrying out in the nearest future the computations to analyze the safety of potential NPP projects at a qualitatively higher level.

Performance assessment of KORAT-3D on the ANL IBM-SP computer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexeyev, A.V.; Zvenigorodskaya, O.A.; Shagaliev, R.M.

1999-09-01

The TENAR code is currently being developed at the Russian Federal Nuclear Center (VNIIEF) as a coupled dynamics code for the simulation of transients in VVER and RBMK systems and other nuclear systems. The neutronic module in this code system is KORAT-3D. This module is also one of the most computationally intensive components of the code system. A parallel version of KORAT-3D has been implemented to achieve the goal of obtaining transient solutions in reasonable computational time, particularly for RBMK calculations that involve the application of >100,000 nodes. An evaluation of the KORAT-3D code performance was recently undertaken on themore » Argonne National Laboratory (ANL) IBM ScalablePower (SP) parallel computer located in the Mathematics and Computer Science Division of ANL. At the time of the study, the ANL IBM-SP computer had 80 processors. This study was conducted under the auspices of a technical staff exchange program sponsored by the International Nuclear Safety Center (INSC).« less

Profugus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, Thomas; Hamilton, Steven; Slattery, Stuart

Profugus is an open-source mini-application (mini-app) for radiation transport and reactor applications. It contains the fundamental computational kernels used in the Exnihilo code suite from Oak Ridge National Laboratory. However, Exnihilo is production code with a substantial user base. Furthermore, Exnihilo is export controlled. This makes collaboration with computer scientists and computer engineers difficult. Profugus is designed to bridge that gap. By encapsulating the core numerical algorithms in an abbreviated code base that is open-source, computer scientists can analyze the algorithms and easily make code-architectural changes to test performance without compromising the production code values of Exnihilo. Profugus is notmore » meant to be production software with respect to problem analysis. The computational kernels in Profugus are designed to analyze performance, not correctness. Nonetheless, users of Profugus can setup and run problems with enough real-world features to be useful as proof-of-concept for actual production work.« less

Practical color vision tests for air traffic control applicants: en route center and terminal facilities.

PubMed

Mertens, H W; Milburn, N J; Collins, W E

2000-12-01

Two practical color vision tests were developed and validated for use in screening Air Traffic Control Specialist (ATCS) applicants for work at en route center or terminal facilities. The development of the tests involved careful reproduction/simulation of color-coded materials from the most demanding, safety-critical color task performed in each type of facility. The tests were evaluated using 106 subjects with normal color vision and 85 with color vision deficiency. The en route center test, named the Flight Progress Strips Test (FPST), required the identification of critical red/black coding in computer printing and handwriting on flight progress strips. The terminal option test, named the Aviation Lights Test (ALT), simulated red/green/white aircraft lights that must be identified in night ATC tower operations. Color-coding is a non-redundant source of safety-critical information in both tasks. The FPST was validated by direct comparison of responses to strip reproductions with responses to the original flight progress strips and a set of strips selected independently. Validity was high; Kappa = 0.91 with original strips as the validation criterion and 0.86 with different strips. The light point stimuli of the ALT were validated physically with a spectroradiometer. The reliabilities of the FPST and ALT were estimated with Chronbach's alpha as 0.93 and 0.98, respectively. The high job-relevance, validity, and reliability of these tests increases the effectiveness and fairness of ATCS color vision testing.

Fast H.264/AVC FRExt intra coding using belief propagation.

PubMed

Milani, Simone

2011-01-01

In the H.264/AVC FRExt coder, the coding performance of Intra coding significantly overcomes the previous still image coding standards, like JPEG2000, thanks to a massive use of spatial prediction. Unfortunately, the adoption of an extensive set of predictors induces a significant increase of the computational complexity required by the rate-distortion optimization routine. The paper presents a complexity reduction strategy that aims at reducing the computational load of the Intra coding with a small loss in the compression performance. The proposed algorithm relies on selecting a reduced set of prediction modes according to their probabilities, which are estimated adopting a belief-propagation procedure. Experimental results show that the proposed method permits saving up to 60 % of the coding time required by an exhaustive rate-distortion optimization method with a negligible loss in performance. Moreover, it permits an accurate control of the computational complexity unlike other methods where the computational complexity depends upon the coded sequence.

2,445 Hours of Code: What I Learned from Facilitating Hour of Code Events in High School Libraries

ERIC Educational Resources Information Center

Colby, Jennifer

2015-01-01

This article describes a school librarian's experience with initiating an Hour of Code event for her school's student body. Hadi Partovi of Code.org conceived the Hour of Code "to get ten million students to try one hour of computer science" (Partovi, 2013a), which is implemented during Computer Science Education Week with a goal of…

Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

1991-01-01

Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

User's Manual for FEMOM3DR. Version 1.0

NASA Technical Reports Server (NTRS)

Reddy, C. J.

1998-01-01

FEMoM3DR is a computer code written in FORTRAN 77 to compute radiation characteristics of antennas on 3D body using combined Finite Element Method (FEM)/Method of Moments (MoM) technique. The code is written to handle different feeding structures like coaxial line, rectangular waveguide, and circular waveguide. This code uses the tetrahedral elements, with vector edge basis functions for FEM and triangular elements with roof-top basis functions for MoM. By virtue of FEM, this code can handle any arbitrary shaped three dimensional bodies with inhomogeneous lossy materials; and due to MoM the computational domain can be terminated in any arbitrary shape. The User's Manual is written to make the user acquainted with the operation of the code. The user is assumed to be familiar with the FORTRAN 77 language and the operating environment of the computers on which the code is intended to run.

Selection of a computer code for Hanford low-level waste engineered-system performance assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGrail, B.P.; Mahoney, L.A.

Planned performance assessments for the proposed disposal of low-level waste (LLW) glass produced from remediation of wastes stored in underground tanks at Hanford, Washington will require calculations of radionuclide release rates from the subsurface disposal facility. These calculations will be done with the aid of computer codes. Currently available computer codes were ranked in terms of the feature sets implemented in the code that match a set of physical, chemical, numerical, and functional capabilities needed to assess release rates from the engineered system. The needed capabilities were identified from an analysis of the important physical and chemical process expected tomore » affect LLW glass corrosion and the mobility of radionuclides. The highest ranked computer code was found to be the ARES-CT code developed at PNL for the US Department of Energy for evaluation of and land disposal sites.« less

Optimization of a Lattice Boltzmann Computation on State-of-the-Art Multicore Platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Samuel; Carter, Jonathan; Oliker, Leonid

2009-04-10

We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Xeon E5345 (Clovertown), AMD Opteron 2214 (Santa Rosa), AMD Opteron 2356 (Barcelona), Sun T5140 T2+ (Victoria Falls), as well asmore » a QS20 IBM Cell Blade. Rather than hand-tuning LBMHD for each system, we develop a code generator that allows us to identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto-tuned LBMHD application achieves up to a 15x improvement compared with the original code at a given concurrency. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications.« less

User's manual for a material transport code on the Octopus Computer Network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Naymik, T.G.; Mendez, G.D.

1978-09-15

A code to simulate material transport through porous media was developed at Oak Ridge National Laboratory. This code has been modified and adapted for use at Lawrence Livermore Laboratory. This manual, in conjunction with report ORNL-4928, explains the input, output, and execution of the code on the Octopus Computer Network.

Advanced Applications of Adifor 3.0 for Efficient Calculation of First-and Second-Order CFD Sensitivity Derivatives

NASA Technical Reports Server (NTRS)

Taylor, Arthur C., III

2004-01-01

This final report will document the accomplishments of the work of this project. 1) The incremental-iterative (II) form of the reverse-mode (adjoint) method for computing first-order (FO) aerodynamic sensitivity derivatives (SDs) has been successfully implemented and tested in a 2D CFD code (called ANSERS) using the reverse-mode capability of ADIFOR 3.0. These preceding results compared very well with similar SDS computed via a black-box (BB) application of the reverse-mode capability of ADIFOR 3.0, and also with similar SDs calculated via the method of finite differences. 2) Second-order (SO) SDs have been implemented in the 2D ASNWERS code using the very efficient strategy that was originally proposed (but not previously tested) of Reference 3, Appendix A. Furthermore, these SO SOs have been validated for accuracy and computational efficiency. 3) Studies were conducted in Quasi-1D and 2D concerning the smoothness (or lack of smoothness) of the FO and SO SD's for flows with shock waves. The phenomenon is documented in the publications of this study (listed subsequently), however, the specific numerical mechanism which is responsible for this unsmoothness phenomenon was not discovered. 4) The FO and SO derivatives for Quasi-1D and 2D flows were applied to predict aerodynamic design uncertainties, and were also applied in robust design optimization studies.

Toward an Improvement of the Analysis of Neural Coding.

PubMed

Alegre-Cortés, Javier; Soto-Sánchez, Cristina; Albarracín, Ana L; Farfán, Fernando D; Val-Calvo, Mikel; Ferrandez, José M; Fernandez, Eduardo

2017-01-01

Machine learning and artificial intelligence have strong roots on principles of neural computation. Some examples are the structure of the first perceptron, inspired in the retina, neuroprosthetics based on ganglion cell recordings or Hopfield networks. In addition, machine learning provides a powerful set of tools to analyze neural data, which has already proved its efficacy in so distant fields of research as speech recognition, behavioral states classification, or LFP recordings. However, despite the huge technological advances in neural data reduction of dimensionality, pattern selection, and clustering during the last years, there has not been a proportional development of the analytical tools used for Time-Frequency (T-F) analysis in neuroscience. Bearing this in mind, we introduce the convenience of using non-linear, non-stationary tools, EMD algorithms in particular, for the transformation of the oscillatory neural data (EEG, EMG, spike oscillations…) into the T-F domain prior to its analysis with machine learning tools. We support that to achieve meaningful conclusions, the transformed data we analyze has to be as faithful as possible to the original recording, so that the transformations forced into the data due to restrictions in the T-F computation are not extended to the results of the machine learning analysis. Moreover, bioinspired computation such as brain-machine interface may be enriched from a more precise definition of neuronal coding where non-linearities of the neuronal dynamics are considered.

Compact Models for Defect Diffusivity in Semiconductor Alloys.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, Alan F.; Modine, Normand A.; Lee, Stephen R.

Predicting transient effects caused by short - pulse neutron irradiation of electronic devices is an important part of Sandia's mission. For example , predicting the diffusion of radiation - induced point defects is needed with in Sandia's Qualification Alternative to the Sandia Pulsed Reactor (QASPR) pro gram since defect diffusion mediates transient gain recovery in QASPR electronic devices. Recently, the semiconductors used to fabricate radiation - hard electronic devices have begun to shift from silicon to III - V compounds such as GaAs, InAs , GaP and InP . An advantage of this shift is that it allows engineers tomore » optimize the radiation hardness of electronic devices by using alloy s such as InGaAs and InGaP . However, the computer codes currently being used to simulate transient radiation effects in QASP R devices will need to be modified since they presume that defect properties (charge states, energy levels, and diffusivities) in these alloys do not change with time. This is not realistic since the energy and properties of a defect depend on the types of atoms near it and , therefore, on its location in the alloy. In particular, radiation - induced defects are created at nearly random locations in an alloy and the distribution of their local environments - and thus their energies and properties - evolves with time as the defects diffuse through the alloy . To incorporate these consequential effects into computer codes used to simulate transient radiation effects, we have developed procedures to accurately compute the time dependence of defect energies and properties and then formulate them within compact models that can be employed in these computer codes. In this document, we demonstrate these procedures for the case of the highly mobile P interstitial (I P ) in an InGaP alloy. Further dissemination only as authorized to U.S. Government agencies and their contractors; other requests shall be approved by the originating facility or higher DOE programmatic authority.« less

Performance analysis of three dimensional integral equation computations on a massively parallel computer. M.S. Thesis

NASA Technical Reports Server (NTRS)

Logan, Terry G.

1994-01-01

The purpose of this study is to investigate the performance of the integral equation computations using numerical source field-panel method in a massively parallel processing (MPP) environment. A comparative study of computational performance of the MPP CM-5 computer and conventional Cray-YMP supercomputer for a three-dimensional flow problem is made. A serial FORTRAN code is converted into a parallel CM-FORTRAN code. Some performance results are obtained on CM-5 with 32, 62, 128 nodes along with those on Cray-YMP with a single processor. The comparison of the performance indicates that the parallel CM-FORTRAN code near or out-performs the equivalent serial FORTRAN code for some cases.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexander E; Gschwind, Michael K; Gunnels, John A

2013-10-29

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexandre E [Chappaqua, NY; Gschwind, Michael K [Chappaqua, NY; Gunnels, John A [Yorktown Heights, NY

2012-08-28

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Computer Description of the M561 Utility Truck

DTIC Science & Technology

1984-10-01

GIFT Computer Code Sustainabi1ity Predictions for Army Spare Components Requirements for Combat (SPARC) 20. ABSTRACT (Caotfmia «a NWM eitim ft...used as input to the GIFT computer code to generate target vulnerability data. DO FORM V JAM 73 1473 EDITION OF I NOV 65 IS OBSOLETE Unclass i f ied...anaLyiis requires input from the Geometric Information for Targets ( GIFT ) ’ computer code. This report documents the combina- torial geometry (Com-Geom

TEMPEST: A three-dimensional time-dependent computer program for hydrothermal analysis: Volume 2, Assessment and verification results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eyler, L L; Trent, D S; Budden, M J

During the course of the TEMPEST computer code development a concurrent effort was conducted to assess the code's performance and the validity of computed results. The results of this work are presented in this document. The principal objective of this effort was to assure the code's computational correctness for a wide range of hydrothermal phenomena typical of fast breeder reactor application. 47 refs., 94 figs., 6 tabs.

The influence of commenting validity, placement, and style on perceptions of computer code trustworthiness: A heuristic-systematic processing approach.

PubMed

Alarcon, Gene M; Gamble, Rose F; Ryan, Tyler J; Walter, Charles; Jessup, Sarah A; Wood, David W; Capiola, August

2018-07-01

Computer programs are a ubiquitous part of modern society, yet little is known about the psychological processes that underlie reviewing code. We applied the heuristic-systematic model (HSM) to investigate the influence of computer code comments on perceptions of code trustworthiness. The study explored the influence of validity, placement, and style of comments in code on trustworthiness perceptions and time spent on code. Results indicated valid comments led to higher trust assessments and more time spent on the code. Properly placed comments led to lower trust assessments and had a marginal effect on time spent on code; however, the effect was no longer significant after controlling for effects of the source code. Low style comments led to marginally higher trustworthiness assessments, but high style comments led to longer time spent on the code. Several interactions were also found. Our findings suggest the relationship between code comments and perceptions of code trustworthiness is not as straightforward as previously thought. Additionally, the current paper extends the HSM to the programming literature. Copyright © 2018 Elsevier Ltd. All rights reserved.

Adiabatic topological quantum computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Adiabatic topological quantum computing

DOE PAGES

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave; ...

2015-07-31

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Coil Design for Low Aspect Ratio Stellarators

NASA Astrophysics Data System (ADS)

Miner, W. H., Jr.; Valanju, P. M.; Wiley, J. C.; Hirshman, S. P.; Whitson, J. C.

1998-11-01

Two compact stellarator designs have recently been under investigation because of their potential as a reactor featuring steady-state, disruption-free operation, low recirculating power and good confinement and beta. Both quasi-axisymmetric (QA) equilibria and quasi-omnigenous (QO) equilibria have been obtained by using the 3-D MHD equilibrium code VMEC. In order to build an experiment, coil sets must be obtained that are compatable with these equilibria. We have been using both the NESCOIL(Merkel, P., Nucl. Fus. 27, 5 (1987) 867.) code and the COILOPT code to find coilsets for both of these types of equilibria. We are considering three types of coil configurations. The first is a combination of modular coils and vertical field coils. The second configuration is a combination of toroidal field coils, vertical field coils and saddle coils. A third configuration is a combination of modular coils and a single helical winding. The quality of each coil set will be evaluated by computing its magnetic field and using that as input to VMEC in free boundary mode to see how accurately the original equilibrium can be reconstructed.

Fast Computation of the Two-Point Correlation Function in the Age of Big Data

NASA Astrophysics Data System (ADS)

Pellegrino, Andrew; Timlin, John

2018-01-01

We present a new code which quickly computes the two-point correlation function for large sets of astronomical data. This code combines the ease of use of Python with the speed of parallel shared libraries written in C. We include the capability to compute the auto- and cross-correlation statistics, and allow the user to calculate the three-dimensional and angular correlation functions. Additionally, the code automatically divides the user-provided sky masks into contiguous subsamples of similar size, using the HEALPix pixelization scheme, for the purpose of resampling. Errors are computed using jackknife and bootstrap resampling in a way that adds negligible extra runtime, even with many subsamples. We demonstrate comparable speed with other clustering codes, and code accuracy compared to known and analytic results.

Grid generation about complex three-dimensional aircraft configurations

NASA Technical Reports Server (NTRS)

Klopfer, Goetz H.

1991-01-01

The problem of obtaining three dimensional grids with sufficient resolution to resolve all the flow or other physical features of interest is addressed. The generation of a computational grid involves a series of compromises to resolve several conflicting requirements. On one hand, one would like the grid to be fine enough and not too skewed to reduce the numerical errors and to adequately resolve the pertinent physical features of the flow field about the aircraft. On the other hand, the capabilities of present or even future supercomputers are finite and the number of mesh points must be limited to a reasonable number: one which is usually much less than desired for numerical accuracy. One technique to overcome this limitation is the 'zonal' grid approach. In this method, the overall field is subdivided into smaller zones or blocks in each of which an independent grid is generated with enough grid density to resolve the flow features in that zone. The zonal boundaries or interfaces require special boundary conditions such that the conservation properties of the governing equations are observed. Much work was done in 3-D zonal approaches with nonconservative zonal interfaces. A 3-D zonal conservative interfacing method that is efficient and easy to implement was developed during the past year. During the course of the work, it became apparent that it would be much more feasible to do the conservative interfacing with cell-centered finite volume codes instead of the originally planned finite difference codes. Accordingly, the CNS code was converted to finite volume form. This new version of the code is named CNSFV. The original multi-zonal interfacing capability of the CNS code was enhanced by generalizing the procedure to allow for completely arbitrarily shaped zones with no mesh continuity between the zones. While this zoning capability works well for most flow situations, it is, however, still nonconservative. The conservative interface algorithm was also implemented but was not completely validated.

On-board attitude determination for the Explorer Platform satellite

NASA Technical Reports Server (NTRS)

Jayaraman, C.; Class, B.

1992-01-01

This paper describes the attitude determination algorithm for the Explorer Platform satellite. The algorithm, which is baselined on the Landsat code, is a six-element linear quadratic state estimation processor, in the form of a Kalman filter augmented by an adaptive filter process. Improvements to the original Landsat algorithm were required to meet mission pointing requirements. These consisted of a more efficient sensor processing algorithm and the addition of an adaptive filter which acts as a check on the Kalman filter during satellite slew maneuvers. A 1750A processor will be flown on board the satellite for the first time as a coprocessor (COP) in addition to the NASA Standard Spacecraft Computer. The attitude determination algorithm, which will be resident in the COP's memory, will make full use of its improved processing capabilities to meet mission requirements. Additional benefits were gained by writing the attitude determination code in Ada.

SSME Bearing and Seal Tester Data Compilation, Analysis and Reporting; and Refinement of the Cryogenic Bearing Analysis Mathematical Model

NASA Technical Reports Server (NTRS)

Moore, James; Marty, Dave; Cody, Joe

2000-01-01

SRS and NASA/MSFC have developed software with unique capabilities to couple bearing kinematic modeling with high fidelity thermal modeling. The core thermomechanical modeling software was developed by SRS and others in the late 1980's and early 1990's under various different contractual efforts. SRS originally developed software that enabled SHABERTH (Shaft Bearing Thermal Model) and SINDA (Systems Improved Numerical Differencing Analyzer) to exchange data and autonomously allowing bearing component temperature effects to propagate into the steady state bearing mechanical model. A separate contract was issued in 1990 to create a personal computer version of the software. At that time SRS performed major improvements to the code. Both SHABERTH and SINDA were independently ported to the PC and compiled. SRS them integrated the two programs into a single program that was named SINSHA. This was a major code improvement.

SSME Bearing and Seal Tester Data Compilation, Analysis, and Reporting; and Refinement of the Cryogenic Bearing Analysis Mathematical Model

NASA Technical Reports Server (NTRS)

Moore, James; Marty, Dave; Cody, Joe

2000-01-01

SRS and NASA/MSFC have developed software with unique capabilities to couple bearing kinematic modeling with high fidelity thermal modeling. The core thermomechanical modeling software was developed by SRS and others in the late 1980's and early 1990's under various different contractual efforts. SRS originally developed software that enabled SHABERTH (Shaft Bearing Thermal Model) and SINDA (Systems Improved Numerical Differencing Analyzer) to exchange data and autonomously allowing bearing component temperature effects to propagate into the steady state bearing mechanical model. A separate contract was issued in 1990 to create a personal computer version of the software. At that time SRS performed major improvements to the code. Both SHABERTH and SINDA were independently ported to the PC and compiled. SRS them integrated the two programs into a single program that was named SINSHA. This was a major code improvement.

High speed corner and gap-seal computations using an LU-SGS scheme

NASA Technical Reports Server (NTRS)

Coirier, William J.

1989-01-01

The hybrid Lower-Upper Symmetric Gauss-Seidel (LU-SGS) algorithm was added to a widely used series of 2D/3D Euler/Navier-Stokes solvers and was demonstrated for a particular class of high-speed flows. A limited study was conducted to compare the hybrid LU-SGS for approximate Newton iteration and diagonalized Beam-Warming (DBW) schemes on a work and convergence history basis. The hybrid LU-SGS algorithm is more efficient and easier to implement than the DBW scheme originally present in the code for the cases considered. The code was validated for the hypersonic flow through two mutually perpendicular flat plates and then used to investigate the flow field in and around a simplified scramjet module gap seal configuration. Due to the similarities, the gap seal flow was compared to hypersonic corner flow at the same freestream conditions and Reynolds number.

SPRAI: coupling of radiative feedback and primordial chemistry in moving mesh hydrodynamics

NASA Astrophysics Data System (ADS)

Jaura, O.; Glover, S. C. O.; Klessen, R. S.; Paardekooper, J.-P.

2018-04-01

In this paper, we introduce a new radiative transfer code SPRAI (Simplex Photon Radiation in the Arepo Implementation) based on the SIMPLEX radiation transfer method. This method, originally used only for post-processing, is now directly integrated into the AREPO code and takes advantage of its adaptive unstructured mesh. Radiated photons are transferred from the sources through the series of Voronoi gas cells within a specific solid angle. From the photon attenuation, we derive corresponding photon fluxes and ionization rates and feed them to a primordial chemistry module. This gives us a self-consistent method for studying dynamical and chemical processes caused by ionizing sources in primordial gas. Since the computational cost of the SIMPLEX method does not scale directly with the number of sources, it is convenient for studying systems such as primordial star-forming haloes that may form multiple ionizing sources.

Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.

PubMed

Palkowski, Marek; Bielecki, Wlodzimierz

2017-06-02

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. Polyhedral compilation techniques have proven to be a powerful tool for optimization of dense array codes. However, classical affine loop nest transformations used with these techniques do not optimize effectively codes of dynamic programming of RNA structure predictions. The purpose of this paper is to present a novel approach allowing for generation of a parallel tiled Nussinov RNA loop nest exposing significantly higher performance than that of known related code. This effect is achieved due to improving code locality and calculation parallelization. In order to improve code locality, we apply our previously published technique of automatic loop nest tiling to all the three loops of the Nussinov loop nest. This approach first forms original rectangular 3D tiles and then corrects them to establish their validity by means of applying the transitive closure of a dependence graph. To produce parallel code, we apply the loop skewing technique to a tiled Nussinov loop nest. The technique is implemented as a part of the publicly available polyhedral source-to-source TRACO compiler. Generated code was run on modern Intel multi-core processors and coprocessors. We present the speed-up factor of generated Nussinov RNA parallel code and demonstrate that it is considerably faster than related codes in which only the two outer loops of the Nussinov loop nest are tiled.

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.

1983-01-01

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

Design of convolutional tornado code

NASA Astrophysics Data System (ADS)

Zhou, Hui; Yang, Yao; Gao, Hongmin; Tan, Lu

2017-09-01

As a linear block code, the traditional tornado (tTN) code is inefficient in burst-erasure environment and its multi-level structure may lead to high encoding/decoding complexity. This paper presents a convolutional tornado (cTN) code which is able to improve the burst-erasure protection capability by applying the convolution property to the tTN code, and reduce computational complexity by abrogating the multi-level structure. The simulation results show that cTN code can provide a better packet loss protection performance with lower computation complexity than tTN code.

Three-dimensional turbopump flowfield analysis

NASA Technical Reports Server (NTRS)

Sharma, O. P.; Belford, K. A.; Ni, R. H.

1992-01-01

A program was conducted to develop a flow prediction method applicable to rocket turbopumps. The complex nature of a flowfield in turbopumps is described and examples of flowfields are discussed to illustrate that physics based models and analytical calculation procedures based on computational fluid dynamics (CFD) are needed to develop reliable design procedures for turbopumps. A CFD code developed at NASA ARC was used as the base code. The turbulence model and boundary conditions in the base code were modified, respectively, to: (1) compute transitional flows and account for extra rates of strain, e.g., rotation; and (2) compute surface heat transfer coefficients and allow computation through multistage turbomachines. Benchmark quality data from two and three-dimensional cascades were used to verify the code. The predictive capabilities of the present CFD code were demonstrated by computing the flow through a radial impeller and a multistage axial flow turbine. Results of the program indicate that the present code operated in a two-dimensional mode is a cost effective alternative to full three-dimensional calculations, and that it permits realistic predictions of unsteady loadings and losses for multistage machines.

High altitude chemically reacting gas particle mixtures. Volume 3: Computer code user's and applications manual. [rocket nozzle and orbital plume flow fields

NASA Technical Reports Server (NTRS)

Smith, S. D.

1984-01-01

A users manual for the RAMP2 computer code is provided. The RAMP2 code can be used to model the dominant phenomena which affect the prediction of liquid and solid rocket nozzle and orbital plume flow fields. The general structure and operation of RAMP2 are discussed. A user input/output guide for the modified TRAN72 computer code and the RAMP2F code is given. The application and use of the BLIMPJ module are considered. Sample problems involving the space shuttle main engine and motor are included.

Development of numerical methods for overset grids with applications for the integrated Space Shuttle vehicle

NASA Technical Reports Server (NTRS)

Chan, William M.

1995-01-01

Algorithms and computer code developments were performed for the overset grid approach to solving computational fluid dynamics problems. The techniques developed are applicable to compressible Navier-Stokes flow for any general complex configurations. The computer codes developed were tested on different complex configurations with the Space Shuttle launch vehicle configuration as the primary test bed. General, efficient and user-friendly codes were produced for grid generation, flow solution and force and moment computation.

Research in Computational Aeroscience Applications Implemented on Advanced Parallel Computing Systems

NASA Technical Reports Server (NTRS)

Wigton, Larry

1996-01-01

Improving the numerical linear algebra routines for use in new Navier-Stokes codes, specifically Tim Barth's unstructured grid code, with spin-offs to TRANAIR is reported. A fast distance calculation routine for Navier-Stokes codes using the new one-equation turbulence models is written. The primary focus of this work was devoted to improving matrix-iterative methods. New algorithms have been developed which activate the full potential of classical Cray-class computers as well as distributed-memory parallel computers.

ISSYS: An integrated synergistic Synthesis System

NASA Technical Reports Server (NTRS)

Dovi, A. R.

1980-01-01

Integrated Synergistic Synthesis System (ISSYS), an integrated system of computer codes in which the sequence of program execution and data flow is controlled by the user, is discussed. The commands available to exert such control, the ISSYS major function and rules, and the computer codes currently available in the system are described. Computational sequences frequently used in the aircraft structural analysis and synthesis are defined. External computer codes utilized by the ISSYS system are documented. A bibliography on the programs is included.

Building black holes: supercomputer cinema.

PubMed

Shapiro, S L; Teukolsky, S A

1988-07-22

A new computer code can solve Einstein's equations of general relativity for the dynamical evolution of a relativistic star cluster. The cluster may contain a large number of stars that move in a strong gravitational field at speeds approaching the speed of light. Unstable star clusters undergo catastrophic collapse to black holes. The collapse of an unstable cluster to a supermassive black hole at the center of a galaxy may explain the origin of quasars and active galactic nuclei. By means of a supercomputer simulation and color graphics, the whole process can be viewed in real time on a movie screen.

Bond order potential module for LAMMPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-09-11

pair_bop is a module for performing energy calculations using the Bond Order Potential (BOP) for use in the parallel molecular dynamics code LAMMPS. The bop pair style computes BOP based upon quantum mechanical incorporating both sigma and pi bondings. By analytically deriving the BOP pair bop from quantum mechanical theory its transferability to different phases can approach that of quantum mechanical methods. This potential is extremely effective at modeling 111-V and II-VI compounds such as GaAs and CdTe. This potential is similar to the original BOP developed by Pettifor and later updated by Murdock et al. and Ward et al.

User's manual for a two-dimensional, ground-water flow code on the Octopus computer network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Naymik, T.G.

1978-08-30

A ground-water hydrology computer code, programmed by R.L. Taylor (in Proc. American Society of Civil Engineers, Journal of Hydraulics Division, 93(HY2), pp. 25-33 (1967)), has been adapted to the Octopus computer system at Lawrence Livermore Laboratory. Using an example problem, this manual details the input, output, and execution options of the code.

Interactive Synthesis of Code Level Security Rules

DTIC Science & Technology

2017-04-01

Interactive Synthesis of Code-Level Security Rules A Thesis Presented by Leo St. Amour to The Department of Computer Science in partial fulfillment...of the requirements for the degree of Master of Science in Computer Science Northeastern University Boston, Massachusetts April 2017 DISTRIBUTION...Abstract of the Thesis Interactive Synthesis of Code-Level Security Rules by Leo St. Amour Master of Science in Computer Science Northeastern University

Agricultural Spraying

NASA Technical Reports Server (NTRS)

1986-01-01

AGDISP, a computer code written for Langley by Continuum Dynamics, Inc., aids crop dusting airplanes in targeting pesticides. The code is commercially available and can be run on a personal computer by an inexperienced operator. Called SWA+H, it is used by the Forest Service, FAA, DuPont, etc. DuPont uses the code to "test" equipment on the computer using a laser system to measure particle characteristics of various spray compounds.

The adaption and use of research codes for performance assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebetrau, A.M.

1987-05-01

Models of real-world phenomena are developed for many reasons. The models are usually, if not always, implemented in the form of a computer code. The characteristics of a code are determined largely by its intended use. Realizations or implementations of detailed mathematical models of complex physical and/or chemical processes are often referred to as research or scientific (RS) codes. Research codes typically require large amounts of computing time. One example of an RS code is a finite-element code for solving complex systems of differential equations that describe mass transfer through some geologic medium. Considerable computing time is required because computationsmore » are done at many points in time and/or space. Codes used to evaluate the overall performance of real-world physical systems are called performance assessment (PA) codes. Performance assessment codes are used to conduct simulated experiments involving systems that cannot be directly observed. Thus, PA codes usually involve repeated simulations of system performance in situations that preclude the use of conventional experimental and statistical methods. 3 figs.« less

Modeling the source of GW150914 with targeted numerical-relativity simulations

NASA Astrophysics Data System (ADS)

Lovelace, Geoffrey; Lousto, Carlos O.; Healy, James; Scheel, Mark A.; Garcia, Alyssa; O'Shaughnessy, Richard; Boyle, Michael; Campanelli, Manuela; Hemberger, Daniel A.; Kidder, Lawrence E.; Pfeiffer, Harald P.; Szilágyi, Béla; Teukolsky, Saul A.; Zlochower, Yosef

2016-12-01

In fall of 2015, the two LIGO detectors measured the gravitational wave signal GW150914, which originated from a pair of merging black holes (Abbott et al Virgo, LIGO Scientific 2016 Phys. Rev. Lett. 116 061102). In the final 0.2 s (about 8 gravitational-wave cycles) before the amplitude reached its maximum, the observed signal swept up in amplitude and frequency, from 35 Hz to 150 Hz. The theoretical gravitational-wave signal for merging black holes, as predicted by general relativity, can be computed only by full numerical relativity, because analytic approximations fail near the time of merger. Moreover, the nearly-equal masses, moderate spins, and small number of orbits of GW150914 are especially straightforward and efficient to simulate with modern numerical-relativity codes. In this paper, we report the modeling of GW150914 with numerical-relativity simulations, using black-hole masses and spins consistent with those inferred from LIGO’s measurement (Abbott et al LIGO Scientific Collaboration, Virgo Collaboration 2016 Phys. Rev. Lett. 116 241102). In particular, we employ two independent numerical-relativity codes that use completely different analytical and numerical methods to model the same merging black holes and to compute the emitted gravitational waveform; we find excellent agreement between the waveforms produced by the two independent codes. These results demonstrate the validity, impact, and potential of current and future studies using rapid-response, targeted numerical-relativity simulations for better understanding gravitational-wave observations.

Topological color codes on Union Jack lattices: a stable implementation of the whole Clifford group

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katzgraber, Helmut G.; Theoretische Physik, ETH Zurich, CH-8093 Zurich; Bombin, H.

We study the error threshold of topological color codes on Union Jack lattices that allow for the full implementation of the whole Clifford group of quantum gates. After mapping the error-correction process onto a statistical mechanical random three-body Ising model on a Union Jack lattice, we compute its phase diagram in the temperature-disorder plane using Monte Carlo simulations. Surprisingly, topological color codes on Union Jack lattices have a similar error stability to color codes on triangular lattices, as well as to the Kitaev toric code. The enhanced computational capabilities of the topological color codes on Union Jack lattices with respectmore » to triangular lattices and the toric code combined with the inherent robustness of this implementation show good prospects for future stable quantum computer implementations.« less

Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system.

PubMed

Kawano, Tomonori

2013-03-01

There have been a wide variety of approaches for handling the pieces of DNA as the "unplugged" tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given "passwords" and/or secret numbers using DNA sequences. The "passwords" of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the non-coding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original "passwords." The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the chains. Lastly, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed.

Modeling IrisCode and its variants as convex polyhedral cones and its security implications.

PubMed

Kong, Adams Wai-Kin

2013-03-01

IrisCode, developed by Daugman, in 1993, is the most influential iris recognition algorithm. A thorough understanding of IrisCode is essential, because over 100 million persons have been enrolled by this algorithm and many biometric personal identification and template protection methods have been developed based on IrisCode. This paper indicates that a template produced by IrisCode or its variants is a convex polyhedral cone in a hyperspace. Its central ray, being a rough representation of the original biometric signal, can be computed by a simple algorithm, which can often be implemented in one Matlab command line. The central ray is an expected ray and also an optimal ray of an objective function on a group of distributions. This algorithm is derived from geometric properties of a convex polyhedral cone but does not rely on any prior knowledge (e.g., iris images). The experimental results show that biometric templates, including iris and palmprint templates, produced by different recognition methods can be matched through the central rays in their convex polyhedral cones and that templates protected by a method extended from IrisCode can be broken into. These experimental results indicate that, without a thorough security analysis, convex polyhedral cone templates cannot be assumed secure. Additionally, the simplicity of the algorithm implies that even junior hackers without knowledge of advanced image processing and biometric databases can still break into protected templates and reveal relationships among templates produced by different recognition methods.

An Upgrade of the Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) Software

NASA Technical Reports Server (NTRS)

Mason, Michelle L.; Rufer, Shann J.

2015-01-01

The Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) code is used at NASA Langley Research Center to analyze global aeroheating data on wind tunnel models tested in the Langley Aerothermodynamics Laboratory. One-dimensional, semi-infinite heating data derived from IHEAT are used to design thermal protection systems to mitigate the risks due to the aeroheating loads on hypersonic vehicles, such as re-entry vehicles during descent and landing procedures. This code was originally written in the PV-WAVE programming language to analyze phosphor thermography data from the two-color, relativeintensity system developed at Langley. To increase the efficiency, functionality, and reliability of IHEAT, the code was migrated to MATLAB syntax and compiled as a stand-alone executable file labeled version 4.0. New features of IHEAT 4.0 include the options to batch process all of the data from a wind tunnel run, to map the two-dimensional heating distribution to a three-dimensional computer-aided design model of the vehicle to be viewed in Tecplot, and to extract data from a segmented line that follows an interesting feature in the data. Results from IHEAT 4.0 were compared on a pixel level to the output images from the legacy code to validate the program. The differences between the two codes were on the order of 10-5 to 10-7. IHEAT 4.0 replaces the PV-WAVE version as the production code for aeroheating experiments conducted in the hypersonic facilities at NASA Langley.

Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer.

PubMed

Suplatov, Dmitry; Popova, Nina; Zhumatiy, Sergey; Voevodin, Vladimir; Švedas, Vytas

2016-04-01

Rapid expansion of online resources providing access to genomic, structural, and functional information associated with biological macromolecules opens an opportunity to gain a deeper understanding of the mechanisms of biological processes due to systematic analysis of large datasets. This, however, requires novel strategies to optimally utilize computer processing power. Some methods in bioinformatics and molecular modeling require extensive computational resources. Other algorithms have fast implementations which take at most several hours to analyze a common input on a modern desktop station, however, due to multiple invocations for a large number of subtasks the full task requires a significant computing power. Therefore, an efficient computational solution to large-scale biological problems requires both a wise parallel implementation of resource-hungry methods as well as a smart workflow to manage multiple invocations of relatively fast algorithms. In this work, a new computer software mpiWrapper has been developed to accommodate non-parallel implementations of scientific algorithms within the parallel supercomputing environment. The Message Passing Interface has been implemented to exchange information between nodes. Two specialized threads - one for task management and communication, and another for subtask execution - are invoked on each processing unit to avoid deadlock while using blocking calls to MPI. The mpiWrapper can be used to launch all conventional Linux applications without the need to modify their original source codes and supports resubmission of subtasks on node failure. We show that this approach can be used to process huge amounts of biological data efficiently by running non-parallel programs in parallel mode on a supercomputer. The C++ source code and documentation are available from http://biokinet.belozersky.msu.ru/mpiWrapper .

Accurate Modeling of Ionospheric Electromagnetic Fields Generated by a Low-Altitude VLF Transmitter

DTIC Science & Technology

2007-08-31

latitude) for 3 different grid spacings. 14 8. Low-altitude fields produced by a 10-kHz source computed using the FD and TD codes. The agreement is...excellent, validating the new FD code. 16 9. High-altitude fields produced by a 10-kHz source computed using the FD and TD codes. The agreement is...again excellent. 17 10. Low-altitude fields produced by a 20-k.Hz source computed using the FD and TD codes. 17 11. High-altitude fields produced

SRGULL - AN ADVANCED ENGINEERING MODEL FOR THE PREDICTION OF AIRFRAME INTEGRATED SCRAMJET CYCLE PERFORMANCE

NASA Technical Reports Server (NTRS)

Walton, J. T.

1994-01-01

The development of a single-stage-to-orbit aerospace vehicle intended to be launched horizontally into low Earth orbit, such as the National Aero-Space Plane (NASP), has concentrated on the use of the supersonic combustion ramjet (scramjet) propulsion cycle. SRGULL, a scramjet cycle analysis code, is an engineer's tool capable of nose-to-tail, hydrogen-fueled, airframe-integrated scramjet simulation in a real gas flow with equilibrium thermodynamic properties. This program facilitates initial estimates of scramjet cycle performance by linking a two-dimensional forebody, inlet and nozzle code with a one-dimensional combustor code. Five computer codes (SCRAM, SEAGUL, INLET, Progam HUD, and GASH) originally developed at NASA Langley Research Center in support of hypersonic technology are integrated in this program to analyze changing flow conditions. The one-dimensional combustor code is based on the combustor subroutine from SCRAM and the two-dimensional coding is based on an inviscid Euler program (SEAGUL). Kinetic energy efficiency input for sidewall area variation modeling can be calculated by the INLET program code. At the completion of inviscid component analysis, Program HUD, an integral boundary layer code based on the Spaulding-Chi method, is applied to determine the friction coefficient which is then used in a modified Reynolds Analogy to calculate heat transfer. Real gas flow properties such as flow composition, enthalpy, entropy, and density are calculated by the subroutine GASH. Combustor input conditions are taken from one-dimensionalizing the two-dimensional inlet exit flow. The SEAGUL portions of this program are limited to supersonic flows, but the combustor (SCRAM) section can handle supersonic and dual-mode operation. SRGULL has been compared to scramjet engine tests with excellent results. SRGULL was written in FORTRAN 77 on an IBM PC compatible using IBM's FORTRAN/2 or Microway's NDP386 F77 compiler. The program is fully user interactive, but can also run in batch mode. It operates under the UNIX, VMS, NOS, and DOS operating systems. The source code is not directly compatible with all PC compilers (e.g., Lahey or Microsoft FORTRAN) due to block and segment size requirements. SRGULL executable code requires about 490K RAM and a math coprocessor on PC's. The SRGULL program was developed in 1989, although the component programs originated in the 1960's and 1970's. IBM, IBM PC, and DOS are registered trademarks of International Business Machines. VMS is a registered trademark of Digital Equipment Corporation. UNIX is a registered trademark of Bell Laboratories. NOS is a registered trademark of Control Data Corporation.

ANITA-2000 activation code package - updating of the decay data libraries and validation on the experimental data of the 14 MeV Frascati Neutron Generator

NASA Astrophysics Data System (ADS)

Frisoni, Manuela

2016-03-01

ANITA-2000 is a code package for the activation characterization of materials exposed to neutron irradiation released by ENEA to OECD-NEADB and ORNL-RSICC. The main component of the package is the activation code ANITA-4M that computes the radioactive inventory of a material exposed to neutron irradiation. The code requires the decay data library (file fl1) containing the quantities describing the decay properties of the unstable nuclides and the library (file fl2) containing the gamma ray spectra emitted by the radioactive nuclei. The fl1 and fl2 files of the ANITA-2000 code package, originally based on the evaluated nuclear data library FENDL/D-2.0, were recently updated on the basis of the JEFF-3.1.1 Radioactive Decay Data Library. This paper presents the results of the validation of the new fl1 decay data library through the comparison of the ANITA-4M calculated values with the measured electron and photon decay heats and activities of fusion material samples irradiated at the 14 MeV Frascati Neutron Generator (FNG) of the NEA-Frascati Research Centre. Twelve material samples were considered, namely: Mo, Cu, Hf, Mg, Ni, Cd, Sn, Re, Ti, W, Ag and Al. The ratios between calculated and experimental values (C/E) are shown and discussed in this paper.

Parallelization of a Monte Carlo particle transport simulation code

NASA Astrophysics Data System (ADS)

Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

2010-05-01

We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

Effect of the diffusion parameters on the observed γ-ray spectrum of sources and their contribution to the local all-electron spectrum: The EDGE code

NASA Astrophysics Data System (ADS)

López-Coto, R.; Hahn, J.; BenZvi, S.; Dingus, B.; Hinton, J.; Nisa, M. U.; Parsons, R. D.; Greus, F. Salesa; Zhang, H.; Zhou, H.

2018-11-01

The positron excess measured by PAMELA and AMS can only be explained if there is one or several sources injecting them. Moreover, at the highest energies, it requires the presence of nearby ( ∼ hundreds of parsecs) and middle age (maximum of ∼ hundreds of kyr) sources. Pulsars, as factories of electrons and positrons, are one of the proposed candidates to explain the origin of this excess. To calculate the contribution of these sources to the electron and positron flux at the Earth, we developed EDGE (Electron Diffusion and Gamma rays to the Earth), a code to treat the propagation of electrons and compute their diffusion from a central source with a flexible injection spectrum. Using this code, we can derive the source's gamma-ray spectrum, spatial extension, the all-electron density in space, the electron and positron flux reaching the Earth and the positron fraction measured at the Earth. We present in this paper the foundations of the code and study how different parameters affect the gamma-ray spectrum of a source and the electron flux measured at the Earth. We also studied the effect of several approximations usually performed in these studies. This code has been used to derive the results of the positron flux measured at the Earth in [1].

Multidisciplinary High-Fidelity Analysis and Optimization of Aerospace Vehicles. Part 1; Formulation

NASA Technical Reports Server (NTRS)

Walsh, J. L.; Townsend, J. C.; Salas, A. O.; Samareh, J. A.; Mukhopadhyay, V.; Barthelemy, J.-F.

2000-01-01

An objective of the High Performance Computing and Communication Program at the NASA Langley Research Center is to demonstrate multidisciplinary shape and sizing optimization of a complete aerospace vehicle configuration by using high-fidelity, finite element structural analysis and computational fluid dynamics aerodynamic analysis in a distributed, heterogeneous computing environment that includes high performance parallel computing. A software system has been designed and implemented to integrate a set of existing discipline analysis codes, some of them computationally intensive, into a distributed computational environment for the design of a highspeed civil transport configuration. The paper describes the engineering aspects of formulating the optimization by integrating these analysis codes and associated interface codes into the system. The discipline codes are integrated by using the Java programming language and a Common Object Request Broker Architecture (CORBA) compliant software product. A companion paper presents currently available results.

An implicit higher-order spatially accurate scheme for solving time dependent flows on unstructured meshes

NASA Astrophysics Data System (ADS)

Tomaro, Robert F.

1998-07-01

The present research is aimed at developing a higher-order, spatially accurate scheme for both steady and unsteady flow simulations using unstructured meshes. The resulting scheme must work on a variety of general problems to ensure the creation of a flexible, reliable and accurate aerodynamic analysis tool. To calculate the flow around complex configurations, unstructured grids and the associated flow solvers have been developed. Efficient simulations require the minimum use of computer memory and computational times. Unstructured flow solvers typically require more computer memory than a structured flow solver due to the indirect addressing of the cells. The approach taken in the present research was to modify an existing three-dimensional unstructured flow solver to first decrease the computational time required for a solution and then to increase the spatial accuracy. The terms required to simulate flow involving non-stationary grids were also implemented. First, an implicit solution algorithm was implemented to replace the existing explicit procedure. Several test cases, including internal and external, inviscid and viscous, two-dimensional, three-dimensional and axi-symmetric problems, were simulated for comparison between the explicit and implicit solution procedures. The increased efficiency and robustness of modified code due to the implicit algorithm was demonstrated. Two unsteady test cases, a plunging airfoil and a wing undergoing bending and torsion, were simulated using the implicit algorithm modified to include the terms required for a moving and/or deforming grid. Secondly, a higher than second-order spatially accurate scheme was developed and implemented into the baseline code. Third- and fourth-order spatially accurate schemes were implemented and tested. The original dissipation was modified to include higher-order terms and modified near shock waves to limit pre- and post-shock oscillations. The unsteady cases were repeated using the higher-order spatially accurate code. The new solutions were compared with those obtained using the second-order spatially accurate scheme. Finally, the increased efficiency of using an implicit solution algorithm in a production Computational Fluid Dynamics flow solver was demonstrated for steady and unsteady flows. A third- and fourth-order spatially accurate scheme has been implemented creating a basis for a state-of-the-art aerodynamic analysis tool.

Analysis of airborne antenna systems using geometrical theory of diffraction and moment method computer codes

NASA Technical Reports Server (NTRS)

Hartenstein, Richard G., Jr.

1985-01-01

Computer codes have been developed to analyze antennas on aircraft and in the presence of scatterers. The purpose of this study is to use these codes to develop accurate computer models of various aircraft and antenna systems. The antenna systems analyzed are a P-3B L-Band antenna, an A-7E UHF relay pod antenna, and traffic advisory antenna system installed on a Bell Long Ranger helicopter. Computer results are compared to measured ones with good agreement. These codes can be used in the design stage of an antenna system to determine the optimum antenna location and save valuable time and costly flight hours.

Code of Ethical Conduct for Computer-Using Educators: An ICCE Policy Statement.

ERIC Educational Resources Information Center

Computing Teacher, 1987

1987-01-01

Prepared by the International Council for Computers in Education's Ethics and Equity Committee, this code of ethics for educators using computers covers nine main areas: curriculum issues, issues relating to computer access, privacy/confidentiality issues, teacher-related issues, student issues, the community, school organizational issues,…

Learning-Based Just-Noticeable-Quantization- Distortion Modeling for Perceptual Video Coding.

PubMed

Ki, Sehwan; Bae, Sung-Ho; Kim, Munchurl; Ko, Hyunsuk

2018-07-01

Conventional predictive video coding-based approaches are reaching the limit of their potential coding efficiency improvements, because of severely increasing computation complexity. As an alternative approach, perceptual video coding (PVC) has attempted to achieve high coding efficiency by eliminating perceptual redundancy, using just-noticeable-distortion (JND) directed PVC. The previous JNDs were modeled by adding white Gaussian noise or specific signal patterns into the original images, which were not appropriate in finding JND thresholds due to distortion with energy reduction. In this paper, we present a novel discrete cosine transform-based energy-reduced JND model, called ERJND, that is more suitable for JND-based PVC schemes. Then, the proposed ERJND model is extended to two learning-based just-noticeable-quantization-distortion (JNQD) models as preprocessing that can be applied for perceptual video coding. The two JNQD models can automatically adjust JND levels based on given quantization step sizes. One of the two JNQD models, called LR-JNQD, is based on linear regression and determines the model parameter for JNQD based on extracted handcraft features. The other JNQD model is based on a convolution neural network (CNN), called CNN-JNQD. To our best knowledge, our paper is the first approach to automatically adjust JND levels according to quantization step sizes for preprocessing the input to video encoders. In experiments, both the LR-JNQD and CNN-JNQD models were applied to high efficiency video coding (HEVC) and yielded maximum (average) bitrate reductions of 38.51% (10.38%) and 67.88% (24.91%), respectively, with little subjective video quality degradation, compared with the input without preprocessing applied.

Embedding Secure Coding Instruction into the IDE: Complementing Early and Intermediate CS Courses with ESIDE

ERIC Educational Resources Information Center

Whitney, Michael; Lipford, Heather Richter; Chu, Bill; Thomas, Tyler

2018-01-01

Many of the software security vulnerabilities that people face today can be remediated through secure coding practices. A critical step toward the practice of secure coding is ensuring that our computing students are educated on these practices. We argue that secure coding education needs to be included across a computing curriculum. We are…

PFMCal : Photonic force microscopy calibration extended for its application in high-frequency microrheology

NASA Astrophysics Data System (ADS)

Butykai, A.; Domínguez-García, P.; Mor, F. M.; Gaál, R.; Forró, L.; Jeney, S.

2017-11-01

The present document is an update of the previously published MatLab code for the calibration of optical tweezers in the high-resolution detection of the Brownian motion of non-spherical probes [1]. In this instance, an alternative version of the original code, based on the same physical theory [2], but focused on the automation of the calibration of measurements using spherical probes, is outlined. The new added code is useful for high-frequency microrheology studies, where the probe radius is known but the viscosity of the surrounding fluid maybe not. This extended calibration methodology is automatic, without the need of a user's interface. A code for calibration by means of thermal noise analysis [3] is also included; this is a method that can be applied when using viscoelastic fluids if the trap stiffness is previously estimated [4]. The new code can be executed in MatLab and using GNU Octave. Program Files doi:http://dx.doi.org/10.17632/s59f3gz729.1 Licensing provisions: GPLv3 Programming language: MatLab 2016a (MathWorks Inc.) and GNU Octave 4.0 Operating system: Linux and Windows. Supplementary material: A new document README.pdf includes basic running instructions for the new code. Journal reference of previous version: Computer Physics Communications, 196 (2015) 599 Does the new version supersede the previous version?: No. It adds alternative but compatible code while providing similar calibration factors. Nature of problem (approx. 50-250 words): The original code uses a MatLab-provided user's interface, which is not available in GNU Octave, and cannot be used outside of a proprietary software as MatLab. Besides, the process of calibration when using spherical probes needs an automatic method when calibrating big amounts of different data focused to microrheology. Solution method (approx. 50-250 words): The new code can be executed in the latest version of MatLab and using GNU Octave, a free and open-source alternative to MatLab. This code generates an automatic calibration process which requires only to write the input data in the main script. Additionally, we include a calibration method based on thermal noise statistics, which can be used with viscoelastic fluids if the trap stiffness is previously estimated. Reasons for the new version: This version extends the functionality of PFMCal for the particular case of spherical probes and unknown fluid viscosities. The extended code is automatic, works in different operating systems and it is compatible with GNU Octave. Summary of revisions: The original MatLab program in the previous version, which is executed by PFMCal.m, is not changed. Here, we have added two additional main archives named PFMCal_auto.m and PFMCal_histo.m, which implement automatic calculations of the calibration process and calibration through Boltzmann statistics, respectively. The process of calibration using this code for spherical beads is described in the README.pdf file provided in the new code submission. Here, we obtain different calibration factors, β (given in μm/V), according to [2], related to two statistical quantities: the mean-squared displacement (MSD), βMSD, and the velocity autocorrelation function (VAF), βVAF. Using that methodology, the trap stiffness, k, and the zero-shear viscosity of the fluid, η, can be calculated if the value of the particle's radius, a, is previously known. For comparison, we include in the extended code the method of calibration using the corner frequency of the power-spectral density (PSD) [5], providing a calibration factor βPSD. Besides, with the prior estimation of the trap stiffness, along with the known value of the particle's radius, we can use thermal noise statistics to obtain calibration factors, β, according to the quadratic form of the optical potential, βE, and related to the Gaussian distribution of the bead's positions, βσ2. This method has been demonstrated to be applicable to the calibration of optical tweezers when using non-Newtonian viscoelastic polymeric liquids [4]. An example of the results using this calibration process is summarized in Table 1. Using the data provided in the new code submission, for water and acetone fluids, we calculate all the calibration factors by using the original PFMCal.m and by the new non-GUI code PFMCal_auto.m and PFMCal_histo.m. Regarding the new code, PFMCal_auto.m returns η, k, βMSD, βVAF and βPSD, while PFMCal_histo.m provides βσ2 and βE. Table 1 shows how we obtain the expected viscosity of the two fluids at this temperature and how the different methods provide good agreement between trap stiffnesses and calibration factors. Additional comments including Restrictions and Unusual features (approx. 50-250 words): The original code, PFMCal.m, runs under MatLab using the Statistics Toolbox. The extended code, PFMCal_auto.m and PFMCal_histo.m, can be executed without modification using MatLab or GNU Octave. The code has been tested in Linux and Windows operating systems.

Addition and Removal Energies via the In-Medium Similarity Renormalization Group Method

NASA Astrophysics Data System (ADS)

Yuan, Fei

The in-medium similarity renormalization group (IM-SRG) is an ab initio many-body method suitable for systems with moderate numbers of particles due to its polynomial scaling in computational cost. The formalism is highly flexible and admits a variety of modifications that extend its utility beyond the original goal of computing ground state energies of closed-shell systems. In this work, we present an extension of IM-SRG through quasidegenerate perturbation theory (QDPT) to compute addition and removal energies (single particle energies) near the Fermi level at low computational cost. This expands the range of systems that can be studied from closed-shell ones to nearby systems that differ by one particle. The method is applied to circular quantum dot systems and nuclei, and compared against other methods including equations-of-motion (EOM) IM-SRG and EOM coupled-cluster (CC) theory. The results are in good agreement for most cases. As part of this work, we present an open-source implementation of our flexible and easy-to-use J-scheme framework as well as the HF, IM-SRG, and QDPT codes built upon this framework. We include an overview of the overall structure, the implementation details, and strategies for maintaining high code quality and efficiency. Lastly, we also present a graphical application for manipulation of angular momentum coupling coefficients through a diagrammatic notation for angular momenta (Jucys diagrams). The tool enables rapid derivations of equations involving angular momentum coupling--such as in J-scheme--and significantly reduces the risk of human errors.

Calculation of water drop trajectories to and about arbitrary three-dimensional lifting and nonlifting bodies in potential airflow

NASA Technical Reports Server (NTRS)

Norment, H. G.

1985-01-01

Subsonic, external flow about nonlifting bodies, lifting bodies or combinations of lifting and nonlifting bodies is calculated by a modified version of the Hess lifting code. Trajectory calculations can be performed for any atmospheric conditions and for all water drop sizes, from the smallest cloud droplet to large raindrops. Experimental water drop drag relations are used in the water drop equations of motion and effects of gravity settling are included. Inlet flow can be accommodated, and high Mach number compressibility effects are corrected for approximately. Seven codes are described: (1) a code used to debug and plot body surface description data; (2) a code that processes the body surface data to yield the potential flow field; (3) a code that computes flow velocities at arrays of points in space; (4) a code that computes water drop trajectories from an array of points in space; (5) a code that computes water drop trajectories and fluxes to arbitrary target points; (6) a code that computes water drop trajectories tangent to the body; and (7) a code that produces stereo pair plots which include both the body and trajectories. Accuracy of the calculations is discussed, and trajectory calculation results are compared with prior calculations and with experimental data.

Debugging Techniques Used by Experienced Programmers to Debug Their Own Code.

DTIC Science & Technology

1990-09-01

IS. NUMBER OF PAGES code debugging 62 computer programmers 16. PRICE CODE debug programming 17. SECURITY CLASSIFICATION 18. SECURITY CLASSIFICATION 119...Davis, and Schultz (1987) also compared experts and novices, but focused on the way a computer program is represented cognitively and how that...of theories in the emerging computer programming domain (Fisher, 1987). In protocol analysis, subjects are asked to talk/think aloud as they solve

A COTS-Based Replacement Strategy for Aging Avionics Computers

DTIC Science & Technology

2001-12-01

Communication Control Unit. A COTS-Based Replacement Strategy for Aging Avionics Computers COTS Microprocessor Real Time Operating System New Native Code...Native Code Objec ts Native Code Thread Real - Time Operating System Legacy Function x Virtual Component Environment Context Switch Thunk Add-in Replace

PARAVT: Parallel Voronoi tessellation code

NASA Astrophysics Data System (ADS)

González, R. E.

2016-10-01

In this study, we present a new open source code for massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition takes into account consistent boundary computation between tasks, and includes periodic conditions. In addition, the code computes neighbors list, Voronoi density, Voronoi cell volume, density gradient for each particle, and densities on a regular grid. Code implementation and user guide are publicly available at https://github.com/regonzar/paravt.

The STAGS computer code

NASA Technical Reports Server (NTRS)

Almroth, B. O.; Brogan, F. A.

1978-01-01

Basic information about the computer code STAGS (Structural Analysis of General Shells) is presented to describe to potential users the scope of the code and the solution procedures that are incorporated. Primarily, STAGS is intended for analysis of shell structures, although it has been extended to more complex shell configurations through the inclusion of springs and beam elements. The formulation is based on a variational approach in combination with local two dimensional power series representations of the displacement components. The computer code includes options for analysis of linear or nonlinear static stress, stability, vibrations, and transient response. Material as well as geometric nonlinearities are included. A few examples of applications of the code are presented for further illustration of its scope.

Holonomic surface codes for fault-tolerant quantum computation

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Devitt, Simon J.; You, J. Q.; Nori, Franco

2018-02-01

Surface codes can protect quantum information stored in qubits from local errors as long as the per-operation error rate is below a certain threshold. Here we propose holonomic surface codes by harnessing the quantum holonomy of the system. In our scheme, the holonomic gates are built via auxiliary qubits rather than the auxiliary levels in multilevel systems used in conventional holonomic quantum computation. The key advantage of our approach is that the auxiliary qubits are in their ground state before and after each gate operation, so they are not involved in the operation cycles of surface codes. This provides an advantageous way to implement surface codes for fault-tolerant quantum computation.

Comparison of two- and three-dimensional flow computations with laser anemometer measurements in a transonic compressor rotor

NASA Technical Reports Server (NTRS)

Chima, R. V.; Strazisar, A. J.

1982-01-01

Two and three dimensional inviscid solutions for the flow in a transonic axial compressor rotor at design speed are compared with probe and laser anemometers measurements at near-stall and maximum-flow operating points. Experimental details of the laser anemometer system and computational details of the two dimensional axisymmetric code and three dimensional Euler code are described. Comparisons are made between relative Mach number and flow angle contours, shock location, and shock strength. A procedure for using an efficient axisymmetric code to generate downstream pressure input for computationally expensive Euler codes is discussed. A film supplement shows the calculations of the two operating points with the time-marching Euler code.

Performance Analysis and Portability of the PLUM Load Balancing System

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Biswas, Rupak; Gabow, Harold N.

1998-01-01

The ability to dynamically adapt an unstructured mesh is a powerful tool for solving computational problems with evolving physical features; however, an efficient parallel implementation is rather difficult. To address this problem, we have developed PLUM, an automatic portable framework for performing adaptive numerical computations in a message-passing environment. PLUM requires that all data be globally redistributed after each mesh adaption to achieve load balance. We present an algorithm for minimizing this remapping overhead by guaranteeing an optimal processor reassignment. We also show that the data redistribution cost can be significantly reduced by applying our heuristic processor reassignment algorithm to the default mapping of the parallel partitioner. Portability is examined by comparing performance on a SP2, an Origin2000, and a T3E. Results show that PLUM can be successfully ported to different platforms without any code modifications.

Development of MCNPX-ESUT computer code for simulation of neutron/gamma pulse height distribution

NASA Astrophysics Data System (ADS)

Abolfazl Hosseini, Seyed; Vosoughi, Naser; Zangian, Mehdi

2015-05-01

In this paper, the development of the MCNPX-ESUT (MCNPX-Energy Engineering of Sharif University of Technology) computer code for simulation of neutron/gamma pulse height distribution is reported. Since liquid organic scintillators like NE-213 are well suited and routinely used for spectrometry in mixed neutron/gamma fields, this type of detectors is selected for simulation in the present study. The proposed algorithm for simulation includes four main steps. The first step is the modeling of the neutron/gamma particle transport and their interactions with the materials in the environment and detector volume. In the second step, the number of scintillation photons due to charged particles such as electrons, alphas, protons and carbon nuclei in the scintillator material is calculated. In the third step, the transport of scintillation photons in the scintillator and lightguide is simulated. Finally, the resolution corresponding to the experiment is considered in the last step of the simulation. Unlike the similar computer codes like SCINFUL, NRESP7 and PHRESP, the developed computer code is applicable to both neutron and gamma sources. Hence, the discrimination of neutron and gamma in the mixed fields may be performed using the MCNPX-ESUT computer code. The main feature of MCNPX-ESUT computer code is that the neutron/gamma pulse height simulation may be performed without needing any sort of post processing. In the present study, the pulse height distributions due to a monoenergetic neutron/gamma source in NE-213 detector using MCNPX-ESUT computer code is simulated. The simulated neutron pulse height distributions are validated through comparing with experimental data (Gohil et al. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 664 (2012) 304-309.) and the results obtained from similar computer codes like SCINFUL, NRESP7 and Geant4. The simulated gamma pulse height distribution for a 137Cs source is also compared with the experimental data.

EAC: A program for the error analysis of STAGS results for plates

NASA Technical Reports Server (NTRS)

Sistla, Rajaram; Thurston, Gaylen A.; Bains, Nancy Jane C.

1989-01-01

A computer code is now available for estimating the error in results from the STAGS finite element code for a shell unit consisting of a rectangular orthotropic plate. This memorandum contains basic information about the computer code EAC (Error Analysis and Correction) and describes the connection between the input data for the STAGS shell units and the input data necessary to run the error analysis code. The STAGS code returns a set of nodal displacements and a discrete set of stress resultants; the EAC code returns a continuous solution for displacements and stress resultants. The continuous solution is defined by a set of generalized coordinates computed in EAC. The theory and the assumptions that determine the continuous solution are also outlined in this memorandum. An example of application of the code is presented and instructions on its usage on the Cyber and the VAX machines have been provided.

CFD Modeling of Free-Piston Stirling Engines

NASA Technical Reports Server (NTRS)

Ibrahim, Mounir B.; Zhang, Zhi-Guo; Tew, Roy C., Jr.; Gedeon, David; Simon, Terrence W.

2001-01-01

NASA Glenn Research Center (GRC) is funding Cleveland State University (CSU) to develop a reliable Computational Fluid Dynamics (CFD) code that can predict engine performance with the goal of significant improvements in accuracy when compared to one-dimensional (1-D) design code predictions. The funding also includes conducting code validation experiments at both the University of Minnesota (UMN) and CSU. In this paper a brief description of the work-in-progress is provided in the two areas (CFD and Experiments). Also, previous test results are compared with computational data obtained using (1) a 2-D CFD code obtained from Dr. Georg Scheuerer and further developed at CSU and (2) a multidimensional commercial code CFD-ACE+. The test data and computational results are for (1) a gas spring and (2) a single piston/cylinder with attached annular heat exchanger. The comparisons among the codes are discussed. The paper also discusses plans for conducting code validation experiments at CSU and UMN.

Data Bank 5 - Origin and Destination Survey City/Airport Nomenclature : fourth quarter : [2006-01

DOT National Transportation Integrated Search

2006-01-01

This CD presents the letter alphabetic codes, numeric codes, full name spelling (up to 30 characters), abbreviated name spelling (up to 20 characters), and geographic coordinates for all cities in flight itineraries reported in the Passenger Origin a...

On the error statistics of Viterbi decoding and the performance of concatenated codes

NASA Technical Reports Server (NTRS)

Miller, R. L.; Deutsch, L. J.; Butman, S. A.

1981-01-01

Computer simulation results are presented on the performance of convolutional codes of constraint lengths 7 and 10 concatenated with the (255, 223) Reed-Solomon code (a proposed NASA standard). These results indicate that as much as 0.8 dB can be gained by concatenating this Reed-Solomon code with a (10, 1/3) convolutional code, instead of the (7, 1/2) code currently used by the DSN. A mathematical model of Viterbi decoder burst-error statistics is developed and is validated through additional computer simulations.

New double-byte error-correcting codes for memory systems

NASA Technical Reports Server (NTRS)

Feng, Gui-Liang; Wu, Xinen; Rao, T. R. N.

1996-01-01

Error-correcting or error-detecting codes have been used in the computer industry to increase reliability, reduce service costs, and maintain data integrity. The single-byte error-correcting and double-byte error-detecting (SbEC-DbED) codes have been successfully used in computer memory subsystems. There are many methods to construct double-byte error-correcting (DBEC) codes. In the present paper we construct a class of double-byte error-correcting codes, which are more efficient than those known to be optimum, and a decoding procedure for our codes is also considered.

Computational Hemodynamic Simulation of Human Circulatory System under Altered Gravity

NASA Technical Reports Server (NTRS)

Kim. Chang Sung; Kiris, Cetin; Kwak, Dochan

2003-01-01

A computational hemodynamics approach is presented to simulate the blood flow through the human circulatory system under altered gravity conditions. Numerical techniques relevant to hemodynamics issues are introduced to non-Newtonian modeling for flow characteristics governed by red blood cells, distensible wall motion due to the heart pulse, and capillary bed modeling for outflow boundary conditions. Gravitational body force terms are added to the Navier-Stokes equations to study the effects of gravity on internal flows. Six-type gravity benchmark problems are originally presented to provide the fundamental understanding of gravitational effects on the human circulatory system. For code validation, computed results are compared with steady and unsteady experimental data for non-Newtonian flows in a carotid bifurcation model and a curved circular tube, respectively. This computational approach is then applied to the blood circulation in the human brain as a target problem. A three-dimensional, idealized Circle of Willis configuration is developed with minor arteries truncated based on anatomical data. Demonstrated is not only the mechanism of the collateral circulation but also the effects of gravity on the distensible wall motion and resultant flow patterns.

A heterogeneous computing accelerated SCE-UA global optimization method using OpenMP, OpenCL, CUDA, and OpenACC.

PubMed

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Liang, Ke; Hong, Yang

2017-10-01

The shuffled complex evolution optimization developed at the University of Arizona (SCE-UA) has been successfully applied in various kinds of scientific and engineering optimization applications, such as hydrological model parameter calibration, for many years. The algorithm possesses good global optimality, convergence stability and robustness. However, benchmark and real-world applications reveal the poor computational efficiency of the SCE-UA. This research aims at the parallelization and acceleration of the SCE-UA method based on powerful heterogeneous computing technology. The parallel SCE-UA is implemented on Intel Xeon multi-core CPU (by using OpenMP and OpenCL) and NVIDIA Tesla many-core GPU (by using OpenCL, CUDA, and OpenACC). The serial and parallel SCE-UA were tested based on the Griewank benchmark function. Comparison results indicate the parallel SCE-UA significantly improves computational efficiency compared to the original serial version. The OpenCL implementation obtains the best overall acceleration results however, with the most complex source code. The parallel SCE-UA has bright prospects to be applied in real-world applications.

Multifidelity-CMA: a multifidelity approach for efficient personalisation of 3D cardiac electromechanical models.

PubMed

Molléro, Roch; Pennec, Xavier; Delingette, Hervé; Garny, Alan; Ayache, Nicholas; Sermesant, Maxime

2018-02-01

Personalised computational models of the heart are of increasing interest for clinical applications due to their discriminative and predictive abilities. However, the simulation of a single heartbeat with a 3D cardiac electromechanical model can be long and computationally expensive, which makes some practical applications, such as the estimation of model parameters from clinical data (the personalisation), very slow. Here we introduce an original multifidelity approach between a 3D cardiac model and a simplified "0D" version of this model, which enables to get reliable (and extremely fast) approximations of the global behaviour of the 3D model using 0D simulations. We then use this multifidelity approximation to speed-up an efficient parameter estimation algorithm, leading to a fast and computationally efficient personalisation method of the 3D model. In particular, we show results on a cohort of 121 different heart geometries and measurements. Finally, an exploitable code of the 0D model with scripts to perform parameter estimation will be released to the community.

The 1991 version of the plume impingement computer program. Volume 2: User's input guide

NASA Technical Reports Server (NTRS)

Bender, Robert L.; Somers, Richard E.; Prendergast, Maurice J.; Clayton, Joseph P.; Smith, Sheldon D.

1991-01-01

The Plume Impingement Program (PLIMP) is a computer code used to predict impact pressures, forces, moments, heating rates, and contamination on surfaces due to direct impingement flowfields. Typically, it has been used to analyze the effects of rocket exhaust plumes on nearby structures from ground level to the vacuum of space. The program normally uses flowfields generated by the MOC, RAMP2, SPF/2, or SFPGEN computer programs. It is capable of analyzing gaseous and gas/particle flows. A number of simple subshapes are available to model the surfaces of any structure. The original PLIMP program has been modified many times of the last 20 years. The theoretical bases for the referenced major changes, and additional undocumented changes and enhancements since 1988 are summarized in volume 1 of this report. This volume is the User's Input Guide and should be substituted for all previous guides when running the latest version of the program. This version can operate on VAX and UNIX machines with NCAR graphics ability.

Rovibrational bound states of SO2 isotopologues. I: Total angular momentum J = 0-10

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Ellis, Joseph; Poirier, Bill

2015-04-01

Isotopic variation of the rovibrational bound states of SO2 for the four stable sulfur isotopes 32-34,36S is investigated in comprehensive detail. In a two-part series, we compute the low-lying energy levels for all values of total angular momentum in the range J = 0-20. All rovibrational levels are computed, to an extremely high level of numerical convergence. The calculations have been carried out using the ScalIT suite of parallel codes. The present study (Paper I) examines the J = 0-10 rovibrational levels, providing unambiguous symmetry and rovibrational label assignments for each computed state. The calculated vibrational energy levels exhibit very good agreement with previously reported experimental and theoretical data. Rovibrational energy levels, calculated without any Coriolis approximations, are reported here for the first time. Among other potential ramifications, this data will facilitate understanding of the origin of mass-independent fractionation of sulfur isotopes in the Archean rock record-of great relevance for understanding the "oxygen revolution".

SOURCELESS STARTUP. A MACHINE CODE FOR COMPUTING LOW-SOURCE REACTOR STARTUPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacMillan, D.B.

1960-06-01

>A revision to the sourceless start-up code is presented. The code solves a system of differential equations encountered in computing the probability distribution of activity at an observed power level during reactor start-up from a very low source level. (J.R.D.)

Computer-assisted coding and clinical documentation: first things first.

PubMed

Tully, Melinda; Carmichael, Angela

2012-10-01

Computer-assisted coding tools have the potential to drive improvements in seven areas: Transparency of coding. Productivity (generally by 20 to 25 percent for inpatient claims). Accuracy (by improving specificity of documentation). Cost containment (by reducing overtime expenses, audit fees, and denials). Compliance. Efficiency. Consistency.

Optical image encryption based on real-valued coding and subtracting with the help of QR code

NASA Astrophysics Data System (ADS)

Deng, Xiaopeng

2015-08-01

A novel optical image encryption based on real-valued coding and subtracting is proposed with the help of quick response (QR) code. In the encryption process, the original image to be encoded is firstly transformed into the corresponding QR code, and then the corresponding QR code is encoded into two phase-only masks (POMs) by using basic vector operations. Finally, the absolute values of the real or imaginary parts of the two POMs are chosen as the ciphertexts. In decryption process, the QR code can be approximately restored by recording the intensity of the subtraction between the ciphertexts, and hence the original image can be retrieved without any quality loss by scanning the restored QR code with a smartphone. Simulation results and actual smartphone collected results show that the method is feasible and has strong tolerance to noise, phase difference and ratio between intensities of the two decryption light beams.

Hypercube matrix computation task

NASA Technical Reports Server (NTRS)

Calalo, R.; Imbriale, W.; Liewer, P.; Lyons, J.; Manshadi, F.; Patterson, J.

1987-01-01

The Hypercube Matrix Computation (Year 1986-1987) task investigated the applicability of a parallel computing architecture to the solution of large scale electromagnetic scattering problems. Two existing electromagnetic scattering codes were selected for conversion to the Mark III Hypercube concurrent computing environment. They were selected so that the underlying numerical algorithms utilized would be different thereby providing a more thorough evaluation of the appropriateness of the parallel environment for these types of problems. The first code was a frequency domain method of moments solution, NEC-2, developed at Lawrence Livermore National Laboratory. The second code was a time domain finite difference solution of Maxwell's equations to solve for the scattered fields. Once the codes were implemented on the hypercube and verified to obtain correct solutions by comparing the results with those from sequential runs, several measures were used to evaluate the performance of the two codes. First, a comparison was provided of the problem size possible on the hypercube with 128 megabytes of memory for a 32-node configuration with that available in a typical sequential user environment of 4 to 8 megabytes. Then, the performance of the codes was anlyzed for the computational speedup attained by the parallel architecture.

Numerical Modeling of Poroelastic-Fluid Systems Using High-Resolution Finite Volume Methods

NASA Astrophysics Data System (ADS)

Lemoine, Grady

Poroelasticity theory models the mechanics of porous, fluid-saturated, deformable solids. It was originally developed by Maurice Biot to model geophysical problems, such as seismic waves in oil reservoirs, but has also been applied to modeling living bone and other porous media. Poroelastic media often interact with fluids, such as in ocean bottom acoustics or propagation of waves from soft tissue into bone. This thesis describes the development and testing of high-resolution finite volume numerical methods, and simulation codes implementing these methods, for modeling systems of poroelastic media and fluids in two and three dimensions. These methods operate on both rectilinear grids and logically rectangular mapped grids. To allow the use of these methods, Biot's equations of poroelasticity are formulated as a first-order hyperbolic system with a source term; this source term is incorporated using operator splitting. Some modifications are required to the classical high-resolution finite volume method. Obtaining correct solutions at interfaces between poroelastic media and fluids requires a novel transverse propagation scheme and the removal of the classical second-order correction term at the interface, and in three dimensions a new wave limiting algorithm is also needed to correctly limit shear waves. The accuracy and convergence rates of the methods of this thesis are examined for a variety of analytical solutions, including simple plane waves, reflection and transmission of waves at an interface between different media, and scattering of acoustic waves by a poroelastic cylinder. Solutions are also computed for a variety of test problems from the computational poroelasticity literature, as well as some original test problems designed to mimic possible applications for the simulation code.

Bistatic radar cross section of a perfectly conducting rhombus-shaped flat plate

NASA Astrophysics Data System (ADS)

Fenn, Alan J.

1990-05-01

The bistatic radar cross section of a perfectly conducting flat plate that has a rhombus shape (equilateral parallelogram) is investigated. The Ohio State University electromagnetic surface patch code (ESP version 4) is used to compute the theoretical bistatic radar cross section of a 35- x 27-in rhombus plate at 1.3 GHz over the bistatic angles 15 deg to 142 deg. The ESP-4 computer code is a method of moments FORTRAN-77 program which can analyze general configurations of plates and wires. This code has been installed and modified at Lincoln Laboratory on a SUN 3 computer network. Details of the code modifications are described. Comparisons of the method of moments simulations and measurements of the rhombus plate are made. It is shown that the ESP-4 computer code provides a high degree of accuracy in the calculation of copolarized and cross-polarized bistatic radar cross section patterns.

ASR4: A computer code for fitting and processing 4-gage anelastic strain recovery data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warpinski, N.R.

A computer code for analyzing four-gage Anelastic Strain Recovery (ASR) data has been modified for use on a personal computer. This code fits the viscoelastic model of Warpinski and Teufel to measured ASR data, calculates the stress orientation directly, and computes stress magnitudes if sufficient input data are available. The code also calculates the stress orientation using strain-rosette equations, and its calculates stress magnitudes using Blanton's approach, assuming sufficient input data are available. The program is written in FORTRAN, compiled with Ryan-McFarland Version 2.4. Graphics use PLOT88 software by Plotworks, Inc., but the graphics software must be obtained by themore » user because of licensing restrictions. A version without graphics can also be run. This code is available through the National Energy Software Center (NESC), operated by Argonne National Laboratory. 5 refs., 3 figs.« less

Navier-Stokes Simulation of Homogeneous Turbulence on the CYBER 205

NASA Technical Reports Server (NTRS)

Wu, C. T.; Ferziger, J. H.; Chapman, D. R.; Rogallo, R. S.

1984-01-01

A computer code which solves the Navier-Stokes equations for three dimensional, time-dependent, homogenous turbulence has been written for the CYBER 205. The code has options for both 64-bit and 32-bit arithmetic. With 32-bit computation, mesh sizes up to 64 (3) are contained within core of a 2 million 64-bit word memory. Computer speed timing runs were made for various vector lengths up to 6144. With this code, speeds a little over 100 Mflops have been achieved on a 2-pipe CYBER 205. Several problems encountered in the coding are discussed.

The investigation of tethered satellite system dynamics

NASA Technical Reports Server (NTRS)

Lorenzini, E.

1985-01-01

The tether control law to retrieve the satellite was modified in order to have a smooth retrieval trajectory of the satellite that minimizes the thruster activation. The satellite thrusters were added to the rotational dynamics computer code and a preliminary control logic was implemented to simulate them during the retrieval maneuver. The high resolution computer code for modelling the three dimensional dynamics of untensioned tether, SLACK3, was made fully operative and a set of computer simulations of possible tether breakages was run. The distribution of the electric field around an electrodynamic tether in vacuo severed at some length from the shuttle was computed with a three dimensional electrodynamic computer code.

Experimental and computational surface and flow-field results for an all-body hypersonic aircraft

NASA Technical Reports Server (NTRS)

Lockman, William K.; Lawrence, Scott L.; Cleary, Joseph W.

1990-01-01

The objective of the present investigation is to establish a benchmark experimental data base for a generic hypersonic vehicle shape for validation and/or calibration of advanced computational fluid dynamics computer codes. This paper includes results from the comprehensive test program conducted in the NASA/Ames 3.5-foot Hypersonic Wind Tunnel for a generic all-body hypersonic aircraft model. Experimental and computational results on flow visualization, surface pressures, surface convective heat transfer, and pitot-pressure flow-field surveys are presented. Comparisons of the experimental results with computational results from an upwind parabolized Navier-Stokes code developed at Ames demonstrate the capabilities of this code.

IGA: A Simplified Introduction and Implementation Details for Finite Element Users

NASA Astrophysics Data System (ADS)

Agrawal, Vishal; Gautam, Sachin S.

2018-05-01

Isogeometric analysis (IGA) is a recently introduced technique that employs the Computer Aided Design (CAD) concept of Non-uniform Rational B-splines (NURBS) tool to bridge the substantial bottleneck between the CAD and finite element analysis (FEA) fields. The simplified transition of exact CAD models into the analysis alleviates the issues originating from geometrical discontinuities and thus, significantly reduces the design-to-analysis time in comparison to traditional FEA technique. Since its origination, the research in the field of IGA is accelerating and has been applied to various problems. However, the employment of CAD tools in the area of FEA invokes the need of adapting the existing implementation procedure for the framework of IGA. Also, the usage of IGA requires the in-depth knowledge of both the CAD and FEA fields. This can be overwhelming for a beginner in IGA. Hence, in this paper, a simplified introduction and implementation details for the incorporation of NURBS based IGA technique within the existing FEA code is presented. It is shown that with little modifications, the available standard code structure of FEA can be adapted for IGA. For the clear and concise explanation of these modifications, step-by-step implementation of a benchmark plate with a circular hole under the action of in-plane tension is included.

Low latency, high bandwidth data communications between compute nodes in a parallel computer

DOEpatents

Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2010-11-02

Methods, parallel computers, and computer program products are disclosed for low latency, high bandwidth data communications between compute nodes in a parallel computer. Embodiments include receiving, by an origin direct memory access (`DMA`) engine of an origin compute node, data for transfer to a target compute node; sending, by the origin DMA engine of the origin compute node to a target DMA engine on the target compute node, a request to send (`RTS`) message; transferring, by the origin DMA engine, a predetermined portion of the data to the target compute node using memory FIFO operation; determining, by the origin DMA engine whether an acknowledgement of the RTS message has been received from the target DMA engine; if the an acknowledgement of the RTS message has not been received, transferring, by the origin DMA engine, another predetermined portion of the data to the target compute node using a memory FIFO operation; and if the acknowledgement of the RTS message has been received by the origin DMA engine, transferring, by the origin DMA engine, any remaining portion of the data to the target compute node using a direct put operation.

Computer search for binary cyclic UEP codes of odd length up to 65

NASA Technical Reports Server (NTRS)

Lin, Mao-Chao; Lin, Chi-Chang; Lin, Shu

1990-01-01

Using an exhaustive computation, the unequal error protection capabilities of all binary cyclic codes of odd length up to 65 that have minimum distances at least 3 are found. For those codes that can only have upper bounds on their unequal error protection capabilities computed, an analytic method developed by Dynkin and Togonidze (1976) is used to show that the upper bounds meet the exact unequal error protection capabilities.

A Combinatorial Geometry Computer Description of the MEP-021A Generator Set

DTIC Science & Technology

1979-02-01

Generator Computer Description Gasoline Generator GIFT MEP-021A 20. ABSTRACT fCbntteu* an rararaa eta* ft namamwaay anal Identify by block number) This... GIFT code is also stored on magnetic tape for future vulnerability analysis. 00,] 󈧚*7,1473 EDITION OF • NOV 65 IS OBSOLETE UNCLASSIFIED SECURITY...the Geometric Information for Targets ( GIFT ) computer code. The GIFT code traces shotlines through a COM-GEOM description from any specified attack

Optimizing a liquid propellant rocket engine with an automated combustor design code (AUTOCOM)

NASA Technical Reports Server (NTRS)

Hague, D. S.; Reichel, R. H.; Jones, R. T.; Glatt, C. R.

1972-01-01

A procedure for automatically designing a liquid propellant rocket engine combustion chamber in an optimal fashion is outlined. The procedure is contained in a digital computer code, AUTOCOM. The code is applied to an existing engine, and design modifications are generated which provide a substantial potential payload improvement over the existing design. Computer time requirements for this payload improvement were small, approximately four minutes in the CDC 6600 computer.

Unaligned instruction relocation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

Computer algorithm for coding gain

NASA Technical Reports Server (NTRS)

Dodd, E. E.

1974-01-01

Development of a computer algorithm for coding gain for use in an automated communications link design system. Using an empirical formula which defines coding gain as used in space communications engineering, an algorithm is constructed on the basis of available performance data for nonsystematic convolutional encoding with soft-decision (eight-level) Viterbi decoding.

Modeling and Qualification of a Modified Emission Unit for Radioactive Air Emissions Stack Sampling Compliance.

PubMed

Barnett, J Matthew; Yu, Xiao-Ying; Recknagle, Kurtis P; Glissmeyer, John A

2016-11-01

A planned laboratory space and exhaust system modification to the Pacific Northwest National Laboratory Material Science and Technology Building indicated that a new evaluation of the mixing at the air sampling system location would be required for compliance to ANSI/HPS N13.1-2011. The modified exhaust system would add a third fan, thereby increasing the overall exhaust rate out the stack, thus voiding the previous mixing study. Prior to modifying the radioactive air emissions exhaust system, a three-dimensional computational fluid dynamics computer model was used to evaluate the mixing at the sampling system location. Modeling of the original three-fan system indicated that not all mixing criteria could be met. A second modeling effort was conducted with the addition of an air blender downstream of the confluence of the three fans, which then showed satisfactory mixing results. The final installation included an air blender, and the exhaust system underwent full-scale tests to verify velocity, cyclonic flow, gas, and particulate uniformity. The modeling results and those of the full-scale tests show agreement between each of the evaluated criteria. The use of a computational fluid dynamics code was an effective aid in the design process and allowed the sampling system to remain in its original location while still meeting the requirements for sampling at a well mixed location.

The effect of unsteady blade loading on the aeroacoustics of a pusher propeller

NASA Astrophysics Data System (ADS)

Mauk, Clay S.; Farokhi, Saeed

1993-06-01

A theoretical/computational approach is developed to predict the change in near-field noise due to a momentum-deficit upstream of a propeller plane, specifically for a pylon wake in a pusher configuration. The acoustic pressure is computed using blade geometry and unsteady blade surface pressure history. The steady blade surface pressure is predicted using blade-momentum theory and two-dimensional airfoil characteristics. Unsteady blade pressures are derived from in-flight measurements. In-flight acoustic measurements are used for code validation purposes. Overall sound pressure levels (OSPL) are computed for an array of observer locations parallel to the propeller axis of rotation. In order to clearly realize the effect of the wake encounter on the radiated sound, the wake signature is eliminated from the unsteady blade pressures. By subtracting the OSPL computed with the smoothed data from that computed with the original unsteady data, the change in noise resulting from the wake encounter is deduced. In general, the noise was increased due to the propeller-wake chopping activity. For all flight conditions, the largest increase in radiated noise occurred for a highly loaded propeller. The results indicate that the propeller noise due to periodic wake encounter may possess a unique directivity pattern.

Revisiting Intel Xeon Phi optimization of Thompson cloud microphysics scheme in Weather Research and Forecasting (WRF) model

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen

2015-10-01

The Thompson cloud microphysics scheme is a sophisticated cloud microphysics scheme in the Weather Research and Forecasting (WRF) model. The scheme is very suitable for massively parallel computation as there are no interactions among horizontal grid points. Compared to the earlier microphysics schemes, the Thompson scheme incorporates a large number of improvements. Thus, we have optimized the speed of this important part of WRF. Intel Many Integrated Core (MIC) ushers in a new era of supercomputing speed, performance, and compatibility. It allows the developers to run code at trillions of calculations per second using the familiar programming model. In this paper, we present our results of optimizing the Thompson microphysics scheme on Intel Many Integrated Core Architecture (MIC) hardware. The Intel Xeon Phi coprocessor is the first product based on Intel MIC architecture, and it consists of up to 61 cores connected by a high performance on-die bidirectional interconnect. The coprocessor supports all important Intel development tools. Thus, the development environment is familiar one to a vast number of CPU developers. Although, getting a maximum performance out of MICs will require using some novel optimization techniques. New optimizations for an updated Thompson scheme are discusses in this paper. The optimizations improved the performance of the original Thompson code on Xeon Phi 7120P by a factor of 1.8x. Furthermore, the same optimizations improved the performance of the Thompson on a dual socket configuration of eight core Intel Xeon E5-2670 CPUs by a factor of 1.8x compared to the original Thompson code.

Frames for exact inversion of the rank order coder.

PubMed

Masmoudi, Khaled; Antonini, Marc; Kornprobst, Pierre

2012-02-01

Our goal is to revisit rank order coding by proposing an original exact decoding procedure for it. Rank order coding was proposed by Thorpe et al. who stated that the order in which the retina cells are activated encodes for the visual stimulus. Based on this idea, the authors proposed in [1] a rank order coder/decoder associated to a retinal model. Though, it appeared that the decoding procedure employed yields reconstruction errors that limit the model bit-cost/quality performances when used as an image codec. The attempts made in the literature to overcome this issue are time consuming and alter the coding procedure, or are lacking mathematical support and feasibility for standard size images. Here we solve this problem in an original fashion by using the frames theory, where a frame of a vector space designates an extension for the notion of basis. Our contribution is twofold. First, we prove that the analyzing filter bank considered is a frame, and then we define the corresponding dual frame that is necessary for the exact image reconstruction. Second, to deal with the problem of memory overhead, we design a recursive out-of-core blockwise algorithm for the computation of this dual frame. Our work provides a mathematical formalism for the retinal model under study and defines a simple and exact reverse transform for it with over than 265 dB of increase in the peak signal-to-noise ratio quality compared to [1]. Furthermore, the framework presented here can be extended to several models of the visual cortical areas using redundant representations.

On the Use of Statistics in Design and the Implications for Deterministic Computer Experiments

NASA Technical Reports Server (NTRS)

Simpson, Timothy W.; Peplinski, Jesse; Koch, Patrick N.; Allen, Janet K.

1997-01-01

Perhaps the most prevalent use of statistics in engineering design is through Taguchi's parameter and robust design -- using orthogonal arrays to compute signal-to-noise ratios in a process of design improvement. In our view, however, there is an equally exciting use of statistics in design that could become just as prevalent: it is the concept of metamodeling whereby statistical models are built to approximate detailed computer analysis codes. Although computers continue to get faster, analysis codes always seem to keep pace so that their computational time remains non-trivial. Through metamodeling, approximations of these codes are built that are orders of magnitude cheaper to run. These metamodels can then be linked to optimization routines for fast analysis, or they can serve as a bridge for integrating analysis codes across different domains. In this paper we first review metamodeling techniques that encompass design of experiments, response surface methodology, Taguchi methods, neural networks, inductive learning, and kriging. We discuss their existing applications in engineering design and then address the dangers of applying traditional statistical techniques to approximate deterministic computer analysis codes. We conclude with recommendations for the appropriate use of metamodeling techniques in given situations and how common pitfalls can be avoided.

SPECT3D - A multi-dimensional collisional-radiative code for generating diagnostic signatures based on hydrodynamics and PIC simulation output

NASA Astrophysics Data System (ADS)

MacFarlane, J. J.; Golovkin, I. E.; Wang, P.; Woodruff, P. R.; Pereyra, N. A.

2007-05-01

SPECT3D is a multi-dimensional collisional-radiative code used to post-process the output from radiation-hydrodynamics (RH) and particle-in-cell (PIC) codes to generate diagnostic signatures (e.g. images, spectra) that can be compared directly with experimental measurements. This ability to post-process simulation code output plays a pivotal role in assessing the reliability of RH and PIC simulation codes and their physics models. SPECT3D has the capability to operate on plasmas in 1D, 2D, and 3D geometries. It computes a variety of diagnostic signatures that can be compared with experimental measurements, including: time-resolved and time-integrated spectra, space-resolved spectra and streaked spectra; filtered and monochromatic images; and X-ray diode signals. Simulated images and spectra can include the effects of backlighters, as well as the effects of instrumental broadening and time-gating. SPECT3D also includes a drilldown capability that shows where frequency-dependent radiation is emitted and absorbed as it propagates through the plasma towards the detector, thereby providing insights on where the radiation seen by a detector originates within the plasma. SPECT3D has the capability to model a variety of complex atomic and radiative processes that affect the radiation seen by imaging and spectral detectors in high energy density physics (HEDP) experiments. LTE (local thermodynamic equilibrium) or non-LTE atomic level populations can be computed for plasmas. Photoabsorption rates can be computed using either escape probability models or, for selected 1D and 2D geometries, multi-angle radiative transfer models. The effects of non-thermal (i.e. non-Maxwellian) electron distributions can also be included. To study the influence of energetic particles on spectra and images recorded in intense short-pulse laser experiments, the effects of both relativistic electrons and energetic proton beams can be simulated. SPECT3D is a user-friendly software package that runs on Windows, Linux, and Mac platforms. A parallel version of SPECT3D is supported for Linux clusters for large-scale calculations. We will discuss the major features of SPECT3D, and present example results from simulations and comparisons with experimental data.

Gompertz type dechanneling functions for protons in <1 0 0>, <1 1 0> and <1 1 1> Si crystal channels

NASA Astrophysics Data System (ADS)

Petrović, S.; Erić, M.; Kokkoris, M.; Nešković, N.

2007-03-01

In this work the energy dependences of the Gompertz type sigmoidal dechanneling function parameters for protons in <1 0 0>, <1 1 0> and <1 1 1> Si crystal channels is investigated theoretically. The proton energy range considered is between 1 and 10 MeV. The original dechanneling functions are generated using a realistic Monte Carlo computer simulation code. We show that the Gompertz type dechanneling function, having two parameters, lc and k, representing the dechanneling range and rate, respectively, approximate accurately the original dechanneling function. It is also shown that the energy dependences of parameters lc and k can be approximated by a linear function and a sum of two exponential functions, respectively. The results obtained can be used for accurate reproduction of experimental proton channeling spectra recorded in the backscattering geometry.

Parallel algorithms for modeling flow in permeable media. Annual report, February 15, 1995 - February 14, 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

G.A. Pope; K. Sephernoori; D.C. McKinney

1996-03-15

This report describes the application of distributed-memory parallel programming techniques to a compositional simulator called UTCHEM. The University of Texas Chemical Flooding reservoir simulator (UTCHEM) is a general-purpose vectorized chemical flooding simulator that models the transport of chemical species in three-dimensional, multiphase flow through permeable media. The parallel version of UTCHEM addresses solving large-scale problems by reducing the amount of time that is required to obtain the solution as well as providing a flexible and portable programming environment. In this work, the original parallel version of UTCHEM was modified and ported to CRAY T3D and CRAY T3E, distributed-memory, multiprocessor computersmore » using CRAY-PVM as the interprocessor communication library. Also, the data communication routines were modified such that the portability of the original code across different computer architectures was mad possible.« less

Design and optimization of a portable LQCD Monte Carlo code using OpenACC

NASA Astrophysics Data System (ADS)

Bonati, Claudio; Coscetti, Simone; D'Elia, Massimo; Mesiti, Michele; Negro, Francesco; Calore, Enrico; Schifano, Sebastiano Fabio; Silvi, Giorgio; Tripiccione, Raffaele

The present panorama of HPC architectures is extremely heterogeneous, ranging from traditional multi-core CPU processors, supporting a wide class of applications but delivering moderate computing performance, to many-core Graphics Processor Units (GPUs), exploiting aggressive data-parallelism and delivering higher performances for streaming computing applications. In this scenario, code portability (and performance portability) become necessary for easy maintainability of applications; this is very relevant in scientific computing where code changes are very frequent, making it tedious and prone to error to keep different code versions aligned. In this work, we present the design and optimization of a state-of-the-art production-level LQCD Monte Carlo application, using the directive-based OpenACC programming model. OpenACC abstracts parallel programming to a descriptive level, relieving programmers from specifying how codes should be mapped onto the target architecture. We describe the implementation of a code fully written in OpenAcc, and show that we are able to target several different architectures, including state-of-the-art traditional CPUs and GPUs, with the same code. We also measure performance, evaluating the computing efficiency of our OpenACC code on several architectures, comparing with GPU-specific implementations and showing that a good level of performance-portability can be reached.

Survey Of Lossless Image Coding Techniques

NASA Astrophysics Data System (ADS)

Melnychuck, Paul W.; Rabbani, Majid

1989-04-01

Many image transmission/storage applications requiring some form of data compression additionally require that the decoded image be an exact replica of the original. Lossless image coding algorithms meet this requirement by generating a decoded image that is numerically identical to the original. Several lossless coding techniques are modifications of well-known lossy schemes, whereas others are new. Traditional Markov-based models and newer arithmetic coding techniques are applied to predictive coding, bit plane processing, and lossy plus residual coding. Generally speaking, the compression ratio offered by these techniques are in the area of 1.6:1 to 3:1 for 8-bit pictorial images. Compression ratios for 12-bit radiological images approach 3:1, as these images have less detailed structure, and hence, their higher pel correlation leads to a greater removal of image redundancy.

Development of a thermal and structural analysis procedure for cooled radial turbines

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Deanna, Russell G.

1988-01-01

A procedure for computing the rotor temperature and stress distributions in a cooled radial turbine is considered. Existing codes for modeling the external mainstream flow and the internal cooling flow are used to compute boundary conditions for the heat transfer and stress analyses. An inviscid, quasi three-dimensional code computes the external free stream velocity. The external velocity is then used in a boundary layer analysis to compute the external heat transfer coefficients. Coolant temperatures are computed by a viscous one-dimensional internal flow code for the momentum and energy equation. These boundary conditions are input to a three-dimensional heat conduction code for calculation of rotor temperatures. The rotor stress distribution may be determined for the given thermal, pressure and centrifugal loading. The procedure is applied to a cooled radial turbine which will be tested at the NASA Lewis Research Center. Representative results from this case are included.

Computational strategies for three-dimensional flow simulations on distributed computer systems. Ph.D. Thesis Semiannual Status Report, 15 Aug. 1993 - 15 Feb. 1994

NASA Technical Reports Server (NTRS)

Weed, Richard Allen; Sankar, L. N.

1994-01-01

An increasing amount of research activity in computational fluid dynamics has been devoted to the development of efficient algorithms for parallel computing systems. The increasing performance to price ratio of engineering workstations has led to research to development procedures for implementing a parallel computing system composed of distributed workstations. This thesis proposal outlines an ongoing research program to develop efficient strategies for performing three-dimensional flow analysis on distributed computing systems. The PVM parallel programming interface was used to modify an existing three-dimensional flow solver, the TEAM code developed by Lockheed for the Air Force, to function as a parallel flow solver on clusters of workstations. Steady flow solutions were generated for three different wing and body geometries to validate the code and evaluate code performance. The proposed research will extend the parallel code development to determine the most efficient strategies for unsteady flow simulations.

Computerized systems analysis and optimization of aircraft engine performance, weight, and life cycle costs

NASA Technical Reports Server (NTRS)

Fishbach, L. H.

1979-01-01

The computational techniques utilized to determine the optimum propulsion systems for future aircraft applications and to identify system tradeoffs and technology requirements are described. The characteristics and use of the following computer codes are discussed: (1) NNEP - a very general cycle analysis code that can assemble an arbitrary matrix fans, turbines, ducts, shafts, etc., into a complete gas turbine engine and compute on- and off-design thermodynamic performance; (2) WATE - a preliminary design procedure for calculating engine weight using the component characteristics determined by NNEP; (3) POD DRG - a table look-up program to calculate wave and friction drag of nacelles; (4) LIFCYC - a computer code developed to calculate life cycle costs of engines based on the output from WATE; and (5) INSTAL - a computer code developed to calculate installation effects, inlet performance and inlet weight. Examples are given to illustrate how these computer techniques can be applied to analyze and optimize propulsion system fuel consumption, weight, and cost for representative types of aircraft and missions.

A Combinatorial Geometry Computer Description of the M9 ACE (Armored Combat Earthmover) Vehicle

DTIC Science & Technology

1984-12-01

program requires as input the M9 target descriptions as processed by the Geometric Information for Targets ( GIFT ) ’ computer code. The first step is...model of the target. This COM-GEOM target description is used as input to the Geometric Information For Targets ( GIFT ) computer code. Among other...things, the GIFT code traces shotlines through a COM-GEOM description from any specified aspect, listing pertinent information about each component hit

DGSA: A Matlab toolbox for distance-based generalized sensitivity analysis of geoscientific computer experiments

NASA Astrophysics Data System (ADS)

Park, Jihoon; Yang, Guang; Satija, Addy; Scheidt, Céline; Caers, Jef

2016-12-01

Sensitivity analysis plays an important role in geoscientific computer experiments, whether for forecasting, data assimilation or model calibration. In this paper we focus on an extension of a method of regionalized sensitivity analysis (RSA) to applications typical in the Earth Sciences. Such applications involve the building of large complex spatial models, the application of computationally extensive forward modeling codes and the integration of heterogeneous sources of model uncertainty. The aim of this paper is to be practical: 1) provide a Matlab code, 2) provide novel visualization methods to aid users in getting a better understanding in the sensitivity 3) provide a method based on kernel principal component analysis (KPCA) and self-organizing maps (SOM) to account for spatial uncertainty typical in Earth Science applications and 4) provide an illustration on a real field case where the above mentioned complexities present themselves. We present methods that extend the original RSA method in several ways. First we present the calculation of conditional effects, defined as the sensitivity of a parameter given a level of another parameters. Second, we show how this conditional effect can be used to choose nominal values or ranges to fix insensitive parameters aiming to minimally affect uncertainty in the response. Third, we develop a method based on KPCA and SOM to assign a rank to spatial models in order to calculate the sensitivity on spatial variability in the models. A large oil/gas reservoir case is used as illustration of these ideas.

Characterizing the Properties of a Woven SiC/SiC Composite Using W-CEMCAN Computer Code

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. N.; Mital, Subodh K.; DiCarlo, James A.

1999-01-01

A micromechanics based computer code to predict the thermal and mechanical properties of woven ceramic matrix composites (CMC) is developed. This computer code, W-CEMCAN (Woven CEramic Matrix Composites ANalyzer), predicts the properties of two-dimensional woven CMC at any temperature and takes into account various constituent geometries and volume fractions. This computer code is used to predict the thermal and mechanical properties of an advanced CMC composed of 0/90 five-harness (5 HS) Sylramic fiber which had been chemically vapor infiltrated (CVI) with boron nitride (BN) and SiC interphase coatings and melt-infiltrated (MI) with SiC. The predictions, based on the bulk constituent properties from the literature, are compared with measured experimental data. Based on the comparison. improved or calibrated properties for the constituent materials are then developed for use by material developers/designers. The computer code is then used to predict the properties of a composite with the same constituents but with different fiber volume fractions. The predictions are compared with measured data and a good agreement is achieved.

Fault tolerant computing: A preamble for assuring viability of large computer systems

NASA Technical Reports Server (NTRS)

Lim, R. S.

1977-01-01

The need for fault-tolerant computing is addressed from the viewpoints of (1) why it is needed, (2) how to apply it in the current state of technology, and (3) what it means in the context of the Phoenix computer system and other related systems. To this end, the value of concurrent error detection and correction is described. User protection, program retry, and repair are among the factors considered. The technology of algebraic codes to protect memory systems and arithmetic codes to protect memory systems and arithmetic codes to protect arithmetic operations is discussed.

The Advanced Software Development and Commercialization Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallopoulos, E.; Canfield, T.R.; Minkoff, M.

1990-09-01

This is the first of a series of reports pertaining to progress in the Advanced Software Development and Commercialization Project, a joint collaborative effort between the Center for Supercomputing Research and Development of the University of Illinois and the Computing and Telecommunications Division of Argonne National Laboratory. The purpose of this work is to apply techniques of parallel computing that were pioneered by University of Illinois researchers to mature computational fluid dynamics (CFD) and structural dynamics (SD) computer codes developed at Argonne. The collaboration in this project will bring this unique combination of expertise to bear, for the first time,more » on industrially important problems. By so doing, it will expose the strengths and weaknesses of existing techniques for parallelizing programs and will identify those problems that need to be solved in order to enable wide spread production use of parallel computers. Secondly, the increased efficiency of the CFD and SD codes themselves will enable the simulation of larger, more accurate engineering models that involve fluid and structural dynamics. In order to realize the above two goals, we are considering two production codes that have been developed at ANL and are widely used by both industry and Universities. These are COMMIX and WHAMS-3D. The first is a computational fluid dynamics code that is used for both nuclear reactor design and safety and as a design tool for the casting industry. The second is a three-dimensional structural dynamics code used in nuclear reactor safety as well as crashworthiness studies. These codes are currently available for both sequential and vector computers only. Our main goal is to port and optimize these two codes on shared memory multiprocessors. In so doing, we shall establish a process that can be followed in optimizing other sequential or vector engineering codes for parallel processors.« less

Source Code Plagiarism--A Student Perspective

ERIC Educational Resources Information Center

Joy, M.; Cosma, G.; Yau, J. Y.-K.; Sinclair, J.

2011-01-01

This paper considers the problem of source code plagiarism by students within the computing disciplines and reports the results of a survey of students in Computing departments in 18 institutions in the U.K. This survey was designed to investigate how well students understand the concept of source code plagiarism and to discover what, if any,…

Poetry in Programs: A Brief Examination of Software Aesthetics, Including Observations on the History of Programming Styles and Speculations on Post-object Programming

NASA Technical Reports Server (NTRS)

Filman, Robert E.

2004-01-01

This viewgraph presentation provides samples of computer code which have characteristics of poetic verse, and addresses the theoretical underpinnings of artistic coding, as well as how computer language influences software style, and the possible style of future coding.

The impact of conventional dietary intake data coding methods on foods typically consumed by low-income African-American and White urban populations.

PubMed

Mason, Marc A; Fanelli Kuczmarski, Marie; Allegro, Deanne; Zonderman, Alan B; Evans, Michele K

2015-08-01

Analysing dietary data to capture how individuals typically consume foods is dependent on the coding variables used. Individual foods consumed simultaneously, like coffee with milk, are given codes to identify these combinations. Our literature review revealed a lack of discussion about using combination codes in analysis. The present study identified foods consumed at mealtimes and by race when combination codes were or were not utilized. Duplicate analysis methods were performed on separate data sets. The original data set consisted of all foods reported; each food was coded as if it was consumed individually. The revised data set was derived from the original data set by first isolating coded foods consumed as individual items from those foods consumed simultaneously and assigning a code to designate a combination. Foods assigned a combination code, like pancakes with syrup, were aggregated and associated with a food group, defined by the major food component (i.e. pancakes), and then appended to the isolated coded foods. Healthy Aging in Neighborhoods of Diversity across the Life Span study. African-American and White adults with two dietary recalls (n 2177). Differences existed in lists of foods most frequently consumed by mealtime and race when comparing results based on original and revised data sets. African Americans reported consumption of sausage/luncheon meat and poultry, while ready-to-eat cereals and cakes/doughnuts/pastries were reported by Whites on recalls. Use of combination codes provided more accurate representation of how foods were consumed by populations. This information is beneficial when creating interventions and exploring diet-health relationships.

Solution of the lossy nonlinear Tricomi equation with application to sonic boom focusing

NASA Astrophysics Data System (ADS)

Salamone, Joseph A., III

Sonic boom focusing theory has been augmented with new terms that account for mean flow effects in the direction of propagation and also for atmospheric absorption/dispersion due to molecular relaxation due to oxygen and nitrogen. The newly derived model equation was numerically implemented using a computer code. The computer code was numerically validated using a spectral solution for nonlinear propagation of a sinusoid through a lossy homogeneous medium. An additional numerical check was performed to verify the linear diffraction component of the code calculations. The computer code was experimentally validated using measured sonic boom focusing data from the NASA sponsored Superboom Caustic and Analysis Measurement Program (SCAMP) flight test. The computer code was in good agreement with both the numerical and experimental validation. The newly developed code was applied to examine the focusing of a NASA low-boom demonstration vehicle concept. The resulting pressure field was calculated for several supersonic climb profiles. The shaping efforts designed into the signatures were still somewhat evident despite the effects of sonic boom focusing.

Modernization and optimization of a legacy open-source CFD code for high-performance computing architectures

NASA Astrophysics Data System (ADS)

Gel, Aytekin; Hu, Jonathan; Ould-Ahmed-Vall, ElMoustapha; Kalinkin, Alexander A.

2017-02-01

Legacy codes remain a crucial element of today's simulation-based engineering ecosystem due to the extensive validation process and investment in such software. The rapid evolution of high-performance computing architectures necessitates the modernization of these codes. One approach to modernization is a complete overhaul of the code. However, this could require extensive investments, such as rewriting in modern languages, new data constructs, etc., which will necessitate systematic verification and validation to re-establish the credibility of the computational models. The current study advocates using a more incremental approach and is a culmination of several modernization efforts of the legacy code MFIX, which is an open-source computational fluid dynamics code that has evolved over several decades, widely used in multiphase flows and still being developed by the National Energy Technology Laboratory. Two different modernization approaches,'bottom-up' and 'top-down', are illustrated. Preliminary results show up to 8.5x improvement at the selected kernel level with the first approach, and up to 50% improvement in total simulated time with the latter were achieved for the demonstration cases and target HPC systems employed.

Visual Computing Environment Workshop

NASA Technical Reports Server (NTRS)

Lawrence, Charles (Compiler)

1998-01-01

The Visual Computing Environment (VCE) is a framework for intercomponent and multidisciplinary computational simulations. Many current engineering analysis codes simulate various aspects of aircraft engine operation. For example, existing computational fluid dynamics (CFD) codes can model the airflow through individual engine components such as the inlet, compressor, combustor, turbine, or nozzle. Currently, these codes are run in isolation, making intercomponent and complete system simulations very difficult to perform. In addition, management and utilization of these engineering codes for coupled component simulations is a complex, laborious task, requiring substantial experience and effort. To facilitate multicomponent aircraft engine analysis, the CFD Research Corporation (CFDRC) is developing the VCE system. This system, which is part of NASA's Numerical Propulsion Simulation System (NPSS) program, can couple various engineering disciplines, such as CFD, structural analysis, and thermal analysis.

Force user's manual: A portable, parallel FORTRAN

NASA Technical Reports Server (NTRS)

Jordan, Harry F.; Benten, Muhammad S.; Arenstorf, Norbert S.; Ramanan, Aruna V.

1990-01-01

The use of Force, a parallel, portable FORTRAN on shared memory parallel computers is described. Force simplifies writing code for parallel computers and, once the parallel code is written, it is easily ported to computers on which Force is installed. Although Force is nearly the same for all computers, specific details are included for the Cray-2, Cray-YMP, Convex 220, Flex/32, Encore, Sequent, Alliant computers on which it is installed.

Monte Carlo simulation of Ising models by multispin coding on a vector computer

NASA Astrophysics Data System (ADS)

Wansleben, Stephan; Zabolitzky, John G.; Kalle, Claus

1984-11-01

Rebbi's efficient multispin coding algorithm for Ising models is combined with the use of the vector computer CDC Cyber 205. A speed of 21.2 million updates per second is reached. This is comparable to that obtained by special- purpose computers.

Thrust chamber performance using Navier-Stokes solution. [space shuttle main engine viscous nozzle calculation

NASA Technical Reports Server (NTRS)

Chan, J. S.; Freeman, J. A.

1984-01-01

The viscous, axisymmetric flow in the thrust chamber of the space shuttle main engine (SSME) was computed on the CRAY 205 computer using the general interpolants method (GIM) code. Results show that the Navier-Stokes codes can be used for these flows to study trends and viscous effects as well as determine flow patterns; but further research and development is needed before they can be used as production tools for nozzle performance calculations. The GIM formulation, numerical scheme, and computer code are described. The actual SSME nozzle computation showing grid points, flow contours, and flow parameter plots is discussed. The computer system and run times/costs are detailed.

Finite difference time domain electromagnetic scattering from frequency-dependent lossy materials

NASA Technical Reports Server (NTRS)

Luebbers, Raymond J.; Beggs, John H.

1991-01-01

Four different FDTD computer codes and companion Radar Cross Section (RCS) conversion codes on magnetic media are submitted. A single three dimensional dispersive FDTD code for both dispersive dielectric and magnetic materials was developed, along with a user's manual. The extension of FDTD to more complicated materials was made. The code is efficient and is capable of modeling interesting radar targets using a modest computer workstation platform. RCS results for two different plate geometries are reported. The FDTD method was also extended to computing far zone time domain results in two dimensions. Also the capability to model nonlinear materials was incorporated into FDTD and validated.

Multitasking the code ARC3D. [for computational fluid dynamics

NASA Technical Reports Server (NTRS)

Barton, John T.; Hsiung, Christopher C.

1986-01-01

The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

Comparison of Origin 2000 and Origin 3000 Using NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Turney, Raymond D.

2001-01-01

This report describes results of benchmark tests on the Origin 3000 system currently being installed at the NASA Ames National Advanced Supercomputing facility. This machine will ultimately contain 1024 R14K processors. The first part of the system, installed in November, 2000 and named mendel, is an Origin 3000 with 128 R12K processors. For comparison purposes, the tests were also run on lomax, an Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to determine system performance and measure the impact of changes on the machine as it evolves. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versiqns used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN 3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

Improving NASA's Multiscale Modeling Framework for Tropical Cyclone Climate Study

NASA Technical Reports Server (NTRS)

Shen, Bo-Wen; Nelson, Bron; Cheung, Samson; Tao, Wei-Kuo

2013-01-01

One of the current challenges in tropical cyclone (TC) research is how to improve our understanding of TC interannual variability and the impact of climate change on TCs. Recent advances in global modeling, visualization, and supercomputing technologies at NASA show potential for such studies. In this article, the authors discuss recent scalability improvement to the multiscale modeling framework (MMF) that makes it feasible to perform long-term TC-resolving simulations. The MMF consists of the finite-volume general circulation model (fvGCM), supplemented by a copy of the Goddard cumulus ensemble model (GCE) at each of the fvGCM grid points, giving 13,104 GCE copies. The original fvGCM implementation has a 1D data decomposition; the revised MMF implementation retains the 1D decomposition for most of the code, but uses a 2D decomposition for the massive copies of GCEs. Because the vast majority of computation time in the MMF is spent computing the GCEs, this approach can achieve excellent speedup without incurring the cost of modifying the entire code. Intelligent process mapping allows differing numbers of processes to be assigned to each domain for load balancing. The revised parallel implementation shows highly promising scalability, obtaining a nearly 80-fold speedup by increasing the number of cores from 30 to 3,335.

An algorithm to identify rheumatoid arthritis in primary care: a Clinical Practice Research Datalink study

PubMed Central

Muller, Sara; Hider, Samantha L; Raza, Karim; Stack, Rebecca J; Hayward, Richard A; Mallen, Christian D

2015-01-01

Objective Rheumatoid arthritis (RA) is a multisystem, inflammatory disorder associated with increased levels of morbidity and mortality. While much research into the condition is conducted in the secondary care setting, routinely collected primary care databases provide an important source of research data. This study aimed to update an algorithm to define RA that was previously developed and validated in the General Practice Research Database (GPRD). Methods The original algorithm consisted of two criteria. Individuals meeting at least one were considered to have RA. Criterion 1: ≥1 RA Read code and a disease modifying antirheumatic drug (DMARD) without an alternative indication. Criterion 2: ≥2 RA Read codes, with at least one ‘strong’ code and no alternative diagnoses. Lists of codes for consultations and prescriptions were obtained from the authors of the original algorithm where these were available, or compiled based on the original description and clinical knowledge. 4161 people with a first Read code for RA between 1 January 2010 and 31 December 2012 were selected from the Clinical Practice Research Datalink (CPRD, successor to the GPRD), and the criteria applied. Results Code lists were updated for the introduction of new Read codes and biological DMARDs. 3577/4161 (86%) of people met the updated algorithm for RA, compared to 61% in the original development study. 62.8% of people fulfilled both Criterion 1 and Criterion 2. Conclusions Those wishing to define RA in the CPRD, should consider using this updated algorithm, rather than a single RA code, if they wish to identify only those who are most likely to have RA. PMID:26700281

Reliability of routinely collected hospital data for child maltreatment surveillance.

PubMed

McKenzie, Kirsten; Scott, Debbie A; Waller, Garry S; Campbell, Margaret

2011-01-05

Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most 'under-coded' by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting.

Reliability of Routinely Collected Hospital Data for Child Maltreatment Surveillance

PubMed Central

2011-01-01

Background Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. Methods A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. Results In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most 'under-coded' by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Conclusion Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting. PMID:21208411

Addressing the challenges of standalone multi-core simulations in molecular dynamics

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-07-01

Computational modelling in material science involves mathematical abstractions of force fields between particles with the aim to postulate, develop and understand materials by simulation. The aggregated pairwise interactions of the material's particles lead to a deduction of its macroscopic behaviours. For practically meaningful macroscopic scales, a large amount of data are generated, leading to vast execution times. Simulation times of hours, days or weeks for moderately sized problems are not uncommon. The reduction of simulation times, improved result accuracy and the associated software and hardware engineering challenges are the main motivations for many of the ongoing researches in the computational sciences. This contribution is concerned mainly with simulations that can be done on a "standalone" computer based on Message Passing Interfaces (MPI), parallel code running on hardware platforms with wide specifications, such as single/multi- processor, multi-core machines with minimal reconfiguration for upward scaling of computational power. The widely available, documented and standardized MPI library provides this functionality through the MPI_Comm_size (), MPI_Comm_rank () and MPI_Reduce () functions. A survey of the literature shows that relatively little is written with respect to the efficient extraction of the inherent computational power in a cluster. In this work, we discuss the main avenues available to tap into this extra power without compromising computational accuracy. We also present methods to overcome the high inertia encountered in single-node-based computational molecular dynamics. We begin by surveying the current state of the art and discuss what it takes to achieve parallelism, efficiency and enhanced computational accuracy through program threads and message passing interfaces. Several code illustrations are given. The pros and cons of writing raw code as opposed to using heuristic, third-party code are also discussed. The growing trend towards graphical processor units and virtual computing clouds for high-performance computing is also discussed. Finally, we present the comparative results of vacancy formation energy calculations using our own parallelized standalone code called Verlet-Stormer velocity (VSV) operating on 30,000 copper atoms. The code is based on the Sutton-Chen implementation of the Finnis-Sinclair pairwise embedded atom potential. A link to the code is also given.

Computing effective properties of random heterogeneous materials on heterogeneous parallel processors

NASA Astrophysics Data System (ADS)

Leidi, Tiziano; Scocchi, Giulio; Grossi, Loris; Pusterla, Simone; D'Angelo, Claudio; Thiran, Jean-Philippe; Ortona, Alberto

2012-11-01

In recent decades, finite element (FE) techniques have been extensively used for predicting effective properties of random heterogeneous materials. In the case of very complex microstructures, the choice of numerical methods for the solution of this problem can offer some advantages over classical analytical approaches, and it allows the use of digital images obtained from real material samples (e.g., using computed tomography). On the other hand, having a large number of elements is often necessary for properly describing complex microstructures, ultimately leading to extremely time-consuming computations and high memory requirements. With the final objective of reducing these limitations, we improved an existing freely available FE code for the computation of effective conductivity (electrical and thermal) of microstructure digital models. To allow execution on hardware combining multi-core CPUs and a GPU, we first translated the original algorithm from Fortran to C, and we subdivided it into software components. Then, we enhanced the C version of the algorithm for parallel processing with heterogeneous processors. With the goal of maximizing the obtained performances and limiting resource consumption, we utilized a software architecture based on stream processing, event-driven scheduling, and dynamic load balancing. The parallel processing version of the algorithm has been validated using a simple microstructure consisting of a single sphere located at the centre of a cubic box, yielding consistent results. Finally, the code was used for the calculation of the effective thermal conductivity of a digital model of a real sample (a ceramic foam obtained using X-ray computed tomography). On a computer equipped with dual hexa-core Intel Xeon X5670 processors and an NVIDIA Tesla C2050, the parallel application version features near to linear speed-up progression when using only the CPU cores. It executes more than 20 times faster when additionally using the GPU.

Uncovering the problem-solving process: cued retrospective reporting versus concurrent and retrospective reporting.

PubMed

van Gog, Tamara; Paas, Fred; van Merriënboer, Jeroen J G; Witte, Puk

2005-12-01

This study investigated the amounts of problem-solving process information ("action," "why," "how," and "metacognitive") elicited by means of concurrent, retrospective, and cued retrospective reporting. In a within-participants design, 26 participants completed electrical circuit troubleshooting tasks under different reporting conditions. The method of cued retrospective reporting used the original computer-based task and a superimposed record of the participant's eye fixations and mouse-keyboard operations as a cue for retrospection. Cued retrospective reporting (with the exception of why information) and concurrent reporting (with the exception of metacognitive information) resulted in a higher number of codes on the different types of information than did retrospective reporting.

An assessment of RELAP5-3D using the Edwards-O'Brien Blowdown problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomlinson, E.T.; Aumiller, D.L.

1999-07-01

The RELAP5-3D (version bt) computer code was used to assess the United States Nuclear Regulatory Commission's Standard Problem 1 (Edwards-O'Brien Blowdown Test). The RELAP5-3D standard installation problem based on the Edwards-O'Brien Blowdown Test was modified to model the appropriate initial conditions and to represent the proper location of the instruments present in the experiment. The results obtained using the modified model are significantly different from the original calculation indicating the need to model accurately the experimental conditions if an accurate assessment of the calculational model is to be obtained.

Superimposed Code Theoretic Analysis of DNA Codes and DNA Computing

DTIC Science & Technology

2008-01-01

complements of one another and the DNA duplex formed is a Watson - Crick (WC) duplex. However, there are many instances when the formation of non-WC...that the user’s requirements for probe selection are met based on the Watson - Crick probe locality within a target. The second type, called...AFRL-RI-RS-TR-2007-288 Final Technical Report January 2008 SUPERIMPOSED CODE THEORETIC ANALYSIS OF DNA CODES AND DNA COMPUTING

Preliminary Results from the Application of Automated Adjoint Code Generation to CFL3D

NASA Technical Reports Server (NTRS)

Carle, Alan; Fagan, Mike; Green, Lawrence L.

1998-01-01

This report describes preliminary results obtained using an automated adjoint code generator for Fortran to augment a widely-used computational fluid dynamics flow solver to compute derivatives. These preliminary results with this augmented code suggest that, even in its infancy, the automated adjoint code generator can accurately and efficiently deliver derivatives for use in transonic Euler-based aerodynamic shape optimization problems with hundreds to thousands of independent design variables.

Aeroacoustic Prediction Codes

NASA Technical Reports Server (NTRS)

Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

2000-01-01

This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor-noise correlation model was developed from engine acoustic test results. This work provided several insights on potential approaches to reducing aircraft engine noise. Code development is described in this report, and those insights are discussed.

Turbine Internal and Film Cooling Modeling For 3D Navier-Stokes Codes

NASA Technical Reports Server (NTRS)

DeWitt, Kenneth; Garg Vijay; Ameri, Ali

2005-01-01

The aim of this research project is to make use of NASA Glenn on-site computational facilities in order to develop, validate and apply aerodynamic, heat transfer, and turbine cooling models for use in advanced 3D Navier-Stokes Computational Fluid Dynamics (CFD) codes such as the Glenn-" code. Specific areas of effort include: Application of the Glenn-HT code to specific configurations made available under Turbine Based Combined Cycle (TBCC), and Ultra Efficient Engine Technology (UEET) projects. Validating the use of a multi-block code for the time accurate computation of the detailed flow and heat transfer of cooled turbine airfoils. The goal of the current research is to improve the predictive ability of the Glenn-HT code. This will enable one to design more efficient turbine components for both aviation and power generation. The models will be tested against specific configurations provided by NASA Glenn.

Run-length encoding graphic rules, biochemically editable designs and steganographical numeric data embedment for DNA-based cryptographical coding system

PubMed Central

Kawano, Tomonori

2013-01-01

There have been a wide variety of approaches for handling the pieces of DNA as the “unplugged” tools for digital information storage and processing, including a series of studies applied to the security-related area, such as DNA-based digital barcodes, water marks and cryptography. In the present article, novel designs of artificial genes as the media for storing the digitally compressed data for images are proposed for bio-computing purpose while natural genes principally encode for proteins. Furthermore, the proposed system allows cryptographical application of DNA through biochemically editable designs with capacity for steganographical numeric data embedment. As a model case of image-coding DNA technique application, numerically and biochemically combined protocols are employed for ciphering the given “passwords” and/or secret numbers using DNA sequences. The “passwords” of interest were decomposed into single letters and translated into the font image coded on the separate DNA chains with both the coding regions in which the images are encoded based on the novel run-length encoding rule, and the non-coding regions designed for biochemical editing and the remodeling processes revealing the hidden orientation of letters composing the original “passwords.” The latter processes require the molecular biological tools for digestion and ligation of the fragmented DNA molecules targeting at the polymerase chain reaction-engineered termini of the chains. Lastly, additional protocols for steganographical overwriting of the numeric data of interests over the image-coding DNA are also discussed. PMID:23750303

Mass transfer effects in a gasification riser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Breault, Ronald W.; Li, Tingwen; Nicoletti, Phillip

2013-07-01

In the development of multiphase reacting computational fluid dynamics (CFD) codes, a number of simplifications were incorporated into the codes and models. One of these simplifications was the use of a simplistic mass transfer correlation for the faster reactions and omission of mass transfer effects completely on the moderate speed and slow speed reactions such as those in a fluidized bed gasifier. Another problem that has propagated is that the mass transfer correlation used in the codes is not universal and is being used far from its developed bubbling fluidized bed regime when applied to circulating fluidized bed (CFB) risermore » reactors. These problems are true for the major CFD codes. To alleviate this problem, a mechanistic based mass transfer coefficient algorithm has been developed based upon an earlier work by Breault et al. This fundamental approach uses the local hydrodynamics to predict a local, time varying mass transfer coefficient. The predicted mass transfer coefficients and the corresponding Sherwood numbers agree well with literature data and are typically about an order of magnitude lower than the correlation noted above. The incorporation of the new mass transfer model gives the expected behavior for all the gasification reactions evaluated in the paper. At the expected and typical design values for the solid flow rate in a CFB riser gasifier an ANOVA analysis has shown the predictions from the new code to be significantly different from the original code predictions. The new algorithm should be used such that the conversions are not over predicted. Additionally, its behaviors with changes in solid flow rate are consistent with the changes in the hydrodynamics.« less

Linear chirp phase perturbing approach for finding binary phased codes

NASA Astrophysics Data System (ADS)

Li, Bing C.

2017-05-01

Binary phased codes have many applications in communication and radar systems. These applications require binary phased codes to have low sidelobes in order to reduce interferences and false detection. Barker codes are the ones that satisfy these requirements and they have lowest maximum sidelobes. However, Barker codes have very limited code lengths (equal or less than 13) while many applications including low probability of intercept radar, and spread spectrum communication, require much higher code lengths. The conventional techniques of finding binary phased codes in literatures include exhaust search, neural network, and evolutionary methods, and they all require very expensive computation for large code lengths. Therefore these techniques are limited to find binary phased codes with small code lengths (less than 100). In this paper, by analyzing Barker code, linear chirp, and P3 phases, we propose a new approach to find binary codes. Experiments show that the proposed method is able to find long low sidelobe binary phased codes (code length >500) with reasonable computational cost.